From 5fdecc72ce2fa10cc3376e014a92e30f3424d6cc Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sun, 13 Mar 2022 22:21:44 +0100
Subject: [PATCH 001/148] Move output into a subpackage

---
 src/eko/{output.py => output/__init__.py} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename src/eko/{output.py => output/__init__.py} (99%)

diff --git a/src/eko/output.py b/src/eko/output/__init__.py
similarity index 99%
rename from src/eko/output.py
rename to src/eko/output/__init__.py
index c6a16af87..6a7de0aac 100644
--- a/src/eko/output.py
+++ b/src/eko/output/__init__.py
@@ -13,8 +13,8 @@
 import numpy as np
 import yaml
 
-from . import basis_rotation as br
-from . import interpolation, version
+from .. import basis_rotation as br
+from .. import interpolation, version
 
 logger = logging.getLogger(__name__)
 

From d9f5fdbef8505abe8b16ffbf2cc7aa5d94670226 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 14 Mar 2022 00:08:42 +0100
Subject: [PATCH 002/148] Split output in modules

---
 src/eko/output/__init__.py   | 422 +----------------------------------
 src/eko/output/legacy.py     | 259 +++++++++++++++++++++
 src/eko/output/manipulate.py | 165 ++++++++++++++
 src/eko/output/struct.py     |   6 +
 4 files changed, 432 insertions(+), 420 deletions(-)
 create mode 100644 src/eko/output/legacy.py
 create mode 100644 src/eko/output/manipulate.py
 create mode 100644 src/eko/output/struct.py

diff --git a/src/eko/output/__init__.py b/src/eko/output/__init__.py
index 6a7de0aac..f278e2860 100644
--- a/src/eko/output/__init__.py
+++ b/src/eko/output/__init__.py
@@ -1,424 +1,6 @@
 # -*- coding: utf-8 -*-
 """
-This file contains the output management
+This subpackage orchestrate the calculation workflow.
 """
-import io
-import logging
-import pathlib
-import tarfile
-import tempfile
-import warnings
 
-import lz4.frame
-import numpy as np
-import yaml
-
-from .. import basis_rotation as br
-from .. import interpolation, version
-
-logger = logging.getLogger(__name__)
-
-
-class Output(dict):
-    """
-    Wrapper for the output to help with application
-    to PDFs and dumping to file.
-    """
-
-    def xgrid_reshape(self, targetgrid=None, inputgrid=None):
-        """
-        Changes the operators to have in the output targetgrid and/or in the input inputgrid.
-
-        The operation is in-place.
-
-        Parameters
-        ----------
-            targetgrid : None or list
-                xgrid for the target
-            inputgrid : None or list
-                xgrid for the input
-        """
-        # calling with no arguments is an error
-        if targetgrid is None and inputgrid is None:
-            raise ValueError("Nor inputgrid nor targetgrid was given")
-        # now check to the current status
-        if (
-            targetgrid is not None
-            and len(targetgrid) == len(self["targetgrid"])
-            and np.allclose(targetgrid, self["targetgrid"])
-        ):
-            targetgrid = None
-            warnings.warn("The new targetgrid is close to the current targetgrid")
-        if (
-            inputgrid is not None
-            and len(inputgrid) == len(self["inputgrid"])
-            and np.allclose(inputgrid, self["inputgrid"])
-        ):
-            inputgrid = None
-            warnings.warn("The new inputgrid is close to the current inputgrid")
-        # after the checks: if there is still nothing to do, skip
-        if targetgrid is None and inputgrid is None:
-            logger.debug("Nothing done.")
-            return
-
-        # construct matrices
-        if targetgrid is not None:
-            b = interpolation.InterpolatorDispatcher(
-                self["targetgrid"],
-                self["interpolation_polynomial_degree"],
-                self["interpolation_is_log"],
-                False,
-            )
-            target_rot = b.get_interpolation(targetgrid)
-            self["targetgrid"] = np.array(targetgrid)
-        if inputgrid is not None:
-            b = interpolation.InterpolatorDispatcher(
-                inputgrid,
-                self["interpolation_polynomial_degree"],
-                self["interpolation_is_log"],
-                False,
-            )
-            input_rot = b.get_interpolation(self["inputgrid"])
-            self["inputgrid"] = np.array(inputgrid)
-
-        # build new grid
-        for elem in self["Q2grid"].values():
-            ops = elem["operators"]
-            errs = elem["operator_errors"]
-            if targetgrid is not None and inputgrid is None:
-                ops = np.einsum("ij,ajbk->aibk", target_rot, ops)
-                errs = np.einsum("ij,ajbk->aibk", target_rot, errs)
-            elif inputgrid is not None and targetgrid is None:
-                ops = np.einsum("ajbk,kl->ajbl", ops, input_rot)
-                errs = np.einsum("ajbk,kl->ajbl", errs, input_rot)
-            else:
-                ops = np.einsum("ij,ajbk,kl->aibl", target_rot, ops, input_rot)
-                errs = np.einsum("ij,ajbk,kl->aibl", target_rot, errs, input_rot)
-            elem["operators"] = ops
-            elem["operator_errors"] = errs
-
-    def flavor_reshape(self, targetbasis=None, inputbasis=None):
-        """
-        Changes the operators to have in the output targetbasis and/or in the input inputbasis.
-
-        The operation is in-place.
-
-        Parameters
-        ----------
-            targetbasis : numpy.ndarray
-                target rotation specified in the flavor basis
-            inputbasis : None or list
-                input rotation specified in the flavor basis
-        """
-        # calling with no arguments is an error
-        if targetbasis is None and inputbasis is None:
-            raise ValueError("Nor inputbasis nor targetbasis was given")
-        # now check to the current status
-        if targetbasis is not None and np.allclose(
-            targetbasis, np.eye(len(self["targetpids"]))
-        ):
-            targetbasis = None
-            warnings.warn("The new targetbasis is close to current basis")
-        if inputbasis is not None and np.allclose(
-            inputbasis, np.eye(len(self["inputpids"]))
-        ):
-            inputbasis = None
-            warnings.warn("The new inputbasis is close to current basis")
-        # after the checks: if there is still nothing to do, skip
-        if targetbasis is None and inputbasis is None:
-            logger.debug("Nothing done.")
-            return
-
-        # flip input around
-        if inputbasis is not None:
-            inv_inputbasis = np.linalg.inv(inputbasis)
-
-        # build new grid
-        for elem in self["Q2grid"].values():
-            ops = elem["operators"]
-            errs = elem["operator_errors"]
-            if targetbasis is not None and inputbasis is None:
-                ops = np.einsum("ca,ajbk->cjbk", targetbasis, ops)
-                errs = np.einsum("ca,ajbk->cjbk", targetbasis, errs)
-            elif inputbasis is not None and targetbasis is None:
-                ops = np.einsum("ajbk,bd->ajdk", ops, inv_inputbasis)
-                errs = np.einsum("ajbk,bd->ajdk", errs, inv_inputbasis)
-            else:
-                ops = np.einsum("ca,ajbk,bd->cjdk", targetbasis, ops, inv_inputbasis)
-                errs = np.einsum("ca,ajbk,bd->cjdk", targetbasis, errs, inv_inputbasis)
-            elem["operators"] = ops
-            elem["operator_errors"] = errs
-        # drop PIDs - keeping them int nevertheless
-        if inputbasis is not None:
-            self["inputpids"] = [0] * len(self["inputpids"])
-        if targetbasis is not None:
-            self["targetpids"] = [0] * len(self["targetpids"])
-
-    def to_evol(self, source=True, target=False):
-        """
-        Rotate the operator into evolution basis.
-
-        This also assigns also the pids. The operation is in-place.
-
-        Parameters
-        ----------
-            source : bool
-                rotate on the input tensor
-            target : bool
-                rotate on the output tensor
-        """
-        # rotate
-        inputbasis = br.rotate_flavor_to_evolution if source else None
-        targetbasis = br.rotate_flavor_to_evolution if target else None
-        self.flavor_reshape(inputbasis=inputbasis, targetbasis=targetbasis)
-        # assign pids
-        if source:
-            self["inputpids"] = br.evol_basis_pids
-        if target:
-            self["targetpids"] = br.evol_basis_pids
-
-    def get_raw(self, binarize=True, skip_q2_grid=False):
-        """
-        Serialize result as dict/YAML.
-
-        This maps the original numpy matrices to lists.
-
-        Parameters
-        ----------
-            binarize : bool
-                dump in binary format (instead of list format)
-
-        Returns
-        -------
-            out : dict
-                dictionary which will be written on output
-        """
-        # prepare output dict
-        out = {"Q2grid": {}, "eko_version": version.__version__}
-        # dump raw elements
-        for f in [
-            "interpolation_polynomial_degree",
-            "interpolation_is_log",
-            "q2_ref",
-        ]:
-            out[f] = self[f]
-
-        # list() work both for tuple and list
-        out["inputpids"] = list(self["inputpids"])
-        out["targetpids"] = list(self["targetpids"])
-        # make raw lists
-        # TODO: is interpolation_xgrid really needed in the output?
-        for k in ["interpolation_xgrid", "targetgrid", "inputgrid"]:
-            out[k] = self[k].tolist()
-        # make operators raw
-        if not skip_q2_grid:
-            for q2, op in self["Q2grid"].items():
-                out["Q2grid"][q2] = {}
-                for k, v in op.items():
-                    if k == "alphas":
-                        out["Q2grid"][q2][k] = float(v)
-                        continue
-                    if binarize:
-                        out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
-                    else:
-                        out["Q2grid"][q2][k] = v.tolist()
-        else:
-            out["Q2grid"] = self["Q2grid"]
-        return out
-
-    def dump_yaml(self, stream=None, binarize=True, skip_q2_grid=False):
-        """
-        Serialize result as YAML.
-
-        Parameters
-        ----------
-            stream : None or stream
-                if given, dump is written on it
-            binarize : bool
-                dump in binary format (instead of list format)
-            skip_q2_grid : bool
-                avoid dumping Q2grid (i.e. the actual operators) into the yaml
-                file (default: ``False``)
-
-        Returns
-        -------
-            dump : any
-                result of dump(output, stream), i.e. a string, if no stream is given or
-                Null, if written successfully to stream
-        """
-        # TODO explicitly silence yaml
-        out = self.get_raw(binarize, skip_q2_grid=skip_q2_grid)
-        return yaml.dump(out, stream)
-
-    def dump_yaml_to_file(self, filename, binarize=True, skip_q2_grid=False):
-        """
-        Writes YAML representation to a file.
-
-        Parameters
-        ----------
-            filename : str
-                target file name
-            binarize : bool
-                dump in binary format (instead of list format)
-            skip_q2_grid : bool
-                avoid dumping Q2grid (i.e. the actual operators) into the yaml
-                file (default: ``False``)
-
-        Returns
-        -------
-            ret : any
-                result of dump(output, stream), i.e. Null if written successfully
-        """
-        with open(filename, "w", encoding="utf-8") as f:
-            ret = self.dump_yaml(f, binarize, skip_q2_grid=skip_q2_grid)
-        return ret
-
-    def dump_tar(self, tarname):
-        """
-        Writes representation into a tar archive containing:
-
-        - metadata (in YAML)
-        - operator (in numpy ``.npy`` format)
-
-        Parameters
-        ----------
-            tarname : str
-                target file name
-        """
-        tarpath = pathlib.Path(tarname)
-        if tarpath.suffix != ".tar":
-            raise ValueError(f"'{tarname}' is not a valid tar filename, wrong suffix")
-
-        with tempfile.TemporaryDirectory() as tmpdir:
-            tmpdir = pathlib.Path(tmpdir)
-
-            cls = self.__class__
-            metadata = cls(**{str(k): v for k, v in self.items() if k != "Q2grid"})
-            metadata["Q2grid"] = list(self["Q2grid"].keys())
-
-            yamlname = tmpdir / "metadata.yaml"
-            metadata.dump_yaml_to_file(yamlname, skip_q2_grid=True)
-
-            for kind in next(iter(self["Q2grid"].values())).keys():
-                operator = np.stack([q2[kind] for q2 in self["Q2grid"].values()])
-                stream = io.BytesIO()
-                np.save(stream, operator)
-                stream.seek(0)
-                with lz4.frame.open(
-                    (tmpdir / kind).with_suffix(".npy.lz4"), "wb"
-                ) as fo:
-                    fo.write(stream.read())
-
-            with tarfile.open(tarpath, "w") as tar:
-                tar.add(tmpdir, arcname=tarpath.stem)
-
-    @classmethod
-    def load_yaml(cls, stream, skip_q2_grid=False):
-        """
-        Load YAML representation from stream
-
-        Parameters
-        ----------
-            stream : any
-                source stream
-            skip_q2_grid : bool
-                avoid loading Q2grid (i.e. the actual operators) from the yaml
-                file (default: ``False``)
-
-        Returns
-        -------
-            obj : output
-                loaded object
-        """
-        obj = yaml.safe_load(stream)
-        len_tpids = len(obj["targetpids"])
-        len_ipids = len(obj["inputpids"])
-        len_tgrid = len(obj["targetgrid"])
-        len_igrid = len(obj["inputgrid"])
-        # cast lists to numpy
-        for k in ["interpolation_xgrid", "inputgrid", "targetgrid"]:
-            obj[k] = np.array(obj[k])
-        # make operators numpy
-        if not skip_q2_grid:
-            for op in obj["Q2grid"].values():
-                for k, v in op.items():
-                    if k == "alphas":
-                        v = float(v)
-                    elif isinstance(v, list):
-                        v = np.array(v)
-                    elif isinstance(v, bytes):
-                        v = np.frombuffer(lz4.frame.decompress(v))
-                        v = v.reshape(len_tpids, len_tgrid, len_ipids, len_igrid)
-                    op[k] = v
-        return cls(obj)
-
-    @classmethod
-    def load_yaml_from_file(cls, filename, skip_q2_grid=False):
-        """
-        Load YAML representation from file
-
-        Parameters
-        ----------
-            filename : str
-                source file name
-            skip_q2_grid : bool
-                avoid loading Q2grid (i.e. the actual operators) from the yaml
-                file (default: ``False``)
-
-        Returns
-        -------
-            obj : output
-                loaded object
-        """
-        obj = None
-        with open(filename, encoding="utf-8") as o:
-            obj = Output.load_yaml(o, skip_q2_grid)
-        return obj
-
-    @classmethod
-    def load_tar(cls, tarname):
-        """
-        Load tar representation from file (compliant with :meth:`dump_tar`
-        output).
-
-        Parameters
-        ----------
-            tarname : str
-                source tar name
-
-        Returns
-        -------
-            obj : output
-                loaded object
-        """
-        tarpath = pathlib.Path(tarname)
-
-        with tempfile.TemporaryDirectory() as tmpdir:
-            tmpdir = pathlib.Path(tmpdir)
-
-            with tarfile.open(tarpath, "r") as tar:
-                tar.extractall(tmpdir)
-
-            # metadata = cls(**{str(k): v for k, v in self.items() if k != "Q2grid"})
-            # metadata["Q2grid"] = list(self["Q2grid"].keys())
-
-            innerdir = list(tmpdir.glob("*"))[0]
-            yamlname = innerdir / "metadata.yaml"
-            metadata = cls.load_yaml_from_file(yamlname, skip_q2_grid=True)
-
-            grids = {}
-            for fp in innerdir.glob("*.npy.lz4"):
-                with lz4.frame.open(fp, "rb") as fd:
-                    stream = io.BytesIO(fd.read())
-                    stream.seek(0)
-                    grids[pathlib.Path(fp.stem).stem] = np.load(stream)
-
-                fp.unlink()
-
-            q2grid = metadata["Q2grid"]
-            operator_grid = {}
-            for q2, slices in zip(q2grid, zip(*grids.values())):
-                operator_grid[q2] = dict(zip(grids.keys(), slices))
-            metadata["Q2grid"] = operator_grid
-
-        return metadata
+from .struct import Eko
diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
new file mode 100644
index 000000000..9e9849ee3
--- /dev/null
+++ b/src/eko/output/legacy.py
@@ -0,0 +1,259 @@
+# -*- coding: utf-8 -*-
+import io
+import pathlib
+import tarfile
+import tempfile
+
+import lz4.frame
+import numpy as np
+import yaml
+
+from .. import version
+
+
+def get_raw(obj, binarize=True, skip_q2_grid=False):
+    """
+    Serialize result as dict/YAML.
+
+    This maps the original numpy matrices to lists.
+
+    Parameters
+    ----------
+        binarize : bool
+            dump in binary format (instead of list format)
+
+    Returns
+    -------
+        out : dict
+            dictionary which will be written on output
+    """
+    # prepare output dict
+    out = {"Q2grid": {}, "eko_version": version.__version__}
+    # dump raw elements
+    for f in [
+        "interpolation_polynomial_degree",
+        "interpolation_is_log",
+        "q2_ref",
+    ]:
+        out[f] = obj[f]
+
+    # list() work both for tuple and list
+    out["inputpids"] = list(obj["inputpids"])
+    out["targetpids"] = list(obj["targetpids"])
+    # make raw lists
+    # TODO: is interpolation_xgrid really needed in the output?
+    for k in ["interpolation_xgrid", "targetgrid", "inputgrid"]:
+        out[k] = obj[k].tolist()
+    # make operators raw
+    if not skip_q2_grid:
+        for q2, op in obj["Q2grid"].items():
+            out["Q2grid"][q2] = {}
+            for k, v in op.items():
+                if k == "alphas":
+                    out["Q2grid"][q2][k] = float(v)
+                    continue
+                if binarize:
+                    out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
+                else:
+                    out["Q2grid"][q2][k] = v.tolist()
+    else:
+        out["Q2grid"] = obj["Q2grid"]
+    return out
+
+
+def dump_yaml(obj, stream=None, binarize=True, skip_q2_grid=False):
+    """
+    Serialize result as YAML.
+
+    Parameters
+    ----------
+        stream : None or stream
+            if given, dump is written on it
+        binarize : bool
+            dump in binary format (instead of list format)
+        skip_q2_grid : bool
+            avoid dumping Q2grid (i.e. the actual operators) into the yaml
+            file (default: ``False``)
+
+    Returns
+    -------
+        dump : any
+            result of dump(output, stream), i.e. a string, if no stream is given or
+            Null, if written successfully to stream
+    """
+    # TODO explicitly silence yaml
+    out = obj.get_raw(binarize, skip_q2_grid=skip_q2_grid)
+    return yaml.dump(out, stream)
+
+
+def dump_yaml_to_file(obj, filename, binarize=True, skip_q2_grid=False):
+    """
+    Writes YAML representation to a file.
+
+    Parameters
+    ----------
+        filename : str
+            target file name
+        binarize : bool
+            dump in binary format (instead of list format)
+        skip_q2_grid : bool
+            avoid dumping Q2grid (i.e. the actual operators) into the yaml
+            file (default: ``False``)
+
+    Returns
+    -------
+        ret : any
+            result of dump(output, stream), i.e. Null if written successfully
+    """
+    with open(filename, "w", encoding="utf-8") as f:
+        ret = obj.dump_yaml(f, binarize, skip_q2_grid=skip_q2_grid)
+    return ret
+
+
+def dump_tar(obj, tarname):
+    """
+    Writes representation into a tar archive containing:
+
+    - metadata (in YAML)
+    - operator (in numpy ``.npy`` format)
+
+    Parameters
+    ----------
+        tarname : str
+            target file name
+    """
+    tarpath = pathlib.Path(tarname)
+    if tarpath.suffix != ".tar":
+        raise ValueError(f"'{tarname}' is not a valid tar filename, wrong suffix")
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tmpdir = pathlib.Path(tmpdir)
+
+        cls = obj.__class__
+        metadata = cls(**{str(k): v for k, v in obj.items() if k != "Q2grid"})
+        metadata["Q2grid"] = list(obj["Q2grid"].keys())
+
+        yamlname = tmpdir / "metadata.yaml"
+        metadata.dump_yaml_to_file(yamlname, skip_q2_grid=True)
+
+        for kind in next(iter(obj["Q2grid"].values())).keys():
+            operator = np.stack([q2[kind] for q2 in obj["Q2grid"].values()])
+            stream = io.BytesIO()
+            np.save(stream, operator)
+            stream.seek(0)
+            with lz4.frame.open((tmpdir / kind).with_suffix(".npy.lz4"), "wb") as fo:
+                fo.write(stream.read())
+
+        with tarfile.open(tarpath, "w") as tar:
+            tar.add(tmpdir, arcname=tarpath.stem)
+
+
+def load_yaml(stream, skip_q2_grid=False):
+    """
+    Load YAML representation from stream
+
+    Parameters
+    ----------
+        stream : any
+            source stream
+        skip_q2_grid : bool
+            avoid loading Q2grid (i.e. the actual operators) from the yaml
+            file (default: ``False``)
+
+    Returns
+    -------
+        obj : output
+            loaded object
+    """
+    obj = yaml.safe_load(stream)
+    len_tpids = len(obj["targetpids"])
+    len_ipids = len(obj["inputpids"])
+    len_tgrid = len(obj["targetgrid"])
+    len_igrid = len(obj["inputgrid"])
+    # cast lists to numpy
+    for k in ["interpolation_xgrid", "inputgrid", "targetgrid"]:
+        obj[k] = np.array(obj[k])
+    # make operators numpy
+    if not skip_q2_grid:
+        for op in obj["Q2grid"].values():
+            for k, v in op.items():
+                if k == "alphas":
+                    v = float(v)
+                elif isinstance(v, list):
+                    v = np.array(v)
+                elif isinstance(v, bytes):
+                    v = np.frombuffer(lz4.frame.decompress(v))
+                    v = v.reshape(len_tpids, len_tgrid, len_ipids, len_igrid)
+                op[k] = v
+    return cls(obj)
+
+
+def load_yaml_from_file(filename, skip_q2_grid=False):
+    """
+    Load YAML representation from file
+
+    Parameters
+    ----------
+        filename : str
+            source file name
+        skip_q2_grid : bool
+            avoid loading Q2grid (i.e. the actual operators) from the yaml
+            file (default: ``False``)
+
+    Returns
+    -------
+        obj : output
+            loaded object
+    """
+    obj = None
+    with open(filename, encoding="utf-8") as o:
+        obj = load_yaml(o, skip_q2_grid)
+    return obj
+
+
+def load_tar(tarname):
+    """
+    Load tar representation from file (compliant with :meth:`dump_tar`
+    output).
+
+    Parameters
+    ----------
+        tarname : str
+            source tar name
+
+    Returns
+    -------
+        obj : output
+            loaded object
+    """
+    tarpath = pathlib.Path(tarname)
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tmpdir = pathlib.Path(tmpdir)
+
+        with tarfile.open(tarpath, "r") as tar:
+            tar.extractall(tmpdir)
+
+        # metadata = cls(**{str(k): v for k, v in obj.items() if k != "Q2grid"})
+        # metadata["Q2grid"] = list(obj["Q2grid"].keys())
+
+        innerdir = list(tmpdir.glob("*"))[0]
+        yamlname = innerdir / "metadata.yaml"
+        metadata = load_yaml_from_file(yamlname, skip_q2_grid=True)
+
+        grids = {}
+        for fp in innerdir.glob("*.npy.lz4"):
+            with lz4.frame.open(fp, "rb") as fd:
+                stream = io.BytesIO(fd.read())
+                stream.seek(0)
+                grids[pathlib.Path(fp.stem).stem] = np.load(stream)
+
+            fp.unlink()
+
+        q2grid = metadata["Q2grid"]
+        operator_grid = {}
+        for q2, slices in zip(q2grid, zip(*grids.values())):
+            operator_grid[q2] = dict(zip(grids.keys(), slices))
+        metadata["Q2grid"] = operator_grid
+
+    return metadata
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
new file mode 100644
index 000000000..aa1e79f79
--- /dev/null
+++ b/src/eko/output/manipulate.py
@@ -0,0 +1,165 @@
+# -*- coding: utf-8 -*-
+import logging
+import warnings
+
+import numpy as np
+
+from .. import basis_rotation as br
+from .. import interpolation
+
+logger = logging.getLogger(__name__)
+
+
+def xgrid_reshape(obj, targetgrid=None, inputgrid=None):
+    """
+    Changes the operators to have in the output targetgrid and/or in the input inputgrid.
+
+    The operation is in-place.
+
+    Parameters
+    ----------
+        targetgrid : None or list
+            xgrid for the target
+        inputgrid : None or list
+            xgrid for the input
+    """
+    # calling with no arguments is an error
+    if targetgrid is None and inputgrid is None:
+        raise ValueError("Nor inputgrid nor targetgrid was given")
+    # now check to the current status
+    if (
+        targetgrid is not None
+        and len(targetgrid) == len(obj["targetgrid"])
+        and np.allclose(targetgrid, obj["targetgrid"])
+    ):
+        targetgrid = None
+        warnings.warn("The new targetgrid is close to the current targetgrid")
+    if (
+        inputgrid is not None
+        and len(inputgrid) == len(obj["inputgrid"])
+        and np.allclose(inputgrid, obj["inputgrid"])
+    ):
+        inputgrid = None
+        warnings.warn("The new inputgrid is close to the current inputgrid")
+    # after the checks: if there is still nothing to do, skip
+    if targetgrid is None and inputgrid is None:
+        logger.debug("Nothing done.")
+        return
+
+    # construct matrices
+    if targetgrid is not None:
+        b = interpolation.InterpolatorDispatcher(
+            obj["targetgrid"],
+            obj["interpolation_polynomial_degree"],
+            obj["interpolation_is_log"],
+            False,
+        )
+        target_rot = b.get_interpolation(targetgrid)
+        obj["targetgrid"] = np.array(targetgrid)
+    if inputgrid is not None:
+        b = interpolation.InterpolatorDispatcher(
+            inputgrid,
+            obj["interpolation_polynomial_degree"],
+            obj["interpolation_is_log"],
+            False,
+        )
+        input_rot = b.get_interpolation(obj["inputgrid"])
+        obj["inputgrid"] = np.array(inputgrid)
+
+    # build new grid
+    for elem in obj["Q2grid"].values():
+        ops = elem["operators"]
+        errs = elem["operator_errors"]
+        if targetgrid is not None and inputgrid is None:
+            ops = np.einsum("ij,ajbk->aibk", target_rot, ops)
+            errs = np.einsum("ij,ajbk->aibk", target_rot, errs)
+        elif inputgrid is not None and targetgrid is None:
+            ops = np.einsum("ajbk,kl->ajbl", ops, input_rot)
+            errs = np.einsum("ajbk,kl->ajbl", errs, input_rot)
+        else:
+            ops = np.einsum("ij,ajbk,kl->aibl", target_rot, ops, input_rot)
+            errs = np.einsum("ij,ajbk,kl->aibl", target_rot, errs, input_rot)
+        elem["operators"] = ops
+        elem["operator_errors"] = errs
+
+
+def flavor_reshape(obj, targetbasis=None, inputbasis=None):
+    """
+    Changes the operators to have in the output targetbasis and/or in the input inputbasis.
+
+    The operation is in-place.
+
+    Parameters
+    ----------
+        targetbasis : numpy.ndarray
+            target rotation specified in the flavor basis
+        inputbasis : None or list
+            input rotation specified in the flavor basis
+    """
+    # calling with no arguments is an error
+    if targetbasis is None and inputbasis is None:
+        raise ValueError("Nor inputbasis nor targetbasis was given")
+    # now check to the current status
+    if targetbasis is not None and np.allclose(
+        targetbasis, np.eye(len(obj["targetpids"]))
+    ):
+        targetbasis = None
+        warnings.warn("The new targetbasis is close to current basis")
+    if inputbasis is not None and np.allclose(
+        inputbasis, np.eye(len(obj["inputpids"]))
+    ):
+        inputbasis = None
+        warnings.warn("The new inputbasis is close to current basis")
+    # after the checks: if there is still nothing to do, skip
+    if targetbasis is None and inputbasis is None:
+        logger.debug("Nothing done.")
+        return
+
+    # flip input around
+    if inputbasis is not None:
+        inv_inputbasis = np.linalg.inv(inputbasis)
+
+    # build new grid
+    for elem in obj["Q2grid"].values():
+        ops = elem["operators"]
+        errs = elem["operator_errors"]
+        if targetbasis is not None and inputbasis is None:
+            ops = np.einsum("ca,ajbk->cjbk", targetbasis, ops)
+            errs = np.einsum("ca,ajbk->cjbk", targetbasis, errs)
+        elif inputbasis is not None and targetbasis is None:
+            ops = np.einsum("ajbk,bd->ajdk", ops, inv_inputbasis)
+            errs = np.einsum("ajbk,bd->ajdk", errs, inv_inputbasis)
+        else:
+            ops = np.einsum("ca,ajbk,bd->cjdk", targetbasis, ops, inv_inputbasis)
+            errs = np.einsum("ca,ajbk,bd->cjdk", targetbasis, errs, inv_inputbasis)
+        elem["operators"] = ops
+        elem["operator_errors"] = errs
+    # drop PIDs - keeping them int nevertheless
+    if inputbasis is not None:
+        obj["inputpids"] = [0] * len(obj["inputpids"])
+    if targetbasis is not None:
+        obj["targetpids"] = [0] * len(obj["targetpids"])
+
+
+def to_evol(obj, source=True, target=False):
+    """
+    Rotate the operator into evolution basis.
+
+    This also assigns also the pids. The operation is in-place.
+
+    Parameters
+    ----------
+        source : bool
+            rotate on the input tensor
+        target : bool
+            rotate on the output tensor
+    """
+    # rotate
+    inputbasis = br.rotate_flavor_to_evolution if source else None
+    targetbasis = br.rotate_flavor_to_evolution if target else None
+    obj.flavor_reshape(inputbasis=inputbasis, targetbasis=targetbasis)
+    # assign pids
+    if source:
+        obj["inputpids"] = br.evol_basis_pids
+    if target:
+        obj["targetpids"] = br.evol_basis_pids
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
new file mode 100644
index 000000000..939eef3f7
--- /dev/null
+++ b/src/eko/output/struct.py
@@ -0,0 +1,6 @@
+# -*- coding: utf-8 -*-
+class Eko:
+    """
+    Wrapper for the output to help with application
+    to PDFs and dumping to file.
+    """

From 10b50f769d08f63e2d678f6388d9fcfa6d67c231 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:43:26 +0200
Subject: [PATCH 003/148] Break output into modules (and break everything)

---
 src/eko/output/__init__.py   |   3 +-
 src/eko/output/manipulate.py |  66 ++++++++-------
 src/eko/output/struct.py     |  54 +++++++++++-
 tests/eko/test_output.py     | 155 ++++++++++++++++++-----------------
 tests/eko/test_runner.py     |  17 ++--
 5 files changed, 176 insertions(+), 119 deletions(-)

diff --git a/src/eko/output/__init__.py b/src/eko/output/__init__.py
index f278e2860..312c35bb0 100644
--- a/src/eko/output/__init__.py
+++ b/src/eko/output/__init__.py
@@ -3,4 +3,5 @@
 This subpackage orchestrate the calculation workflow.
 """
 
-from .struct import Eko
+from . import manipulate
+from .struct import EKO
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index aa1e79f79..386815fd7 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -10,7 +10,7 @@
 logger = logging.getLogger(__name__)
 
 
-def xgrid_reshape(obj, targetgrid=None, inputgrid=None):
+def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
     """
     Changes the operators to have in the output targetgrid and/or in the input inputgrid.
 
@@ -29,15 +29,15 @@ def xgrid_reshape(obj, targetgrid=None, inputgrid=None):
     # now check to the current status
     if (
         targetgrid is not None
-        and len(targetgrid) == len(obj["targetgrid"])
-        and np.allclose(targetgrid, obj["targetgrid"])
+        and len(targetgrid) == len(eko.targetgrid)
+        and np.allclose(targetgrid, eko.targetgrid)
     ):
         targetgrid = None
         warnings.warn("The new targetgrid is close to the current targetgrid")
     if (
         inputgrid is not None
-        and len(inputgrid) == len(obj["inputgrid"])
-        and np.allclose(inputgrid, obj["inputgrid"])
+        and len(inputgrid) == len(eko.inputgrid)
+        and np.allclose(inputgrid, eko.inputgrid)
     ):
         inputgrid = None
         warnings.warn("The new inputgrid is close to the current inputgrid")
@@ -49,27 +49,27 @@ def xgrid_reshape(obj, targetgrid=None, inputgrid=None):
     # construct matrices
     if targetgrid is not None:
         b = interpolation.InterpolatorDispatcher(
-            obj["targetgrid"],
-            obj["interpolation_polynomial_degree"],
-            obj["interpolation_is_log"],
+            eko.targetgrid,
+            eko.interpolation_polynomial_degree,
+            eko.interpolation_is_log,
             False,
         )
         target_rot = b.get_interpolation(targetgrid)
-        obj["targetgrid"] = np.array(targetgrid)
+        eko.targetgrid = np.array(targetgrid)
     if inputgrid is not None:
         b = interpolation.InterpolatorDispatcher(
             inputgrid,
-            obj["interpolation_polynomial_degree"],
-            obj["interpolation_is_log"],
+            eko.interpolation_polynomial_degree,
+            eko.interpolation_is_log,
             False,
         )
-        input_rot = b.get_interpolation(obj["inputgrid"])
-        obj["inputgrid"] = np.array(inputgrid)
+        input_rot = b.get_interpolation(eko.inputgrid)
+        eko.inputgrid = np.array(inputgrid)
 
     # build new grid
-    for elem in obj["Q2grid"].values():
-        ops = elem["operators"]
-        errs = elem["operator_errors"]
+    for elem in eko.Q2grid.values():
+        ops = elem.operators
+        errs = elem.operator_errors
         if targetgrid is not None and inputgrid is None:
             ops = np.einsum("ij,ajbk->aibk", target_rot, ops)
             errs = np.einsum("ij,ajbk->aibk", target_rot, errs)
@@ -79,11 +79,11 @@ def xgrid_reshape(obj, targetgrid=None, inputgrid=None):
         else:
             ops = np.einsum("ij,ajbk,kl->aibl", target_rot, ops, input_rot)
             errs = np.einsum("ij,ajbk,kl->aibl", target_rot, errs, input_rot)
-        elem["operators"] = ops
-        elem["operator_errors"] = errs
+        elem.operators = ops
+        elem.operator_errors = errs
 
 
-def flavor_reshape(obj, targetbasis=None, inputbasis=None):
+def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
     """
     Changes the operators to have in the output targetbasis and/or in the input inputbasis.
 
@@ -101,13 +101,11 @@ def flavor_reshape(obj, targetbasis=None, inputbasis=None):
         raise ValueError("Nor inputbasis nor targetbasis was given")
     # now check to the current status
     if targetbasis is not None and np.allclose(
-        targetbasis, np.eye(len(obj["targetpids"]))
+        targetbasis, np.eye(len(eko.targetpids))
     ):
         targetbasis = None
         warnings.warn("The new targetbasis is close to current basis")
-    if inputbasis is not None and np.allclose(
-        inputbasis, np.eye(len(obj["inputpids"]))
-    ):
+    if inputbasis is not None and np.allclose(inputbasis, np.eye(len(eko.inputpids))):
         inputbasis = None
         warnings.warn("The new inputbasis is close to current basis")
     # after the checks: if there is still nothing to do, skip
@@ -120,9 +118,9 @@ def flavor_reshape(obj, targetbasis=None, inputbasis=None):
         inv_inputbasis = np.linalg.inv(inputbasis)
 
     # build new grid
-    for elem in obj["Q2grid"].values():
-        ops = elem["operators"]
-        errs = elem["operator_errors"]
+    for elem in eko.Q2grid.values():
+        ops = elem.operators
+        errs = elem.operator_errors
         if targetbasis is not None and inputbasis is None:
             ops = np.einsum("ca,ajbk->cjbk", targetbasis, ops)
             errs = np.einsum("ca,ajbk->cjbk", targetbasis, errs)
@@ -132,16 +130,16 @@ def flavor_reshape(obj, targetbasis=None, inputbasis=None):
         else:
             ops = np.einsum("ca,ajbk,bd->cjdk", targetbasis, ops, inv_inputbasis)
             errs = np.einsum("ca,ajbk,bd->cjdk", targetbasis, errs, inv_inputbasis)
-        elem["operators"] = ops
-        elem["operator_errors"] = errs
+        elem.operators = ops
+        elem.operator_errors = errs
     # drop PIDs - keeping them int nevertheless
     if inputbasis is not None:
-        obj["inputpids"] = [0] * len(obj["inputpids"])
+        eko.inputpids = [0] * len(eko.inputpids)
     if targetbasis is not None:
-        obj["targetpids"] = [0] * len(obj["targetpids"])
+        eko.targetpids = [0] * len(eko.targetpids)
 
 
-def to_evol(obj, source=True, target=False):
+def to_evol(eko, source=True, target=False, inplace=True):
     """
     Rotate the operator into evolution basis.
 
@@ -157,9 +155,9 @@ def to_evol(obj, source=True, target=False):
     # rotate
     inputbasis = br.rotate_flavor_to_evolution if source else None
     targetbasis = br.rotate_flavor_to_evolution if target else None
-    obj.flavor_reshape(inputbasis=inputbasis, targetbasis=targetbasis)
+    eko.flavor_reshape(inputbasis=inputbasis, targetbasis=targetbasis)
     # assign pids
     if source:
-        obj["inputpids"] = br.evol_basis_pids
+        eko.inputpids = br.evol_basis_pids
     if target:
-        obj["targetpids"] = br.evol_basis_pids
+        eko.targetpids = br.evol_basis_pids
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 939eef3f7..5126b4a44 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,6 +1,58 @@
 # -*- coding: utf-8 -*-
-class Eko:
+from dataclasses import dataclass
+from typing import Dict, Optional
+
+import numpy as np
+
+
+@dataclass
+class Operator:
+    alphas: float
+    operators: np.ndarray
+    operator_errors: Optional[np.ndarray] = None
+
+    @classmethod
+    def from_dict(cls, dictionary):
+        return cls(**dictionary)
+
+
+@dataclass
+class Debug:
+    skip_singlet: bool
+    skip_non_singlet: bool
+
+
+@dataclass
+class Configs:
+    ev_op_max_order: int
+    ev_op_iterations: int
+    interpolation_polynomial_degree: int
+    interpolation_is_log: bool
+    backward_inversion: str
+
+
+@dataclass
+class EKO:
     """
     Wrapper for the output to help with application
     to PDFs and dumping to file.
     """
+
+    xgrid: np.ndarray
+    targetgrid: np.ndarray
+    inputgrid: np.ndarray
+    targetpids: np.ndarray
+    inputpids: np.ndarray
+    Q02: float
+    Q2grid: Dict[float, Operator]
+    # _operators: Dict[float, Optional[Operator]]
+    configs: Configs
+    debug: Debug
+
+    # @property
+    # def Q2grid(self):
+    #    return np.ndarray(self._operators.keys())
+
+    @classmethod
+    def from_dict(cls, dictionary):
+        return cls(**dictionary)
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 6e7fc2617..1d21b6fe1 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -11,6 +11,7 @@
 
 from eko import basis_rotation as br
 from eko import output
+from eko.output import legacy, manipulate
 
 
 def eko_identity(shape):
@@ -23,101 +24,103 @@ def eko_identity(shape):
 def chk_keys(a, b):
     """Check all keys are preserved"""
     assert sorted(a.keys()) == sorted(b.keys())
-    for q2, op in a["Q2grid"].items():
-        assert q2 in b["Q2grid"]
-        opb = b["Q2grid"][q2]
+    for q2, op in a.Q2grid.items():
+        assert q2 in b.Q2grid
+        opb = b.Q2grid[q2]
         assert sorted(op.keys()) == sorted(opb.keys())
         assert op["alphas"] == opb["alphas"]
 
 
-class TestOutput:
+class TestLegacy:
     def test_io(self, fake_output):
         # create object
-        o1 = output.Output(fake_output)
+        o1 = output.EKO.from_dict(fake_output)
         # test streams
         stream = io.StringIO()
-        o1.dump_yaml(stream)
+        legacy.dump_yaml(o1, stream)
         # rewind and read again
         stream.seek(0)
-        o2 = output.Output.load_yaml(stream)
+        o2 = legacy.load_yaml(stream)
         np.testing.assert_almost_equal(
-            o1["interpolation_xgrid"], fake_output["interpolation_xgrid"]
+            o1.interpolation_xgrid, fake_output["interpolation_xgrid"]
         )
         np.testing.assert_almost_equal(
-            o2["interpolation_xgrid"], fake_output["interpolation_xgrid"]
+            o2.interpolation_xgrid, fake_output["interpolation_xgrid"]
         )
         # fake output files
         m_out = mock.mock_open(read_data="")
         with mock.patch("builtins.open", m_out) as mock_file:
             fn = "test.yaml"
-            o1.dump_yaml_to_file(fn)
+            legacy.dump_yaml_to_file(o1, fn)
             mock_file.assert_called_with(fn, "w", encoding="utf-8")
         # fake input file
         stream.seek(0)
         m_in = mock.mock_open(read_data=stream.getvalue())
         with mock.patch("builtins.open", m_in) as mock_file:
             fn = "test.yaml"
-            o3 = output.Output.load_yaml_from_file(fn)
+            o3 = legacy.load_yaml_from_file(fn)
             mock_file.assert_called_with(fn, encoding="utf-8")
             np.testing.assert_almost_equal(
-                o3["interpolation_xgrid"], fake_output["interpolation_xgrid"]
+                o3.interpolation_xgrid, fake_output["interpolation_xgrid"]
             )
         # repeat for tar
         fn = "test.tar"
         with tempfile.TemporaryDirectory() as folder:
             fp = pathlib.Path(folder) / fn
-            o1.dump_tar(fp)
-            o4 = output.Output.load_tar(fp)
+            legacy.dump_tar(o1, fp)
+            o4 = legacy.load_tar(fp)
             np.testing.assert_almost_equal(
-                o4["interpolation_xgrid"], fake_output["interpolation_xgrid"]
+                o4.interpolation_xgrid, fake_output["interpolation_xgrid"]
             )
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
-            o1.dump_tar(fn)
+            legacy.dump_tar(o1, fn)
 
     def test_rename_issue81(self, fake_output):
         # https://github.com/N3PDF/eko/issues/81
         # create object
-        o1 = output.Output(fake_output)
+        o1 = output.EKO.from_dict(fake_output)
 
         with tempfile.TemporaryDirectory() as folder:
             # dump
             p = pathlib.Path(folder)
             fp1 = p / "test1.tar"
             fp2 = p / "test2.tar"
-            o1.dump_tar(fp1)
+            legacy.dump_tar(o1, fp1)
             # rename
             shutil.move(fp1, fp2)
             # reload
-            o4 = output.Output.load_tar(fp2)
+            o4 = legacy.load_tar(fp2)
             np.testing.assert_almost_equal(
                 o4["interpolation_xgrid"], fake_output["interpolation_xgrid"]
             )
 
     def test_io_bin(self, fake_output):
         # create object
-        o1 = output.Output(fake_output)
+        o1 = output.EKO.from_dict(fake_output)
         # test streams
         stream = io.StringIO()
         o1.dump_yaml(stream, False)
         # rewind and read again
         stream.seek(0)
-        o2 = output.Output.load_yaml(stream)
+        o2 = legacy.load_yaml(stream)
         np.testing.assert_almost_equal(
-            o1["interpolation_xgrid"], fake_output["interpolation_xgrid"]
+            o1.interpolation_xgrid, fake_output.interpolation_xgrid
         )
         np.testing.assert_almost_equal(
-            o2["interpolation_xgrid"], fake_output["interpolation_xgrid"]
+            o2.interpolation_xgrid, fake_output.interpolation_xgrid
         )
 
+
+class TestManipulate:
     def test_xgrid_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
-        o1 = output.Output(fake_output)
-        o1["interpolation_xgrid"] = xg
-        o1["targetgrid"] = xg
-        o1["inputgrid"] = xg
-        o1["Q2grid"] = {
+        o1 = output.EKO.from_dict(fake_output)
+        o1.interpolation_xgrid = xg
+        o1.targetgrid = xg
+        o1.inputgrid = xg
+        o1.Q2grid = {
             10: dict(
                 operators=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
                 operator_errors=np.zeros((2, len(xg), 2, len(xg))),
@@ -127,52 +130,52 @@ def test_xgrid_reshape(self, fake_output):
         xgp = np.geomspace(1e-5, 1.0, 11)
         # only target
         ot = copy.deepcopy(o1)
-        ot.xgrid_reshape(xgp)
+        manipulate.xgrid_reshape(ot, xgp, inplace=True)
         chk_keys(o1, ot)
         assert ot["Q2grid"][10]["operators"].shape == (2, len(xgp), 2, len(xg))
         ott = copy.deepcopy(o1)
         with pytest.warns(Warning):
-            ott.xgrid_reshape(xg)
+            manipulate.xgrid_reshape(ott, xg)
             chk_keys(o1, ott)
             np.testing.assert_allclose(
-                ott["Q2grid"][10]["operators"], o1["Q2grid"][10]["operators"]
+                ott.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
             )
 
         # only input
         oi = copy.deepcopy(o1)
-        oi.xgrid_reshape(inputgrid=xgp)
-        assert oi["Q2grid"][10]["operators"].shape == (2, len(xg), 2, len(xgp))
+        manipulate.xgrid_reshape(o1, inputgrid=xgp)
+        assert oi.Q2grid[10]["operators"].shape == (2, len(xg), 2, len(xgp))
         chk_keys(o1, oi)
         oii = copy.deepcopy(o1)
         with pytest.warns(Warning):
-            oii.xgrid_reshape(inputgrid=xg)
+            manipulate.xgrid_reshape(oii, inputgrid=xg)
             chk_keys(o1, oii)
             np.testing.assert_allclose(
-                oii["Q2grid"][10]["operators"], o1["Q2grid"][10]["operators"]
+                oii.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
             )
 
         # both
         oit = copy.deepcopy(o1)
-        oit.xgrid_reshape(xgp, xgp)
+        manipulate.xgrid_reshape(oit, xgp, xgp)
         chk_keys(o1, oit)
         op = eko_identity([1, 2, len(xgp), 2, len(xgp)])
-        np.testing.assert_allclose(oit["Q2grid"][10]["operators"], op[0], atol=1e-10)
+        np.testing.assert_allclose(oit.Q2grid[10]["operators"], op[0], atol=1e-10)
         # error
         with pytest.raises(ValueError):
-            copy.deepcopy(o1).xgrid_reshape()
+            manipulate.xgrid_reshape(copy.deepcopy(o1))
 
     def test_reshape_io(self, fake_output):
         # create object
-        o1 = output.Output(fake_output)
+        o1 = output.EKO.from_dict(fake_output)
         o2 = copy.deepcopy(o1)
-        o2.xgrid_reshape([0.1, 1.0], [0.1, 1.0])
-        o2.flavor_reshape(inputbasis=np.array([[1, -1], [1, 1]]))
+        manipulate.xgrid_reshape(o2, [0.1, 1.0], [0.1, 1.0])
+        manipulate.flavor_reshape(o2, inputbasis=np.array([[1, -1], [1, 1]]))
         # dump
         stream = io.StringIO()
-        o2.dump_yaml(stream)
+        legacy.dump_yaml(o2, stream)
         # reload
         stream.seek(0)
-        o3 = output.Output.load_yaml(stream)
+        o3 = legacy.load_yaml(stream)
         # eko_version is only added in get_raw
         del o3["eko_version"]
         chk_keys(o1, o3)
@@ -180,11 +183,11 @@ def test_reshape_io(self, fake_output):
     def test_flavor_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
-        o1 = output.Output(fake_output)
-        o1["interpolation_xgrid"] = xg
-        o1["targetgrid"] = xg
-        o1["inputgrid"] = xg
-        o1["Q2grid"] = {
+        o1 = output.EKO.from_dict(fake_output)
+        o1.interpolation_xgrid = xg
+        o1.targetgrid = xg
+        o1.inputgrid = xg
+        o1.Q2grid = {
             10: dict(
                 operators=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
                 operator_errors=np.zeros((2, len(xg), 2, len(xg))),
@@ -194,48 +197,50 @@ def test_flavor_reshape(self, fake_output):
         # only target
         target_r = np.array([[1, -1], [1, 1]])
         ot = copy.deepcopy(o1)
-        ot.flavor_reshape(target_r)
+        manipulate.flavor_reshape(ot, target_r)
         chk_keys(o1, ot)
-        assert ot["Q2grid"][10]["operators"].shape == (2, len(xg), 2, len(xg))
+        assert ot.Q2grid[10]["operators"].shape == (2, len(xg), 2, len(xg))
         ott = copy.deepcopy(ot)
-        ott.flavor_reshape(np.linalg.inv(target_r))
+        manipulate.flavor_reshape(ott, np.linalg.inv(target_r))
         np.testing.assert_allclose(
-            ott["Q2grid"][10]["operators"], o1["Q2grid"][10]["operators"]
+            ott.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
         )
         with pytest.warns(Warning):
-            ott.flavor_reshape(np.eye(2))
+            manipulate.flavor_reshape(ott, np.eye(2))
             chk_keys(o1, ott)
             np.testing.assert_allclose(
-                ott["Q2grid"][10]["operators"], o1["Q2grid"][10]["operators"]
+                ott.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
             )
 
         # only input
         input_r = np.array([[1, -1], [1, 1]])
         oi = copy.deepcopy(o1)
-        oi.flavor_reshape(inputbasis=input_r)
+        manipulate.flavor_reshape(oi, inputbasis=input_r)
         chk_keys(o1, oi)
-        assert oi["Q2grid"][10]["operators"].shape == (2, len(xg), 2, len(xg))
+        assert oi.Q2grid[10]["operators"].shape == (2, len(xg), 2, len(xg))
         oii = copy.deepcopy(oi)
-        oii.flavor_reshape(inputbasis=np.linalg.inv(input_r))
+        manipulate.flavor_reshape(oii, inputbasis=np.linalg.inv(input_r))
         np.testing.assert_allclose(
-            oii["Q2grid"][10]["operators"], o1["Q2grid"][10]["operators"]
+            oii.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
         )
         with pytest.warns(Warning):
-            oii.flavor_reshape(inputbasis=np.eye(2))
+            manipulate.flavor_reshape(oii, inputbasis=np.eye(2))
             chk_keys(o1, oii)
             np.testing.assert_allclose(
-                oii["Q2grid"][10]["operators"], o1["Q2grid"][10]["operators"]
+                oii.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
             )
 
         # both
         oit = copy.deepcopy(o1)
-        oit.flavor_reshape(np.array([[1, -1], [1, 1]]), np.array([[1, -1], [1, 1]]))
+        manipulate.flavor_reshape(
+            oit, np.array([[1, -1], [1, 1]]), np.array([[1, -1], [1, 1]])
+        )
         chk_keys(o1, oit)
         op = eko_identity([1, 2, len(xg), 2, len(xg)]).copy()
-        np.testing.assert_allclose(oit["Q2grid"][10]["operators"], op[0], atol=1e-10)
+        np.testing.assert_allclose(oit.Q2grid[10]["operators"], op[0], atol=1e-10)
         # error
         with pytest.raises(ValueError):
-            copy.deepcopy(o1).flavor_reshape()
+            manipulate.flavor_reshape(copy.deepcopy(o1))
 
     def test_to_evol(self, fake_factory):
         interpolation_xgrid = np.array([0.5, 1.0])
@@ -257,30 +262,30 @@ def test_to_evol(self, fake_factory):
             targetpids=br.flavor_basis_pids,
             Q2grid=Q2grid,
         )
-        o00 = output.Output(d)
+        o00 = output.EKO.from_dict(d)
         o01 = copy.copy(o00)
-        o01.to_evol()
+        manipulate.to_evol(o01)
         o10 = copy.copy(o00)
-        o10.to_evol(False, True)
+        manipulate.to_evol(o10, False, True)
         o11 = copy.copy(o00)
-        o11.to_evol(True, True)
+        manipulate.to_evol(o11, True, True)
         chk_keys(o00, o11)
 
         # check the input rotated one
-        np.testing.assert_allclose(o01["inputpids"], br.evol_basis_pids)
-        np.testing.assert_allclose(o01["targetpids"], br.flavor_basis_pids)
+        np.testing.assert_allclose(o01.inputpids, br.evol_basis_pids)
+        np.testing.assert_allclose(o01.targetpids, br.flavor_basis_pids)
         # rotate also target
-        o01.to_evol(False, True)
+        manipulate.to_evol(o01, False, True)
         np.testing.assert_allclose(
-            o01["Q2grid"][q2_out]["operators"], o11["Q2grid"][q2_out]["operators"]
+            o01.Q2grid[q2_out]["operators"], o11.Q2grid[q2_out]["operators"]
         )
         chk_keys(o00, o01)
         # check the target rotated one
-        np.testing.assert_allclose(o10["inputpids"], br.flavor_basis_pids)
-        np.testing.assert_allclose(o10["targetpids"], br.evol_basis_pids)
+        np.testing.assert_allclose(o10.inputpids, br.flavor_basis_pids)
+        np.testing.assert_allclose(o10.targetpids, br.evol_basis_pids)
         # rotate also input
-        o10.to_evol()
+        manipulate.to_evol(o10)
         np.testing.assert_allclose(
-            o10["Q2grid"][q2_out]["operators"], o11["Q2grid"][q2_out]["operators"]
+            o10.Q2grid[q2_out]["operators"], o11.Q2grid[q2_out]["operators"]
         )
         chk_keys(o00, o10)
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index dc09c214c..6b5c66d5f 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -38,14 +38,15 @@
 operators_card = {
     "Q2grid": [10, 100],
     "interpolation_xgrid": [0.01, 0.1, 1.0],
-    "interpolation_polynomial_degree": 1,
-    "interpolation_is_log": True,
-    "debug_skip_singlet": True,
-    "debug_skip_non_singlet": True,
-    "ev_op_max_order": (2, 0),
-    "ev_op_iterations": 1,
-    "backward_inversion": "exact",
-    "n_integration_cores": 1,
+    "configs": {
+        "interpolation_polynomial_degree": 1,
+        "interpolation_is_log": True,
+        "ev_op_max_order": (2, 0),
+        "ev_op_iterations": 1,
+        "backward_inversion": "exact",
+        "n_integration_cores": 1,
+    },
+    "debug": {"skip_singlet": True, "skip_non_singlet": True},
 }
 
 

From dd9443047ae1867dd6e6da1f5a1822583306f7e6 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:45:39 +0200
Subject: [PATCH 004/148] Add new output serialization

---
 src/eko/output/legacy.py |  5 ++-
 src/eko/output/struct.py | 80 +++++++++++++++++++++++++++++-----------
 src/eko/runner.py        |  6 +--
 tests/conftest.py        | 24 ++++++++----
 tests/eko/test_output.py | 32 +++++-----------
 5 files changed, 90 insertions(+), 57 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 9e9849ee3..86a5030be 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -9,6 +9,7 @@
 import yaml
 
 from .. import version
+from . import struct
 
 
 def get_raw(obj, binarize=True, skip_q2_grid=False):
@@ -82,7 +83,7 @@ def dump_yaml(obj, stream=None, binarize=True, skip_q2_grid=False):
             Null, if written successfully to stream
     """
     # TODO explicitly silence yaml
-    out = obj.get_raw(binarize, skip_q2_grid=skip_q2_grid)
+    out = get_raw(obj, binarize, skip_q2_grid=skip_q2_grid)
     return yaml.dump(out, stream)
 
 
@@ -185,7 +186,7 @@ def load_yaml(stream, skip_q2_grid=False):
                     v = np.frombuffer(lz4.frame.decompress(v))
                     v = v.reshape(len_tpids, len_tgrid, len_ipids, len_igrid)
                 op[k] = v
-    return cls(obj)
+    return struct.EKO.from_dict(obj)
 
 
 def load_yaml_from_file(filename, skip_q2_grid=False):
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 5126b4a44..66cd8b59e 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,34 +1,56 @@
 # -*- coding: utf-8 -*-
-from dataclasses import dataclass
-from typing import Dict, Optional
+from dataclasses import dataclass, fields
+from typing import Dict, Literal, Optional
 
 import numpy as np
 
 
-@dataclass
-class Operator:
-    alphas: float
-    operators: np.ndarray
-    operator_errors: Optional[np.ndarray] = None
+class DictLike:
+    def __init__(self, **kwargs):
+        pass
 
     @classmethod
     def from_dict(cls, dictionary):
         return cls(**dictionary)
 
+    @property
+    def raw(self):
+        dictionary = {}
+        for field in fields(self):
+            value = getattr(self, field.name)
+            dictionary[field.name] = (
+                value if not isinstance(value, np.ndarray) else value.tolist()
+            )
+
+
+@dataclass
+class Operator(DictLike):
+    alphas: float
+    operators: np.ndarray
+    operator_errors: Optional[np.ndarray] = None
+
 
 @dataclass
-class Debug:
-    skip_singlet: bool
-    skip_non_singlet: bool
+class Debug(DictLike):
+    skip_singlet: bool = False
+    skip_non_singlet: bool = False
 
 
 @dataclass
-class Configs:
+class Configs(DictLike):
     ev_op_max_order: int
     ev_op_iterations: int
     interpolation_polynomial_degree: int
     interpolation_is_log: bool
-    backward_inversion: str
+    backward_inversion: Literal["exact", "expanded"]
+
+
+@dataclass
+class Rotations(DictLike):
+    targetgrid: Optional[np.ndarray] = None
+    inputgrid: Optional[np.ndarray] = None
+    targetpids: Optional[np.ndarray] = None
+    inputpids: Optional[np.ndarray] = None
 
 
 @dataclass
@@ -39,20 +61,34 @@ class EKO:
     """
 
     xgrid: np.ndarray
-    targetgrid: np.ndarray
-    inputgrid: np.ndarray
-    targetpids: np.ndarray
-    inputpids: np.ndarray
     Q02: float
-    Q2grid: Dict[float, Operator]
-    # _operators: Dict[float, Optional[Operator]]
+    _operators: Dict[float, Optional[Operator]]
     configs: Configs
+    rotations: Rotations
     debug: Debug
 
-    # @property
-    # def Q2grid(self):
-    #    return np.ndarray(self._operators.keys())
+    @property
+    def Q2grid(self):
+        return np.array(self._operators.keys())
 
     @classmethod
     def from_dict(cls, dictionary):
-        return cls(**dictionary)
+        return cls(
+            xgrid=dictionary["xgrid"],
+            Q02=dictionary["Q0"] ** 2,
+            _operators={q2: None for q2 in dictionary["Q2grid"]},
+            configs=Configs.from_dict(dictionary["configs"]),
+            rotations=Rotations.from_dict(dictionary["rotations"]),
+            debug=Debug.from_dict(dictionary.get("debug", {})),
+        )
+
+    @property
+    def raw(self):
+        return dict(
+            xgrid=self.xgrid.tolist(),
+            Q0=np.sqrt(self.Q02),
+            Q2grid=self.Q2grid,
+            configs=self.configs.raw,
+            rotations=self.rotations.raw,
+            debug=self.debug.raw,
+        )
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 2270f737d..45cc42222 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -11,7 +11,7 @@
 from . import compatibility, interpolation, msbar_masses
 from .couplings import Couplings
 from .evolution_operator.grid import OperatorGrid
-from .output import Output
+from .output import EKO
 from .thresholds import ThresholdsAtlas
 
 logger = logging.getLogger(__name__)
@@ -40,7 +40,7 @@ class Runner:
 """
 
     def __init__(self, theory_card, operators_card):
-        self.out = Output()
+        self.out = EKO()
 
         new_theory, new_operators = compatibility.update(theory_card, operators_card)
 
@@ -82,7 +82,7 @@ def get_output(self):
 
         Returns
         -------
-            ret : eko.output.Output
+            ret : eko.output.EKO
                 output instance
         """
         # add all operators
diff --git a/tests/conftest.py b/tests/conftest.py
index 62d23882d..3ca998106 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -43,14 +43,22 @@ def fake_output(self):
         q2_out = 2
         Q2grid = self.mk_g([q2_out], len(pids), len(interpolation_xgrid))
         d = dict(
-            interpolation_xgrid=interpolation_xgrid,
-            targetgrid=interpolation_xgrid,
-            inputgrid=interpolation_xgrid,
-            interpolation_polynomial_degree=interpolation_polynomial_degree,
-            interpolation_is_log=interpolation_is_log,
-            q2_ref=q2_ref,
-            inputpids=pids,
-            targetpids=pids,
+            xgrid=interpolation_xgrid,
+            rotations=dict(
+                targetgrid=interpolation_xgrid,
+                inputgrid=interpolation_xgrid,
+                inputpids=pids,
+                targetpids=pids,
+            ),
+            Q0=np.sqrt(q2_ref),
+            couplings=dict(),
+            configs=dict(
+                ev_op_max_order=1,
+                ev_op_iterations=1,
+                interpolation_polynomial_degree=interpolation_polynomial_degree,
+                interpolation_is_log=interpolation_is_log,
+                backward_inversion="exact",
+            ),
             Q2grid=Q2grid,
         )
         return d
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 1d21b6fe1..53ddaaf3d 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -41,12 +41,8 @@ def test_io(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(
-            o1.interpolation_xgrid, fake_output["interpolation_xgrid"]
-        )
-        np.testing.assert_almost_equal(
-            o2.interpolation_xgrid, fake_output["interpolation_xgrid"]
-        )
+        np.testing.assert_almost_equal(o1.xgrid, fake_output["interpolation_xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid, fake_output["interpolation_xgrid"])
         # fake output files
         m_out = mock.mock_open(read_data="")
         with mock.patch("builtins.open", m_out) as mock_file:
@@ -60,18 +56,14 @@ def test_io(self, fake_output):
             fn = "test.yaml"
             o3 = legacy.load_yaml_from_file(fn)
             mock_file.assert_called_with(fn, encoding="utf-8")
-            np.testing.assert_almost_equal(
-                o3.interpolation_xgrid, fake_output["interpolation_xgrid"]
-            )
+            np.testing.assert_almost_equal(o3.xgrid, fake_output["interpolation_xgrid"])
         # repeat for tar
         fn = "test.tar"
         with tempfile.TemporaryDirectory() as folder:
             fp = pathlib.Path(folder) / fn
             legacy.dump_tar(o1, fp)
             o4 = legacy.load_tar(fp)
-            np.testing.assert_almost_equal(
-                o4.interpolation_xgrid, fake_output["interpolation_xgrid"]
-            )
+            np.testing.assert_almost_equal(o4.xgrid, fake_output["interpolation_xgrid"])
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
             legacy.dump_tar(o1, fn)
@@ -100,16 +92,12 @@ def test_io_bin(self, fake_output):
         o1 = output.EKO.from_dict(fake_output)
         # test streams
         stream = io.StringIO()
-        o1.dump_yaml(stream, False)
+        legacy.dump_yaml(o1, stream, False)
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(
-            o1.interpolation_xgrid, fake_output.interpolation_xgrid
-        )
-        np.testing.assert_almost_equal(
-            o2.interpolation_xgrid, fake_output.interpolation_xgrid
-        )
+        np.testing.assert_almost_equal(o1.xgrid, fake_output.xgrid)
+        np.testing.assert_almost_equal(o2.xgrid, fake_output.xgrid)
 
 
 class TestManipulate:
@@ -117,7 +105,7 @@ def test_xgrid_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
         o1 = output.EKO.from_dict(fake_output)
-        o1.interpolation_xgrid = xg
+        o1.xgrid = xg
         o1.targetgrid = xg
         o1.inputgrid = xg
         o1.Q2grid = {
@@ -184,7 +172,7 @@ def test_flavor_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
         o1 = output.EKO.from_dict(fake_output)
-        o1.interpolation_xgrid = xg
+        o1.xgrid = xg
         o1.targetgrid = xg
         o1.inputgrid = xg
         o1.Q2grid = {
@@ -252,7 +240,7 @@ def test_to_evol(self, fake_factory):
             [q2_out], len(br.flavor_basis_pids), len(interpolation_xgrid)
         )
         d = dict(
-            interpolation_xgrid=interpolation_xgrid,
+            xgrid=interpolation_xgrid,
             targetgrid=interpolation_xgrid,
             inputgrid=interpolation_xgrid,
             interpolation_polynomial_degree=interpolation_polynomial_degree,

From b3943a1197a9937430bb6573e24f44043d141759 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 16 Mar 2022 17:10:53 +0100
Subject: [PATCH 005/148] Recover one legacy test

---
 src/eko/output/legacy.py | 66 ++++++++++++++++++----------------------
 src/eko/output/struct.py | 19 +++++++++---
 tests/eko/test_output.py | 13 ++++----
 3 files changed, 51 insertions(+), 47 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 86a5030be..34d4b173b 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -12,7 +12,7 @@
 from . import struct
 
 
-def get_raw(obj, binarize=True, skip_q2_grid=False):
+def get_raw(eko, binarize=True, skip_q2_grid=False):
     """
     Serialize result as dict/YAML.
 
@@ -20,43 +20,36 @@ def get_raw(obj, binarize=True, skip_q2_grid=False):
 
     Parameters
     ----------
-        binarize : bool
-            dump in binary format (instead of list format)
+    binarize : bool
+        dump in binary format (instead of list format)
 
     Returns
     -------
-        out : dict
-            dictionary which will be written on output
+    out : dict
+        dictionary which will be written on output
+
     """
+    obj = eko.raw
+
     # prepare output dict
     out = {"Q2grid": {}, "eko_version": version.__version__}
     # dump raw elements
-    for f in [
-        "interpolation_polynomial_degree",
-        "interpolation_is_log",
-        "q2_ref",
-    ]:
+    for f in ["Q0", "xgrid", "configs", "rotations"]:
         out[f] = obj[f]
 
-    # list() work both for tuple and list
-    out["inputpids"] = list(obj["inputpids"])
-    out["targetpids"] = list(obj["targetpids"])
-    # make raw lists
-    # TODO: is interpolation_xgrid really needed in the output?
-    for k in ["interpolation_xgrid", "targetgrid", "inputgrid"]:
-        out[k] = obj[k].tolist()
     # make operators raw
     if not skip_q2_grid:
-        for q2, op in obj["Q2grid"].items():
+        for q2, op in eko.items():
             out["Q2grid"][q2] = {}
-            for k, v in op.items():
-                if k == "alphas":
-                    out["Q2grid"][q2][k] = float(v)
-                    continue
-                if binarize:
-                    out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
-                else:
-                    out["Q2grid"][q2][k] = v.tolist()
+            if op is not None:
+                for k, v in op.items():
+                    if k == "alphas":
+                        out["Q2grid"][q2][k] = float(v)
+                        continue
+                    if binarize:
+                        out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
+                    else:
+                        out["Q2grid"][q2][k] = v.tolist()
     else:
         out["Q2grid"] = obj["Q2grid"]
     return out
@@ -107,7 +100,7 @@ def dump_yaml_to_file(obj, filename, binarize=True, skip_q2_grid=False):
             result of dump(output, stream), i.e. Null if written successfully
     """
     with open(filename, "w", encoding="utf-8") as f:
-        ret = obj.dump_yaml(f, binarize, skip_q2_grid=skip_q2_grid)
+        ret = dump_yaml(obj, f, binarize, skip_q2_grid=skip_q2_grid)
     return ret
 
 
@@ -130,12 +123,11 @@ def dump_tar(obj, tarname):
     with tempfile.TemporaryDirectory() as tmpdir:
         tmpdir = pathlib.Path(tmpdir)
 
-        cls = obj.__class__
-        metadata = cls(**{str(k): v for k, v in obj.items() if k != "Q2grid"})
-        metadata["Q2grid"] = list(obj["Q2grid"].keys())
+        metadata = {str(k): v for k, v in obj.items() if k != "Q2grid"}
+        metadata["Q2grid"] = obj.Q2grid.tolist()
 
         yamlname = tmpdir / "metadata.yaml"
-        metadata.dump_yaml_to_file(yamlname, skip_q2_grid=True)
+        dump_yaml_to_file(metadata, yamlname, skip_q2_grid=True)
 
         for kind in next(iter(obj["Q2grid"].values())).keys():
             operator = np.stack([q2[kind] for q2 in obj["Q2grid"].values()])
@@ -167,13 +159,13 @@ def load_yaml(stream, skip_q2_grid=False):
             loaded object
     """
     obj = yaml.safe_load(stream)
-    len_tpids = len(obj["targetpids"])
-    len_ipids = len(obj["inputpids"])
-    len_tgrid = len(obj["targetgrid"])
-    len_igrid = len(obj["inputgrid"])
+    len_tpids = len(obj["rotations"]["targetpids"])
+    len_ipids = len(obj["rotations"]["inputpids"])
+    len_tgrid = len(obj["rotations"]["targetgrid"])
+    len_igrid = len(obj["rotations"]["inputgrid"])
     # cast lists to numpy
-    for k in ["interpolation_xgrid", "inputgrid", "targetgrid"]:
-        obj[k] = np.array(obj[k])
+    for k, v in obj["rotations"].items():
+        obj["rotations"][k] = np.array(v)
     # make operators numpy
     if not skip_q2_grid:
         for op in obj["Q2grid"].values():
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 66cd8b59e..3bf6b45e8 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from dataclasses import dataclass, fields
+from dataclasses import asdict, dataclass, fields
 from typing import Dict, Literal, Optional
 
 import numpy as np
@@ -22,6 +22,8 @@ def raw(self):
                 value if not isinstance(value, np.ndarray) else value.tolist()
             )
 
+        return dictionary
+
 
 @dataclass
 class Operator(DictLike):
@@ -67,14 +69,23 @@ class EKO:
     rotations: Rotations
     debug: Debug
 
+    def __iter__(self):
+        return iter(self._operators)
+
+    def items(self):
+        return (
+            (k, asdict(v) if v is not None else None)
+            for k, v in self._operators.items()
+        )
+
     @property
     def Q2grid(self):
-        return np.array(self._operators.keys())
+        return np.array(list(self._operators))
 
     @classmethod
     def from_dict(cls, dictionary):
         return cls(
-            xgrid=dictionary["xgrid"],
+            xgrid=np.array(dictionary["xgrid"]),
             Q02=dictionary["Q0"] ** 2,
             _operators={q2: None for q2 in dictionary["Q2grid"]},
             configs=Configs.from_dict(dictionary["configs"]),
@@ -86,7 +97,7 @@ def from_dict(cls, dictionary):
     def raw(self):
         return dict(
             xgrid=self.xgrid.tolist(),
-            Q0=np.sqrt(self.Q02),
+            Q0=float(np.sqrt(self.Q02)),
             Q2grid=self.Q2grid,
             configs=self.configs.raw,
             rotations=self.rotations.raw,
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 53ddaaf3d..421940336 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -41,8 +41,8 @@ def test_io(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid, fake_output["interpolation_xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid, fake_output["interpolation_xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid, fake_output["xgrid"])
         # fake output files
         m_out = mock.mock_open(read_data="")
         with mock.patch("builtins.open", m_out) as mock_file:
@@ -56,14 +56,14 @@ def test_io(self, fake_output):
             fn = "test.yaml"
             o3 = legacy.load_yaml_from_file(fn)
             mock_file.assert_called_with(fn, encoding="utf-8")
-            np.testing.assert_almost_equal(o3.xgrid, fake_output["interpolation_xgrid"])
+            np.testing.assert_almost_equal(o3.xgrid, fake_output["xgrid"])
         # repeat for tar
         fn = "test.tar"
         with tempfile.TemporaryDirectory() as folder:
             fp = pathlib.Path(folder) / fn
             legacy.dump_tar(o1, fp)
             o4 = legacy.load_tar(fp)
-            np.testing.assert_almost_equal(o4.xgrid, fake_output["interpolation_xgrid"])
+            np.testing.assert_almost_equal(o4.xgrid, fake_output["xgrid"])
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
             legacy.dump_tar(o1, fn)
@@ -78,6 +78,7 @@ def test_rename_issue81(self, fake_output):
             p = pathlib.Path(folder)
             fp1 = p / "test1.tar"
             fp2 = p / "test2.tar"
+            __import__("pdb").set_trace()
             legacy.dump_tar(o1, fp1)
             # rename
             shutil.move(fp1, fp2)
@@ -96,8 +97,8 @@ def test_io_bin(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid, fake_output.xgrid)
-        np.testing.assert_almost_equal(o2.xgrid, fake_output.xgrid)
+        np.testing.assert_almost_equal(o1.xgrid, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid, fake_output["xgrid"])
 
 
 class TestManipulate:

From 211be29c5b0996584987d38cd925402e3ff0a60f Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 16 Mar 2022 18:14:00 +0100
Subject: [PATCH 006/148] Recover all legacy tests

---
 src/eko/output/legacy.py | 23 ++++++++++++++++-------
 tests/eko/test_output.py |  5 +----
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 34d4b173b..aea7f244e 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -123,14 +123,22 @@ def dump_tar(obj, tarname):
     with tempfile.TemporaryDirectory() as tmpdir:
         tmpdir = pathlib.Path(tmpdir)
 
-        metadata = {str(k): v for k, v in obj.items() if k != "Q2grid"}
+        metadata = {str(k): v for k, v in obj.raw.items() if k != "Q2grid"}
         metadata["Q2grid"] = obj.Q2grid.tolist()
 
         yamlname = tmpdir / "metadata.yaml"
-        dump_yaml_to_file(metadata, yamlname, skip_q2_grid=True)
-
-        for kind in next(iter(obj["Q2grid"].values())).keys():
-            operator = np.stack([q2[kind] for q2 in obj["Q2grid"].values()])
+        with open(yamlname, "w", encoding="utf-8") as fd:
+            yaml.dump(metadata, fd)
+
+        for kind in ["alphas", "operators", "operator_errors"]:
+            elements = []
+            for q2, op in obj.items():
+                if op is not None:
+                    el = getattr(q2, kind)
+                else:
+                    el = np.zeros((len(obj.xgrid), 14, len(obj.xgrid), 14))
+                elements.append(el)
+            operator = np.stack(elements)
             stream = io.BytesIO()
             np.save(stream, operator)
             stream.seek(0)
@@ -232,7 +240,8 @@ def load_tar(tarname):
 
         innerdir = list(tmpdir.glob("*"))[0]
         yamlname = innerdir / "metadata.yaml"
-        metadata = load_yaml_from_file(yamlname, skip_q2_grid=True)
+        with open(yamlname, encoding="utf-8") as fd:
+            metadata = yaml.safe_load(fd)
 
         grids = {}
         for fp in innerdir.glob("*.npy.lz4"):
@@ -249,4 +258,4 @@ def load_tar(tarname):
             operator_grid[q2] = dict(zip(grids.keys(), slices))
         metadata["Q2grid"] = operator_grid
 
-    return metadata
+    return struct.EKO.from_dict(metadata)
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 421940336..98002d693 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -78,15 +78,12 @@ def test_rename_issue81(self, fake_output):
             p = pathlib.Path(folder)
             fp1 = p / "test1.tar"
             fp2 = p / "test2.tar"
-            __import__("pdb").set_trace()
             legacy.dump_tar(o1, fp1)
             # rename
             shutil.move(fp1, fp2)
             # reload
             o4 = legacy.load_tar(fp2)
-            np.testing.assert_almost_equal(
-                o4["interpolation_xgrid"], fake_output["interpolation_xgrid"]
-            )
+            np.testing.assert_almost_equal(o4.xgrid, fake_output["xgrid"])
 
     def test_io_bin(self, fake_output):
         # create object

From 04a74b640cbb9b2ca032e3864fa3317064d0362c Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 13:30:32 +0100
Subject: [PATCH 007/148] Recover to manipulation tests

---
 src/eko/output/__init__.py   |  2 +-
 src/eko/output/manipulate.py | 51 ++++++++++++++++++++----------------
 src/eko/output/struct.py     | 15 +++++++++--
 src/eko/version.py           |  1 +
 tests/eko/test_output.py     | 50 +++++++++++++++++------------------
 5 files changed, 68 insertions(+), 51 deletions(-)

diff --git a/src/eko/output/__init__.py b/src/eko/output/__init__.py
index 312c35bb0..d8bb6ebaf 100644
--- a/src/eko/output/__init__.py
+++ b/src/eko/output/__init__.py
@@ -4,4 +4,4 @@
 """
 
 from . import manipulate
-from .struct import EKO
+from .struct import EKO, Operator
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 386815fd7..c5a972437 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -29,15 +29,15 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
     # now check to the current status
     if (
         targetgrid is not None
-        and len(targetgrid) == len(eko.targetgrid)
-        and np.allclose(targetgrid, eko.targetgrid)
+        and len(targetgrid) == len(eko.rotations.targetgrid)
+        and np.allclose(targetgrid, eko.rotations.targetgrid)
     ):
         targetgrid = None
         warnings.warn("The new targetgrid is close to the current targetgrid")
     if (
         inputgrid is not None
-        and len(inputgrid) == len(eko.inputgrid)
-        and np.allclose(inputgrid, eko.inputgrid)
+        and len(inputgrid) == len(eko.rotations.inputgrid)
+        and np.allclose(inputgrid, eko.rotations.inputgrid)
     ):
         inputgrid = None
         warnings.warn("The new inputgrid is close to the current inputgrid")
@@ -49,27 +49,29 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
     # construct matrices
     if targetgrid is not None:
         b = interpolation.InterpolatorDispatcher(
-            eko.targetgrid,
-            eko.interpolation_polynomial_degree,
-            eko.interpolation_is_log,
+            eko.rotations.targetgrid,
+            eko.configs.interpolation_polynomial_degree,
+            eko.configs.interpolation_is_log,
             False,
         )
         target_rot = b.get_interpolation(targetgrid)
-        eko.targetgrid = np.array(targetgrid)
+        eko.rotations.targetgrid = np.array(targetgrid)
     if inputgrid is not None:
         b = interpolation.InterpolatorDispatcher(
             inputgrid,
-            eko.interpolation_polynomial_degree,
-            eko.interpolation_is_log,
+            eko.configs.interpolation_polynomial_degree,
+            eko.configs.interpolation_is_log,
             False,
         )
-        input_rot = b.get_interpolation(eko.inputgrid)
-        eko.inputgrid = np.array(inputgrid)
+        input_rot = b.get_interpolation(eko.rotations.inputgrid)
+        eko.rotations.inputgrid = np.array(inputgrid)
 
     # build new grid
-    for elem in eko.Q2grid.values():
-        ops = elem.operators
-        errs = elem.operator_errors
+    for _, elem in eko._operators.items():
+        if elem is None:
+            continue
+        ops = elem.operator
+        errs = elem.error
         if targetgrid is not None and inputgrid is None:
             ops = np.einsum("ij,ajbk->aibk", target_rot, ops)
             errs = np.einsum("ij,ajbk->aibk", target_rot, errs)
@@ -79,8 +81,8 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
         else:
             ops = np.einsum("ij,ajbk,kl->aibl", target_rot, ops, input_rot)
             errs = np.einsum("ij,ajbk,kl->aibl", target_rot, errs, input_rot)
-        elem.operators = ops
-        elem.operator_errors = errs
+        elem.operator = ops
+        elem.error = errs
 
 
 def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
@@ -101,11 +103,13 @@ def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
         raise ValueError("Nor inputbasis nor targetbasis was given")
     # now check to the current status
     if targetbasis is not None and np.allclose(
-        targetbasis, np.eye(len(eko.targetpids))
+        targetbasis, np.eye(len(eko.rotations.targetpids))
     ):
         targetbasis = None
         warnings.warn("The new targetbasis is close to current basis")
-    if inputbasis is not None and np.allclose(inputbasis, np.eye(len(eko.inputpids))):
+    if inputbasis is not None and np.allclose(
+        inputbasis, np.eye(len(eko.rotations.inputpids))
+    ):
         inputbasis = None
         warnings.warn("The new inputbasis is close to current basis")
     # after the checks: if there is still nothing to do, skip
@@ -118,7 +122,9 @@ def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
         inv_inputbasis = np.linalg.inv(inputbasis)
 
     # build new grid
-    for elem in eko.Q2grid.values():
+    for _, elem in eko.items():
+        if elem is None:
+            continue
         ops = elem.operators
         errs = elem.operator_errors
         if targetbasis is not None and inputbasis is None:
@@ -133,10 +139,11 @@ def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
         elem.operators = ops
         elem.operator_errors = errs
     # drop PIDs - keeping them int nevertheless
+    #  there is no meaningful way to set them in general, after rotation
     if inputbasis is not None:
-        eko.inputpids = [0] * len(eko.inputpids)
+        eko.rotations.inputpids = [0] * len(eko.rotations.inputpids)
     if targetbasis is not None:
-        eko.targetpids = [0] * len(eko.targetpids)
+        eko.rotations.targetpids = [0] * len(eko.rotations.targetpids)
 
 
 def to_evol(eko, source=True, target=False, inplace=True):
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 3bf6b45e8..af9f95c40 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -4,6 +4,8 @@
 
 import numpy as np
 
+from .. import version as vmod
+
 
 class DictLike:
     def __init__(self, **kwargs):
@@ -28,8 +30,8 @@ def raw(self):
 @dataclass
 class Operator(DictLike):
     alphas: float
-    operators: np.ndarray
-    operator_errors: Optional[np.ndarray] = None
+    operator: np.ndarray
+    error: Optional[np.ndarray] = None
 
 
 @dataclass
@@ -68,10 +70,19 @@ class EKO:
     configs: Configs
     rotations: Rotations
     debug: Debug
+    version: str = vmod.__version__
+    data_version: str = vmod.__data_version__
 
     def __iter__(self):
         return iter(self._operators)
 
+    def __contains__(self, q2):
+        return q2 in self._operators
+
+    def __getitem__(self, q2):
+        # TODO: autload
+        return self._operators[q2]
+
     def items(self):
         return (
             (k, asdict(v) if v is not None else None)
diff --git a/src/eko/version.py b/src/eko/version.py
index f09cc807b..0aff48f78 100644
--- a/src/eko/version.py
+++ b/src/eko/version.py
@@ -1,2 +1,3 @@
 # -*- coding: utf-8 -*-
 __version__ = "0.0.0"
+__data_version__ = "0.0.1"
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 98002d693..ccf694b3f 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -24,11 +24,9 @@ def eko_identity(shape):
 def chk_keys(a, b):
     """Check all keys are preserved"""
     assert sorted(a.keys()) == sorted(b.keys())
-    for q2, op in a.Q2grid.items():
-        assert q2 in b.Q2grid
-        opb = b.Q2grid[q2]
-        assert sorted(op.keys()) == sorted(opb.keys())
-        assert op["alphas"] == opb["alphas"]
+    for key, value in a.items():
+        if isinstance(value, dict):
+            assert sorted(value.keys()) == sorted(b[key].keys())
 
 
 class TestLegacy:
@@ -104,48 +102,50 @@ def test_xgrid_reshape(self, fake_output):
         xg = np.geomspace(1e-5, 1.0, 21)
         o1 = output.EKO.from_dict(fake_output)
         o1.xgrid = xg
-        o1.targetgrid = xg
-        o1.inputgrid = xg
-        o1.Q2grid = {
-            10: dict(
-                operators=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
-                operator_errors=np.zeros((2, len(xg), 2, len(xg))),
-                alphas=np.random.rand(),
+        o1.rotations.targetgrid = xg
+        o1.rotations.inputgrid = xg
+        o1._operators = {
+            10: output.Operator.from_dict(
+                dict(
+                    operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
+                    error=np.zeros((2, len(xg), 2, len(xg))),
+                    alphas=np.random.rand(),
+                )
             )
         }
         xgp = np.geomspace(1e-5, 1.0, 11)
         # only target
         ot = copy.deepcopy(o1)
         manipulate.xgrid_reshape(ot, xgp, inplace=True)
-        chk_keys(o1, ot)
-        assert ot["Q2grid"][10]["operators"].shape == (2, len(xgp), 2, len(xg))
+        chk_keys(o1.raw, ot.raw)
+        assert ot._operators[10].operator.shape == (2, len(xgp), 2, len(xg))
         ott = copy.deepcopy(o1)
         with pytest.warns(Warning):
             manipulate.xgrid_reshape(ott, xg)
-            chk_keys(o1, ott)
+            chk_keys(o1.raw, ott.raw)
             np.testing.assert_allclose(
-                ott.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
+                ott._operators[10].operator, o1._operators[10].operator
             )
 
         # only input
         oi = copy.deepcopy(o1)
-        manipulate.xgrid_reshape(o1, inputgrid=xgp)
-        assert oi.Q2grid[10]["operators"].shape == (2, len(xg), 2, len(xgp))
-        chk_keys(o1, oi)
+        manipulate.xgrid_reshape(oi, inputgrid=xgp)
+        assert oi._operators[10].operator.shape == (2, len(xg), 2, len(xgp))
+        chk_keys(o1.raw, oi.raw)
         oii = copy.deepcopy(o1)
         with pytest.warns(Warning):
             manipulate.xgrid_reshape(oii, inputgrid=xg)
-            chk_keys(o1, oii)
+            chk_keys(o1.raw, oii.raw)
             np.testing.assert_allclose(
-                oii.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
+                oii._operators[10].operator, o1._operators[10].operator
             )
 
         # both
         oit = copy.deepcopy(o1)
         manipulate.xgrid_reshape(oit, xgp, xgp)
-        chk_keys(o1, oit)
+        chk_keys(o1.raw, oit.raw)
         op = eko_identity([1, 2, len(xgp), 2, len(xgp)])
-        np.testing.assert_allclose(oit.Q2grid[10]["operators"], op[0], atol=1e-10)
+        np.testing.assert_allclose(oit._operators[10].operator, op[0], atol=1e-10)
         # error
         with pytest.raises(ValueError):
             manipulate.xgrid_reshape(copy.deepcopy(o1))
@@ -162,9 +162,7 @@ def test_reshape_io(self, fake_output):
         # reload
         stream.seek(0)
         o3 = legacy.load_yaml(stream)
-        # eko_version is only added in get_raw
-        del o3["eko_version"]
-        chk_keys(o1, o3)
+        chk_keys(o1.raw, o3.raw)
 
     def test_flavor_reshape(self, fake_output):
         # create object

From 08af72a86b21f2e8bbcae828da5cdbaef91d9863 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 13:54:05 +0100
Subject: [PATCH 008/148] Recover all manipulation tests

---
 src/eko/output/manipulate.py |  12 ++--
 src/eko/output/struct.py     |   8 ++-
 tests/conftest.py            |   4 +-
 tests/eko/test_output.py     | 120 ++++++++++++++++++-----------------
 4 files changed, 76 insertions(+), 68 deletions(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index c5a972437..8ddf4d550 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -122,11 +122,11 @@ def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
         inv_inputbasis = np.linalg.inv(inputbasis)
 
     # build new grid
-    for _, elem in eko.items():
+    for _, elem in eko._operators.items():
         if elem is None:
             continue
-        ops = elem.operators
-        errs = elem.operator_errors
+        ops = elem.operator
+        errs = elem.error
         if targetbasis is not None and inputbasis is None:
             ops = np.einsum("ca,ajbk->cjbk", targetbasis, ops)
             errs = np.einsum("ca,ajbk->cjbk", targetbasis, errs)
@@ -162,9 +162,9 @@ def to_evol(eko, source=True, target=False, inplace=True):
     # rotate
     inputbasis = br.rotate_flavor_to_evolution if source else None
     targetbasis = br.rotate_flavor_to_evolution if target else None
-    eko.flavor_reshape(inputbasis=inputbasis, targetbasis=targetbasis)
+    flavor_reshape(eko, inputbasis=inputbasis, targetbasis=targetbasis)
     # assign pids
     if source:
-        eko.inputpids = br.evol_basis_pids
+        eko.rotations.inputpids = br.evol_basis_pids
     if target:
-        eko.targetpids = br.evol_basis_pids
+        eko.rotations.targetpids = br.evol_basis_pids
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index af9f95c40..ecb2bfc84 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -80,9 +80,15 @@ def __contains__(self, q2):
         return q2 in self._operators
 
     def __getitem__(self, q2):
-        # TODO: autload
+        # TODO: autoload
         return self._operators[q2]
 
+    def __setitem__(self, q2, op):
+        # TODO: autodump
+        if isinstance(op, dict):
+            op = Operator.from_dict(op)
+        self._operators[q2] = op
+
     def items(self):
         return (
             (k, asdict(v) if v is not None else None)
diff --git a/tests/conftest.py b/tests/conftest.py
index 3ca998106..03f38fa79 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -27,8 +27,8 @@ def mk_g(self, q2s, lpids, lx):
         Q2grid = {}
         for q2 in q2s:
             Q2grid[q2] = {
-                "operators": np.random.rand(lpids, lx, lpids, lx),
-                "operator_errors": np.random.rand(lpids, lx, lpids, lx),
+                "operator": np.random.rand(lpids, lx, lpids, lx),
+                "error": np.random.rand(lpids, lx, lpids, lx),
                 "alphas": np.random.rand(),
             }
         return Q2grid
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index ccf694b3f..138fd9248 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -33,6 +33,8 @@ class TestLegacy:
     def test_io(self, fake_output):
         # create object
         o1 = output.EKO.from_dict(fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            o1[q2] = output.Operator.from_dict(op)
         # test streams
         stream = io.StringIO()
         legacy.dump_yaml(o1, stream)
@@ -70,6 +72,8 @@ def test_rename_issue81(self, fake_output):
         # https://github.com/N3PDF/eko/issues/81
         # create object
         o1 = output.EKO.from_dict(fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            o1[q2] = output.Operator.from_dict(op)
 
         with tempfile.TemporaryDirectory() as folder:
             # dump
@@ -86,6 +90,8 @@ def test_rename_issue81(self, fake_output):
     def test_io_bin(self, fake_output):
         # create object
         o1 = output.EKO.from_dict(fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            o1[q2] = output.Operator.from_dict(op)
         # test streams
         stream = io.StringIO()
         legacy.dump_yaml(o1, stream, False)
@@ -118,34 +124,30 @@ def test_xgrid_reshape(self, fake_output):
         ot = copy.deepcopy(o1)
         manipulate.xgrid_reshape(ot, xgp, inplace=True)
         chk_keys(o1.raw, ot.raw)
-        assert ot._operators[10].operator.shape == (2, len(xgp), 2, len(xg))
+        assert ot[10].operator.shape == (2, len(xgp), 2, len(xg))
         ott = copy.deepcopy(o1)
         with pytest.warns(Warning):
             manipulate.xgrid_reshape(ott, xg)
             chk_keys(o1.raw, ott.raw)
-            np.testing.assert_allclose(
-                ott._operators[10].operator, o1._operators[10].operator
-            )
+            np.testing.assert_allclose(ott[10].operator, o1[10].operator)
 
         # only input
         oi = copy.deepcopy(o1)
         manipulate.xgrid_reshape(oi, inputgrid=xgp)
-        assert oi._operators[10].operator.shape == (2, len(xg), 2, len(xgp))
+        assert oi[10].operator.shape == (2, len(xg), 2, len(xgp))
         chk_keys(o1.raw, oi.raw)
         oii = copy.deepcopy(o1)
         with pytest.warns(Warning):
             manipulate.xgrid_reshape(oii, inputgrid=xg)
             chk_keys(o1.raw, oii.raw)
-            np.testing.assert_allclose(
-                oii._operators[10].operator, o1._operators[10].operator
-            )
+            np.testing.assert_allclose(oii[10].operator, o1[10].operator)
 
         # both
         oit = copy.deepcopy(o1)
         manipulate.xgrid_reshape(oit, xgp, xgp)
         chk_keys(o1.raw, oit.raw)
         op = eko_identity([1, 2, len(xgp), 2, len(xgp)])
-        np.testing.assert_allclose(oit._operators[10].operator, op[0], atol=1e-10)
+        np.testing.assert_allclose(oit[10].operator, op[0], atol=1e-10)
         # error
         with pytest.raises(ValueError):
             manipulate.xgrid_reshape(copy.deepcopy(o1))
@@ -153,6 +155,8 @@ def test_xgrid_reshape(self, fake_output):
     def test_reshape_io(self, fake_output):
         # create object
         o1 = output.EKO.from_dict(fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            o1[q2] = output.Operator.from_dict(op)
         o2 = copy.deepcopy(o1)
         manipulate.xgrid_reshape(o2, [0.1, 1.0], [0.1, 1.0])
         manipulate.flavor_reshape(o2, inputbasis=np.array([[1, -1], [1, 1]]))
@@ -169,59 +173,53 @@ def test_flavor_reshape(self, fake_output):
         xg = np.geomspace(1e-5, 1.0, 21)
         o1 = output.EKO.from_dict(fake_output)
         o1.xgrid = xg
-        o1.targetgrid = xg
-        o1.inputgrid = xg
-        o1.Q2grid = {
-            10: dict(
-                operators=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
-                operator_errors=np.zeros((2, len(xg), 2, len(xg))),
-                alphas=np.random.rand(),
+        o1.rotations.targetgrid = xg
+        o1.rotations.inputgrid = xg
+        o1._operators = {
+            10: output.Operator.from_dict(
+                dict(
+                    operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
+                    error=np.zeros((2, len(xg), 2, len(xg))),
+                    alphas=np.random.rand(),
+                )
             )
         }
         # only target
         target_r = np.array([[1, -1], [1, 1]])
         ot = copy.deepcopy(o1)
         manipulate.flavor_reshape(ot, target_r)
-        chk_keys(o1, ot)
-        assert ot.Q2grid[10]["operators"].shape == (2, len(xg), 2, len(xg))
+        chk_keys(o1.raw, ot.raw)
+        assert ot[10].operator.shape == (2, len(xg), 2, len(xg))
         ott = copy.deepcopy(ot)
         manipulate.flavor_reshape(ott, np.linalg.inv(target_r))
-        np.testing.assert_allclose(
-            ott.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
-        )
+        np.testing.assert_allclose(ott[10].operator, o1[10].operator)
         with pytest.warns(Warning):
             manipulate.flavor_reshape(ott, np.eye(2))
-            chk_keys(o1, ott)
-            np.testing.assert_allclose(
-                ott.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
-            )
+            chk_keys(o1.raw, ott.raw)
+            np.testing.assert_allclose(ott[10].operator, o1[10].operator)
 
         # only input
         input_r = np.array([[1, -1], [1, 1]])
         oi = copy.deepcopy(o1)
         manipulate.flavor_reshape(oi, inputbasis=input_r)
-        chk_keys(o1, oi)
-        assert oi.Q2grid[10]["operators"].shape == (2, len(xg), 2, len(xg))
+        chk_keys(o1.raw, oi.raw)
+        assert oi[10].operator.shape == (2, len(xg), 2, len(xg))
         oii = copy.deepcopy(oi)
         manipulate.flavor_reshape(oii, inputbasis=np.linalg.inv(input_r))
-        np.testing.assert_allclose(
-            oii.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
-        )
+        np.testing.assert_allclose(oii[10].operator, o1[10].operator)
         with pytest.warns(Warning):
             manipulate.flavor_reshape(oii, inputbasis=np.eye(2))
-            chk_keys(o1, oii)
-            np.testing.assert_allclose(
-                oii.Q2grid[10]["operators"], o1.Q2grid[10]["operators"]
-            )
+            chk_keys(o1.raw, oii.raw)
+            np.testing.assert_allclose(oii[10].operator, o1[10].operator)
 
         # both
         oit = copy.deepcopy(o1)
         manipulate.flavor_reshape(
             oit, np.array([[1, -1], [1, 1]]), np.array([[1, -1], [1, 1]])
         )
-        chk_keys(o1, oit)
+        chk_keys(o1.raw, oit.raw)
         op = eko_identity([1, 2, len(xg), 2, len(xg)]).copy()
-        np.testing.assert_allclose(oit.Q2grid[10]["operators"], op[0], atol=1e-10)
+        np.testing.assert_allclose(oit[10].operator, op[0], atol=1e-10)
         # error
         with pytest.raises(ValueError):
             manipulate.flavor_reshape(copy.deepcopy(o1))
@@ -237,39 +235,43 @@ def test_to_evol(self, fake_factory):
         )
         d = dict(
             xgrid=interpolation_xgrid,
-            targetgrid=interpolation_xgrid,
-            inputgrid=interpolation_xgrid,
-            interpolation_polynomial_degree=interpolation_polynomial_degree,
-            interpolation_is_log=interpolation_is_log,
-            q2_ref=q2_ref,
-            inputpids=br.flavor_basis_pids,
-            targetpids=br.flavor_basis_pids,
+            Q0=np.sqrt(q2_ref),
             Q2grid=Q2grid,
+            rotations=dict(
+                targetgrid=interpolation_xgrid,
+                inputgrid=interpolation_xgrid,
+                inputpids=br.flavor_basis_pids,
+                targetpids=br.flavor_basis_pids,
+            ),
+            configs=dict(
+                interpolation_polynomial_degree=interpolation_polynomial_degree,
+                interpolation_is_log=interpolation_is_log,
+                ev_op_max_order=1,
+                ev_op_iterations=1,
+                backward_inversion="exact",
+            ),
         )
         o00 = output.EKO.from_dict(d)
-        o01 = copy.copy(o00)
+        o00[q2_out] = Q2grid[q2_out]
+        o01 = copy.deepcopy(o00)
         manipulate.to_evol(o01)
-        o10 = copy.copy(o00)
+        o10 = copy.deepcopy(o00)
         manipulate.to_evol(o10, False, True)
-        o11 = copy.copy(o00)
+        o11 = copy.deepcopy(o00)
         manipulate.to_evol(o11, True, True)
-        chk_keys(o00, o11)
+        chk_keys(o00.raw, o11.raw)
 
         # check the input rotated one
-        np.testing.assert_allclose(o01.inputpids, br.evol_basis_pids)
-        np.testing.assert_allclose(o01.targetpids, br.flavor_basis_pids)
+        np.testing.assert_allclose(o01.rotations.inputpids, br.evol_basis_pids)
+        np.testing.assert_allclose(o01.rotations.targetpids, br.flavor_basis_pids)
         # rotate also target
         manipulate.to_evol(o01, False, True)
-        np.testing.assert_allclose(
-            o01.Q2grid[q2_out]["operators"], o11.Q2grid[q2_out]["operators"]
-        )
-        chk_keys(o00, o01)
+        np.testing.assert_allclose(o01[q2_out].operator, o11[q2_out].operator)
+        chk_keys(o00.raw, o01.raw)
         # check the target rotated one
-        np.testing.assert_allclose(o10.inputpids, br.flavor_basis_pids)
-        np.testing.assert_allclose(o10.targetpids, br.evol_basis_pids)
+        np.testing.assert_allclose(o10.rotations.inputpids, br.flavor_basis_pids)
+        np.testing.assert_allclose(o10.rotations.targetpids, br.evol_basis_pids)
         # rotate also input
         manipulate.to_evol(o10)
-        np.testing.assert_allclose(
-            o10.Q2grid[q2_out]["operators"], o11.Q2grid[q2_out]["operators"]
-        )
-        chk_keys(o00, o10)
+        np.testing.assert_allclose(o10[q2_out].operator, o11[q2_out].operator)
+        chk_keys(o00.raw, o10.raw)

From b4d0067b0955c4eb269cd9b325869239d42f3398 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 13:58:30 +0100
Subject: [PATCH 009/148] Recover all output tests

---
 src/eko/output/legacy.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index aea7f244e..c2636b71a 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -130,11 +130,11 @@ def dump_tar(obj, tarname):
         with open(yamlname, "w", encoding="utf-8") as fd:
             yaml.dump(metadata, fd)
 
-        for kind in ["alphas", "operators", "operator_errors"]:
+        for kind in ["alphas", "operator", "error"]:
             elements = []
             for q2, op in obj.items():
                 if op is not None:
-                    el = getattr(q2, kind)
+                    el = op[kind]
                 else:
                     el = np.zeros((len(obj.xgrid), 14, len(obj.xgrid), 14))
                 elements.append(el)

From bc58d46fcdc507672b30153e33817b23892b8664 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 14:15:48 +0100
Subject: [PATCH 010/148] Simplify items iteration

---
 pyproject.toml               |  2 ++
 src/eko/output/legacy.py     |  5 +++--
 src/eko/output/manipulate.py |  4 ++--
 src/eko/output/struct.py     | 19 +++++++++++--------
 4 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1197097cf..ebcbe3e55 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -85,6 +85,8 @@ genpdf = "ekobox.genpdf.cli:cli"
 
 [tool.poe.tasks]
 test = "pytest tests"
+coverage = "$BROWSER htmlcov/index.html"
+test-cov = ["test", "coverage"]
 bench = "pytest benchmarks"
 bench-iso.cmd = "pytest benchmarks -m isolated"
 bench-iso.env.NUMBA_DISABLE_JIT.default = "0"
diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index c2636b71a..44d03836c 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import dataclasses
 import io
 import pathlib
 import tarfile
@@ -42,7 +43,7 @@ def get_raw(eko, binarize=True, skip_q2_grid=False):
         for q2, op in eko.items():
             out["Q2grid"][q2] = {}
             if op is not None:
-                for k, v in op.items():
+                for k, v in dataclasses.asdict(op).items():
                     if k == "alphas":
                         out["Q2grid"][q2][k] = float(v)
                         continue
@@ -134,7 +135,7 @@ def dump_tar(obj, tarname):
             elements = []
             for q2, op in obj.items():
                 if op is not None:
-                    el = op[kind]
+                    el = getattr(op, kind)
                 else:
                     el = np.zeros((len(obj.xgrid), 14, len(obj.xgrid), 14))
                 elements.append(el)
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 8ddf4d550..f9e8b14cb 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -67,7 +67,7 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
         eko.rotations.inputgrid = np.array(inputgrid)
 
     # build new grid
-    for _, elem in eko._operators.items():
+    for _, elem in eko.items():
         if elem is None:
             continue
         ops = elem.operator
@@ -122,7 +122,7 @@ def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
         inv_inputbasis = np.linalg.inv(inputbasis)
 
     # build new grid
-    for _, elem in eko._operators.items():
+    for _, elem in eko.items():
         if elem is None:
             continue
         ops = elem.operator
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index ecb2bfc84..61772572f 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from dataclasses import asdict, dataclass, fields
+from dataclasses import dataclass, fields
 from typing import Dict, Literal, Optional
 
 import numpy as np
@@ -20,9 +20,15 @@ def raw(self):
         dictionary = {}
         for field in fields(self):
             value = getattr(self, field.name)
-            dictionary[field.name] = (
-                value if not isinstance(value, np.ndarray) else value.tolist()
-            )
+
+            # replace numpy arrays with lists
+            if isinstance(value, np.ndarray):
+                value = value.tolist()
+            # replace numpy scalars with python ones
+            elif isinstance(value, float):
+                value = float(value)
+
+            dictionary[field.name] = value
 
         return dictionary
 
@@ -90,10 +96,7 @@ def __setitem__(self, q2, op):
         self._operators[q2] = op
 
     def items(self):
-        return (
-            (k, asdict(v) if v is not None else None)
-            for k, v in self._operators.items()
-        )
+        return self._operators.items()
 
     @property
     def Q2grid(self):

From 7667286a8158f3d983dc4d9a446ce087a098458d Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 15:47:09 +0100
Subject: [PATCH 011/148] Recover apply tests

---
 benchmarks/eko/benchmark_evol_to_unity.py |  2 +-
 src/eko/interpolation.py                  |  6 ++--
 src/ekomark/apply.py                      | 35 +++++++++++------------
 tests/ekomark/test_apply.py               | 29 +++++++++++--------
 4 files changed, 38 insertions(+), 34 deletions(-)

diff --git a/benchmarks/eko/benchmark_evol_to_unity.py b/benchmarks/eko/benchmark_evol_to_unity.py
index 24deb236c..4254327c8 100644
--- a/benchmarks/eko/benchmark_evol_to_unity.py
+++ b/benchmarks/eko/benchmark_evol_to_unity.py
@@ -43,7 +43,7 @@ class BenchmarkBackwardForward:
     operators_card = {
         "Q2grid": [10],
         # here you need a very dense grid
-        "interpolation_xgrid": np.linspace(1e-1, 1, 30),
+        "xgrid": np.linspace(1e-1, 1, 30),
         # "interpolation_xgrid": make_grid(30,30, x_min=1e-3),
         "interpolation_polynomial_degree": 1,
         "interpolation_is_log": True,
diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index 118d8ffa0..8c5d0c513 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -511,7 +511,7 @@ def from_dict(cls, operators_card, mode_N=True):
             *   - Name
                 - Type
                 - description
-            *   - ``interpolation_xgrid``
+            *   - ``xgrid``
                 - :py:obj:`list(float)`
                 - the interpolation grid
             *   - ``interpolation_polynomial_degree``
@@ -527,7 +527,7 @@ def from_dict(cls, operators_card, mode_N=True):
                 input configurations
         """
         # load xgrid
-        xgrid = operators_card["interpolation_xgrid"]
+        xgrid = operators_card["xgrid"]
         if len(xgrid) == 0:
             raise ValueError("Empty xgrid!")
         if xgrid[0] == "make_grid":
@@ -607,7 +607,7 @@ def to_dict(self):
                 full grid configuration
         """
         ret = {
-            "interpolation_xgrid": self.xgrid_raw,
+            "xgrid": self.xgrid_raw,
             "interpolation_polynomial_degree": self.polynomial_degree,
             "interpolation_is_log": self.log,
         }
diff --git a/src/ekomark/apply.py b/src/ekomark/apply.py
index fc216ba62..f91db4659 100644
--- a/src/ekomark/apply.py
+++ b/src/ekomark/apply.py
@@ -5,13 +5,13 @@
 from eko import interpolation
 
 
-def apply_pdf(output, lhapdf_like, targetgrid=None, rotate_to_evolution_basis=False):
+def apply_pdf(eko, lhapdf_like, targetgrid=None, rotate_to_evolution_basis=False):
     """
     Apply all available operators to the input PDFs.
 
     Parameters
     ----------
-        output : eko.output.Output
+        output : eko.output.EKO
             eko output object containing all informations
         lhapdf_like : object
             object that provides an xfxQ2 callable (as `lhapdf <https://lhapdf.hepforge.org/>`_
@@ -28,18 +28,18 @@ def apply_pdf(output, lhapdf_like, targetgrid=None, rotate_to_evolution_basis=Fa
     """
     if rotate_to_evolution_basis:
         return apply_pdf_flavor(
-            output, lhapdf_like, targetgrid, br.rotate_flavor_to_evolution
+            eko, lhapdf_like, targetgrid, br.rotate_flavor_to_evolution
         )
-    return apply_pdf_flavor(output, lhapdf_like, targetgrid)
+    return apply_pdf_flavor(eko, lhapdf_like, targetgrid)
 
 
-def apply_pdf_flavor(output, lhapdf_like, targetgrid=None, flavor_rotation=None):
+def apply_pdf_flavor(eko, lhapdf_like, targetgrid=None, flavor_rotation=None):
     """
     Apply all available operators to the input PDFs.
 
     Parameters
     ----------
-        output : eko.output.Output
+        output : eko.output.EKO
             eko output object containing all informations
         lhapdf_like : object
             object that provides an xfxQ2 callable (as `lhapdf <https://lhapdf.hepforge.org/>`_
@@ -55,25 +55,22 @@ def apply_pdf_flavor(output, lhapdf_like, targetgrid=None, flavor_rotation=None)
             output PDFs and their associated errors for the computed Q2grid
     """
     # create pdfs
-    pdfs = np.zeros((len(output["inputpids"]), len(output["inputgrid"])))
-    for j, pid in enumerate(output["inputpids"]):
+    pdfs = np.zeros((len(eko.rotations.inputpids), len(eko.rotations.inputgrid)))
+    for j, pid in enumerate(eko.rotations.inputpids):
         if not lhapdf_like.hasFlavor(pid):
             continue
         pdfs[j] = np.array(
-            [
-                lhapdf_like.xfxQ2(pid, x, output["q2_ref"]) / x
-                for x in output["inputgrid"]
-            ]
+            [lhapdf_like.xfxQ2(pid, x, eko.Q02) / x for x in eko.rotations.inputgrid]
         )
 
     # build output
     out_grid = {}
-    for q2, elem in output["Q2grid"].items():
-        pdf_final = np.einsum("ajbk,bk", elem["operators"], pdfs)
-        error_final = np.einsum("ajbk,bk", elem["operator_errors"], pdfs)
+    for q2, elem in eko.items():
+        pdf_final = np.einsum("ajbk,bk", elem.operator, pdfs)
+        error_final = np.einsum("ajbk,bk", elem.error, pdfs)
         out_grid[q2] = {
-            "pdfs": dict(zip(output["targetpids"], pdf_final)),
-            "errors": dict(zip(output["targetpids"], error_final)),
+            "pdfs": dict(zip(eko.rotations.targetpids, pdf_final)),
+            "errors": dict(zip(eko.rotations.targetpids, error_final)),
         }
 
     # rotate to evolution basis
@@ -90,7 +87,9 @@ def apply_pdf_flavor(output, lhapdf_like, targetgrid=None, flavor_rotation=None)
 
     # rotate/interpolate to target grid
     if targetgrid is not None:
-        b = interpolation.InterpolatorDispatcher.from_dict(output, False)
+        b = interpolation.InterpolatorDispatcher.from_dict(
+            eko.configs.raw | dict(xgrid=eko.xgrid), False
+        )
         rot = b.get_interpolation(targetgrid)
         for evpdf in out_grid.values():
             for pdf_label in evpdf["pdfs"]:
diff --git a/tests/ekomark/test_apply.py b/tests/ekomark/test_apply.py
index 8869d8201..47b342bdf 100644
--- a/tests/ekomark/test_apply.py
+++ b/tests/ekomark/test_apply.py
@@ -9,18 +9,20 @@ class TestApply:
     def test_apply(self, fake_output, fake_pdf):
         q2_out = list(fake_output["Q2grid"].keys())[0]
         # create object
-        o = output.Output(fake_output)
+        o = output.EKO.from_dict(fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            o[q2] = output.Operator.from_dict(op)
         # fake pdfs
         pdf_grid = apply.apply_pdf(o, fake_pdf)
         assert len(pdf_grid) == len(fake_output["Q2grid"])
         pdfs = pdf_grid[q2_out]["pdfs"]
-        assert list(pdfs.keys()) == fake_output["targetpids"]
-        ref_pid1 = fake_output["Q2grid"][q2_out]["operators"][0, :, 1, :] @ np.ones(
-            len(fake_output["interpolation_xgrid"])
+        assert list(pdfs.keys()) == fake_output["rotations"]["targetpids"]
+        ref_pid1 = fake_output["Q2grid"][q2_out]["operator"][0, :, 1, :] @ np.ones(
+            len(fake_output["xgrid"])
         )
         np.testing.assert_allclose(pdfs[0], ref_pid1)
-        ref_pid2 = fake_output["Q2grid"][q2_out]["operators"][1, :, 1, :] @ np.ones(
-            len(fake_output["interpolation_xgrid"])
+        ref_pid2 = fake_output["Q2grid"][q2_out]["operator"][1, :, 1, :] @ np.ones(
+            len(fake_output["xgrid"])
         )
         np.testing.assert_allclose(pdfs[1], ref_pid2)
         # rotate to target_grid
@@ -28,18 +30,21 @@ def test_apply(self, fake_output, fake_pdf):
         pdf_grid = apply.apply_pdf(o, fake_pdf, target_grid)
         assert len(pdf_grid) == 1
         pdfs = pdf_grid[q2_out]["pdfs"]
-        assert list(pdfs.keys()) == fake_output["targetpids"]
+        assert list(pdfs.keys()) == fake_output["rotations"]["targetpids"]
 
     def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
         q2_out = list(fake_output["Q2grid"].keys())[0]
         # create object
-        o = output.Output(fake_output)
+        o = output.EKO.from_dict(fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            o[q2] = output.Operator.from_dict(op)
         # fake pdfs
         monkeypatch.setattr(
             "eko.basis_rotation.rotate_flavor_to_evolution", np.ones((2, 2))
         )
         monkeypatch.setattr(
-            "eko.basis_rotation.flavor_basis_pids", fake_output["targetpids"]
+            "eko.basis_rotation.flavor_basis_pids",
+            fake_output["rotations"]["targetpids"],
         )
         fake_evol_basis = ("a", "b")
         monkeypatch.setattr("eko.basis_rotation.evol_basis", fake_evol_basis)
@@ -48,7 +53,7 @@ def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
         pdfs = pdf_grid[q2_out]["pdfs"]
         assert list(pdfs.keys()) == list(fake_evol_basis)
         ref_a = (
-            fake_output["Q2grid"][q2_out]["operators"][0, :, 1, :]
-            + fake_output["Q2grid"][q2_out]["operators"][1, :, 1, :]
-        ) @ np.ones(len(fake_output["interpolation_xgrid"]))
+            fake_output["Q2grid"][q2_out]["operator"][0, :, 1, :]
+            + fake_output["Q2grid"][q2_out]["operator"][1, :, 1, :]
+        ) @ np.ones(len(fake_output["xgrid"]))
         np.testing.assert_allclose(pdfs["a"], ref_a)

From d289c4f956c9721febb2323f6ec976a00f687329 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:48:30 +0200
Subject: [PATCH 012/148] Recover everything but runner

---
 benchmarks/eko/benchmark_evol_to_unity.py | 22 +++++---
 src/eko/evolution_operator/grid.py        | 14 ++---
 src/eko/interpolation.py                  | 10 ++--
 src/eko/output/struct.py                  |  1 +
 src/ekomark/apply.py                      |  4 +-
 tests/eko/test_ev_op_grid.py              | 22 +++++---
 tests/eko/test_interpolation.py           | 68 +++++++++++++++--------
 tests/eko/test_ome.py                     | 52 ++++++++++-------
 8 files changed, 118 insertions(+), 75 deletions(-)

diff --git a/benchmarks/eko/benchmark_evol_to_unity.py b/benchmarks/eko/benchmark_evol_to_unity.py
index 4254327c8..e0d38dd70 100644
--- a/benchmarks/eko/benchmark_evol_to_unity.py
+++ b/benchmarks/eko/benchmark_evol_to_unity.py
@@ -44,15 +44,19 @@ class BenchmarkBackwardForward:
         "Q2grid": [10],
         # here you need a very dense grid
         "xgrid": np.linspace(1e-1, 1, 30),
-        # "interpolation_xgrid": make_grid(30,30, x_min=1e-3),
-        "interpolation_polynomial_degree": 1,
-        "interpolation_is_log": True,
-        "debug_skip_singlet": False,
-        "debug_skip_non_singlet": False,
-        "ev_op_max_order": 1,
-        "ev_op_iterations": 1,
-        "backward_inversion": "exact",
-        "n_integration_cores": 1,
+        # "xgrid": make_grid(30,30, x_min=1e-3),
+        "configs": {
+            "interpolation_polynomial_degree": 1,
+            "interpolation_is_log": True,
+            "ev_op_max_order": 1,
+            "ev_op_iterations": 1,
+            "backward_inversion": "exact",
+            "n_integration_cores": 1,
+        },
+        "debug": {
+            "skip_singlet": False,
+            "skip_non_singlet": False,
+        },
     }
     new_theory, new_operators = compatibility.update(theory_card, operators_card)
     g = OperatorGrid.from_dict(
diff --git a/src/eko/evolution_operator/grid.py b/src/eko/evolution_operator/grid.py
index db235f3d1..e8206073f 100644
--- a/src/eko/evolution_operator/grid.py
+++ b/src/eko/evolution_operator/grid.py
@@ -57,7 +57,7 @@ def __init__(
         # check
         order = config["order"]
         method = config["method"]
-        if not method in [
+        if method not in [
             "iterate-exact",
             "iterate-expanded",
             "truncated",
@@ -119,13 +119,13 @@ def from_dict(
         }
         method = mod_ev2method.get(method, method)
         config["method"] = method
-        config["backward_inversion"] = operators_card["backward_inversion"]
+        config["backward_inversion"] = operators_card["configs"]["backward_inversion"]
         config["fact_to_ren"] = (theory_card["fact_to_ren_scale_ratio"]) ** 2
-        config["ev_op_max_order"] = operators_card["ev_op_max_order"]
-        config["ev_op_iterations"] = operators_card["ev_op_iterations"]
-        config["debug_skip_singlet"] = operators_card["debug_skip_singlet"]
-        config["debug_skip_non_singlet"] = operators_card["debug_skip_non_singlet"]
-        config["n_integration_cores"] = operators_card["n_integration_cores"]
+        config["ev_op_max_order"] = operators_card["configs"]["ev_op_max_order"]
+        config["ev_op_iterations"] = operators_card["configs"]["ev_op_iterations"]
+        config["n_integration_cores"] = operators_card["configs"]["n_integration_cores"]
+        config["debug_skip_singlet"] = operators_card["debug"]["skip_singlet"]
+        config["debug_skip_non_singlet"] = operators_card["debug"]["skip_non_singlet"]
         config["HQ"] = theory_card["HQ"]
         config["ModSV"] = theory_card["ModSV"]
         q2_grid = np.array(operators_card["Q2grid"], np.float_)
diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index 8c5d0c513..09f63f7dd 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -534,8 +534,8 @@ def from_dict(cls, operators_card, mode_N=True):
             xgrid = make_grid(*xgrid[1:])
         elif xgrid[0] == "make_lambert_grid":
             xgrid = make_lambert_grid(*xgrid[1:])
-        is_log_interpolation = bool(operators_card["interpolation_is_log"])
-        polynom_rank = operators_card["interpolation_polynomial_degree"]
+        is_log_interpolation = bool(operators_card["configs"]["interpolation_is_log"])
+        polynom_rank = operators_card["configs"]["interpolation_polynomial_degree"]
         return cls(
             xgrid,
             polynom_rank,
@@ -608,8 +608,10 @@ def to_dict(self):
         """
         ret = {
             "xgrid": self.xgrid_raw,
-            "interpolation_polynomial_degree": self.polynomial_degree,
-            "interpolation_is_log": self.log,
+            "configs": {
+                "interpolation_polynomial_degree": self.polynomial_degree,
+                "interpolation_is_log": self.log,
+            },
         }
         return ret
 
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 61772572f..c01ca7838 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -53,6 +53,7 @@ class Configs(DictLike):
     interpolation_polynomial_degree: int
     interpolation_is_log: bool
     backward_inversion: Literal["exact", "expanded"]
+    n_integration_cores: int = 1
 
 
 @dataclass
diff --git a/src/ekomark/apply.py b/src/ekomark/apply.py
index f91db4659..d8dfa3f45 100644
--- a/src/ekomark/apply.py
+++ b/src/ekomark/apply.py
@@ -87,9 +87,7 @@ def apply_pdf_flavor(eko, lhapdf_like, targetgrid=None, flavor_rotation=None):
 
     # rotate/interpolate to target grid
     if targetgrid is not None:
-        b = interpolation.InterpolatorDispatcher.from_dict(
-            eko.configs.raw | dict(xgrid=eko.xgrid), False
-        )
+        b = interpolation.InterpolatorDispatcher.from_dict(eko.raw, False)
         rot = b.get_interpolation(targetgrid)
         for evpdf in out_grid.values():
             for pdf_label in evpdf["pdfs"]:
diff --git a/tests/eko/test_ev_op_grid.py b/tests/eko/test_ev_op_grid.py
index 0b6fdbbc0..86913e6ac 100644
--- a/tests/eko/test_ev_op_grid.py
+++ b/tests/eko/test_ev_op_grid.py
@@ -41,15 +41,19 @@ def _get_setup(self, use_FFNS):
         }
         operators_card = {
             "Q2grid": [1, 100**2],
-            "interpolation_xgrid": [0.1, 1.0],
-            "interpolation_polynomial_degree": 1,
-            "interpolation_is_log": True,
-            "debug_skip_singlet": True,
-            "debug_skip_non_singlet": False,
-            "ev_op_max_order": (2, 0),
-            "ev_op_iterations": 1,
-            "backward_inversion": "exact",
-            "n_integration_cores": 1,
+            "xgrid": [0.1, 1.0],
+            "configs": {
+                "interpolation_polynomial_degree": 1,
+                "interpolation_is_log": True,
+                "ev_op_max_order": (2, 0),
+                "ev_op_iterations": 1,
+                "backward_inversion": "exact",
+                "n_integration_cores": 1,
+            },
+            "debug": {
+                "skip_singlet": True,
+                "skip_non_singlet": False,
+            },
         }
         if use_FFNS:
             theory_card["FNS"] = "FFNS"
diff --git a/tests/eko/test_interpolation.py b/tests/eko/test_interpolation.py
index c4e06b7b6..91e4905ad 100644
--- a/tests/eko/test_interpolation.py
+++ b/tests/eko/test_interpolation.py
@@ -102,9 +102,11 @@ def test_init(self):
 
     def test_from_dict(self):
         d = {
-            "interpolation_xgrid": ["make_grid", 3, 3],
-            "interpolation_is_log": False,
-            "interpolation_polynomial_degree": 1,
+            "xgrid": ["make_grid", 3, 3],
+            "configs": {
+                "interpolation_is_log": False,
+                "interpolation_polynomial_degree": 1,
+            },
         }
         a = interpolation.InterpolatorDispatcher.from_dict(d)
         np.testing.assert_array_almost_equal(
@@ -112,17 +114,21 @@ def test_from_dict(self):
         )
         assert a.polynomial_degree == 1
         dd = {
-            "interpolation_xgrid": ["make_lambert_grid", 20],
-            "interpolation_is_log": False,
-            "interpolation_polynomial_degree": 1,
+            "xgrid": ["make_lambert_grid", 20],
+            "configs": {
+                "interpolation_is_log": False,
+                "interpolation_polynomial_degree": 1,
+            },
         }
         aa = interpolation.InterpolatorDispatcher.from_dict(dd)
         assert len(aa.xgrid) == 20
         with pytest.raises(ValueError):
             d = {
-                "interpolation_xgrid": [],
-                "interpolation_is_log": False,
-                "interpolation_polynomial_degree": 1,
+                "xgrid": [],
+                "configs": {
+                    "interpolation_is_log": False,
+                    "interpolation_polynomial_degree": 1,
+                },
             }
             interpolation.InterpolatorDispatcher.from_dict(d)
 
@@ -211,14 +217,20 @@ def test_eval_N(self):
         p0_cs_ref = [1, -1]
         for act_c, res_c in zip(p0N.areas[0], p0_cs_ref):
             assert_almost_equal(act_c, res_c)
-        p0Nref = lambda N, lnx: (1 / N - 1 / (N + 1)) * np.exp(-N * lnx)
+
+        def p0Nref(N, lnx):
+            return (1 / N - 1 / (N + 1)) * np.exp(-N * lnx)
+
         # p_1(x) = x -> \tilde p_1(N) = 1/(N+1)
         p1N = inter_N[1]
         assert len(p1N.areas) == 1
         p1_cs_ref = [0, 1]
         for act_c, res_c in zip(p1N.areas[0], p1_cs_ref):
             assert_almost_equal(act_c, res_c)
-        p1Nref = lambda N, lnx: (1 / (N + 1)) * np.exp(-N * lnx)
+
+        def p1Nref(N, lnx):
+            return (1 / (N + 1)) * np.exp(-N * lnx)
+
         # iterate configurations
         for N in [1.0, 2.0, complex(1.0, 1.0)]:
             # check skip
@@ -238,22 +250,34 @@ def test_log_eval_N(self):
         p0_cs_ref = [0, -1]
         for act_c, res_c in zip(p0N.areas[0], p0_cs_ref):
             assert_almost_equal(act_c, res_c)
-        # Full -> \tilde p_0(N) = exp(-N)(exp(N)-1-N)/N^2
-        # MMa: Integrate[x^(n-1) (-Log[x]),{x,1/E,1}]
-        p0Nref_full = lambda N, lnx: ((np.exp(N) - 1 - N) / N**2) * np.exp(
-            -N * (lnx + 1)
-        )
-        # partial = lower bound is neglected;
-        p0Nref_partial = lambda N, lnx: (1 / N**2) * np.exp(-N * lnx)
+
+        def p0Nref_full(N, lnx):
+            r"""
+            Full -> \tilde p_0(N) = exp(-N)(exp(N)-1-N)/N^2
+            MMa: Integrate[x^(n-1) (-Log[x]),{x,1/E,1}]
+            """
+            return ((np.exp(N) - 1 - N) / N**2) * np.exp(-N * (lnx + 1))
+
+        def p0Nref_partial(N, lnx):
+            "partial = lower bound is neglected"
+            return (1 / N**2) * np.exp(-N * lnx)
+
         p1N = inter_N[1]
         assert len(p1N.areas) == 1
         p1_cs_ref = [1, 1]
         for act_c, res_c in zip(p1N.areas[0], p1_cs_ref):
             assert_almost_equal(act_c, res_c)
-        # p_1(x) = 1+\ln(x) -> \tilde p_1(N) = (exp(-N)-1+N)/N^2
-        # MMa: Integrate[x^(n-1) (1+Log[x]),{x,1/E,1}]
-        p1Nref_full = lambda N, lnx: ((np.exp(-N) - 1 + N) / N**2) * np.exp(-N * lnx)
-        p1Nref_partial = lambda N, lnx: (1 / N - 1 / N**2) * np.exp(-N * lnx)
+
+        def p1Nref_full(N, lnx):
+            r"""
+            p_1(x) = 1+\ln(x) -> \tilde p_1(N) = (exp(-N)-1+N)/N^2
+            MMa: Integrate[x^(n-1) (1+Log[x]),{x,1/E,1}]
+            """
+            return ((np.exp(-N) - 1 + N) / N**2) * np.exp(-N * lnx)
+
+        def p1Nref_partial(N, lnx):
+            return (1 / N - 1 / N**2) * np.exp(-N * lnx)
+
         # iterate configurations
         for N in [1.0, 2.0, complex(1.0, 1.0)]:
             # check skip
diff --git a/tests/eko/test_ome.py b/tests/eko/test_ome.py
index 6d9be8aad..178058522 100644
--- a/tests/eko/test_ome.py
+++ b/tests/eko/test_ome.py
@@ -330,15 +330,19 @@ def test_labels(self):
             for skip_ns in [True, False]:
                 operators_card = {
                     "Q2grid": [1, 10],
-                    "interpolation_xgrid": [0.1, 1.0],
-                    "interpolation_polynomial_degree": 1,
-                    "interpolation_is_log": True,
-                    "debug_skip_singlet": skip_singlet,
-                    "debug_skip_non_singlet": skip_ns,
-                    "ev_op_max_order": (2, 0),
-                    "ev_op_iterations": 1,
-                    "backward_inversion": "exact",
-                    "n_integration_cores": 1,
+                    "xgrid": [0.1, 1.0],
+                    "configs": {
+                        "interpolation_polynomial_degree": 1,
+                        "interpolation_is_log": True,
+                        "ev_op_max_order": (2, 0),
+                        "ev_op_iterations": 1,
+                        "backward_inversion": "exact",
+                        "n_integration_cores": 1,
+                    },
+                    "debug": {
+                        "skip_singlet": skip_singlet,
+                        "skip_non_singlet": skip_ns,
+                    },
                 }
                 g = OperatorGrid.from_dict(
                     self.theory_card,
@@ -415,8 +419,10 @@ def test_compute_n3lo(self):
             np.testing.assert_allclose(mat, np.triu(mat))
 
     def test_compute_lo(self):
-        self.theory_card.update({"order": (1, 0)})
-        self.operators_card.update({"debug_skip_singlet": False})
+        self.theory_card.update({"PTO": (1, 0)})
+        self.operators_card.update(
+            dict(debug={"debug_skip_singlet": False, "skip_non_singlet": False})
+        )
         g = OperatorGrid.from_dict(
             self.theory_card,
             self.operators_card,
@@ -463,15 +469,19 @@ def test_compute_lo(self):
     def test_compute_nlo(self):
         operators_card = {
             "Q2grid": [20],
-            "interpolation_xgrid": [0.001, 0.01, 0.1, 1.0],
-            "interpolation_polynomial_degree": 1,
-            "interpolation_is_log": True,
-            "debug_skip_singlet": False,
-            "debug_skip_non_singlet": False,
-            "ev_op_max_order": (1, 0),
-            "ev_op_iterations": 1,
-            "backward_inversion": "exact",
-            "n_integration_cores": 1,
+            "xgrid": [0.001, 0.01, 0.1, 1.0],
+            "configs": {
+                "interpolation_polynomial_degree": 1,
+                "interpolation_is_log": True,
+                "ev_op_max_order": (2, 0),
+                "ev_op_iterations": 1,
+                "backward_inversion": "exact",
+                "n_integration_cores": 1,
+            },
+            "debug": {
+                "skip_singlet": False,
+                "skip_non_singlet": False,
+            },
         }
         t = copy.deepcopy(self.theory_card)
         t["order"] = (1, 0)
@@ -493,7 +503,7 @@ def test_compute_nlo(self):
         )
         o.compute()
 
-        dim = len(operators_card["interpolation_xgrid"])
+        dim = len(operators_card["xgrid"])
         shape = (dim, dim)
         for indices in [(100, br.matching_hplus_pid), (200, br.matching_hminus_pid)]:
             assert o.op_members[(indices[0], indices[0])].value.shape == shape

From dde03e4684e70e20190ca2911a6abf883aac4743 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:52:20 +0200
Subject: [PATCH 013/148] Recover all runner tests

---
 src/eko/output/struct.py | 15 ++++++++-
 src/eko/runner.py        | 49 +++++++++++++++++------------
 tests/eko/test_runner.py | 66 ++++++++++++----------------------------
 3 files changed, 62 insertions(+), 68 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index c01ca7838..5717e54b0 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -94,6 +94,8 @@ def __setitem__(self, q2, op):
         # TODO: autodump
         if isinstance(op, dict):
             op = Operator.from_dict(op)
+        if not isinstance(op, Operator):
+            raise ValueError("Only operators can be stored.")
         self._operators[q2] = op
 
     def items(self):
@@ -110,10 +112,21 @@ def from_dict(cls, dictionary):
             Q02=dictionary["Q0"] ** 2,
             _operators={q2: None for q2 in dictionary["Q2grid"]},
             configs=Configs.from_dict(dictionary["configs"]),
-            rotations=Rotations.from_dict(dictionary["rotations"]),
+            rotations=Rotations.from_dict(dictionary.get("rotations", {})),
             debug=Debug.from_dict(dictionary.get("debug", {})),
         )
 
+    @classmethod
+    def load(cls, path):
+        return cls(
+            xgrid=None,
+            Q02=None,
+            _operators={q2: None for q2 in ()},
+            configs=None,
+            rotations=None,
+            debug=None,
+        )
+
     @property
     def raw(self):
         return dict(
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 45cc42222..face895a8 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -11,7 +11,7 @@
 from . import compatibility, interpolation, msbar_masses
 from .couplings import Couplings
 from .evolution_operator.grid import OperatorGrid
-from .output import EKO
+from .output import EKO, manipulate
 from .thresholds import ThresholdsAtlas
 
 logger = logging.getLogger(__name__)
@@ -49,14 +49,13 @@ def __init__(self, theory_card, operators_card):
 
         # setup basis grid
         bfd = interpolation.InterpolatorDispatcher.from_dict(new_operators)
-        self.out.update(bfd.to_dict())
+
         # setup the Threshold path, compute masses if necessary
         masses = None
         if new_theory["HQ"] == "MSBAR":
             masses = msbar_masses.compute(new_theory)
         tc = ThresholdsAtlas.from_dict(new_theory, masses=masses)
 
-        self.out["q2_ref"] = float(tc.q2_ref)
         # strong coupling
         sc = Couplings.from_dict(new_theory, masses=masses)
         # setup operator grid
@@ -67,15 +66,22 @@ def __init__(self, theory_card, operators_card):
             sc,
             bfd,
         )
-        self.out["inputgrid"] = bfd.xgrid_raw
-        self.out["targetgrid"] = bfd.xgrid_raw
+
+        rot = operators_card.get("rotations", {})
         self.post_process = dict(
-            inputgrid=new_operators.get("inputgrid", bfd.xgrid_raw),
-            targetgrid=new_operators.get("targetgrid", bfd.xgrid_raw),
-            inputbasis=new_operators.get("inputbasis"),
-            targetbasis=new_operators.get("targetbasis"),
+            inputgrid=rot.get("inputgrid", bfd.xgrid_raw),
+            targetgrid=rot.get("targetgrid", bfd.xgrid_raw),
+            inputbasis=rot.get("inputbasis"),
+            targetbasis=rot.get("targetbasis"),
         )
 
+        if "rotations" not in operators_card:
+            operators_card["rotations"] = {}
+        operators_card["rotations"]["inputgrid"] = bfd.xgrid_raw
+        operators_card["rotations"]["targetgrid"] = bfd.xgrid_raw
+
+        self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref)) | operators_card)
+
     def get_output(self):
         """
         Collects all data for output (to run the evolution)
@@ -86,27 +92,28 @@ def get_output(self):
                 output instance
         """
         # add all operators
-        Q2grid = {}
-        self.out["inputpids"] = br.flavor_basis_pids
-        self.out["targetpids"] = br.flavor_basis_pids
-        self.out["inputgrid"] = self.out["interpolation_xgrid"]
-        self.out["targetgrid"] = self.out["interpolation_xgrid"]
+        self.out.rotations.inputpids = np.array(br.flavor_basis_pids)
+        self.out.rotations.targetpids = np.array(br.flavor_basis_pids)
+        self.out.rotations.inputgrid = self.out.xgrid
+        self.out.rotations.targetgrid = self.out.xgrid
         for final_scale, op in self.op_grid.compute().items():
-            Q2grid[float(final_scale)] = op
-        self.out["Q2grid"] = Q2grid
+            self.out[float(final_scale)] = op
+
         # reshape xgrid
         inputgrid = (
             self.post_process["inputgrid"]
-            if self.post_process["inputgrid"] is not self.out["interpolation_xgrid"]
+            if self.post_process["inputgrid"] is not self.out.xgrid
             else None
         )
         targetgrid = (
             self.post_process["targetgrid"]
-            if self.post_process["targetgrid"] is not self.out["interpolation_xgrid"]
+            if self.post_process["targetgrid"] is not self.out.xgrid
             else None
         )
         if inputgrid is not None or targetgrid is not None:
-            self.out.xgrid_reshape(targetgrid=targetgrid, inputgrid=inputgrid)
+            manipulate.xgrid_reshape(
+                self.out, targetgrid=targetgrid, inputgrid=inputgrid
+            )
 
         # reshape flavors
         inputbasis = self.post_process["inputbasis"]
@@ -116,5 +123,7 @@ def get_output(self):
         if targetbasis is not None:
             targetbasis = np.array(targetbasis)
         if inputbasis is not None or targetbasis is not None:
-            self.out.flavor_reshape(targetbasis=targetbasis, inputbasis=inputbasis)
+            manipulate.flavor_reshape(
+                self.out, targetbasis=targetbasis, inputbasis=inputbasis
+            )
         return copy.deepcopy(self.out)
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 6b5c66d5f..23ada38f6 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -37,7 +37,7 @@
 }
 operators_card = {
     "Q2grid": [10, 100],
-    "interpolation_xgrid": [0.01, 0.1, 1.0],
+    "xgrid": [0.01, 0.1, 1.0],
     "configs": {
         "interpolation_polynomial_degree": 1,
         "interpolation_is_log": True,
@@ -56,13 +56,7 @@ def test_raw():
     oc = copy.deepcopy(operators_card)
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
-    check_shapes(
-        o,
-        o["interpolation_xgrid"],
-        o["interpolation_xgrid"],
-        tc,
-        oc,
-    )
+    check_shapes(o, o.xgrid, o.xgrid, tc, oc)
 
 
 def test_targetgrid():
@@ -70,16 +64,10 @@ def test_targetgrid():
     tc = copy.deepcopy(theory_card)
     oc = copy.deepcopy(operators_card)
     tgrid = [0.1, 1.0]
-    oc["targetgrid"] = tgrid
+    oc["rotations"] = dict(targetgrid=tgrid)
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
-    check_shapes(
-        o,
-        tgrid,
-        o["interpolation_xgrid"],
-        tc,
-        oc,
-    )
+    check_shapes(o, tgrid, o.xgrid, tc, oc)
 
 
 def test_targetbasis():
@@ -90,37 +78,27 @@ def test_targetbasis():
     oc["inputbasis"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
-    check_shapes(
-        o,
-        o["interpolation_xgrid"],
-        o["interpolation_xgrid"],
-        tc,
-        oc,
-    )
+    check_shapes(o, o.xgrid, o.xgrid, tc, oc)
 
 
 def check_shapes(o, txs, ixs, theory_card, operators_card):
-    tpids = len(o["targetpids"])
-    ipids = len(o["inputpids"])
+    tpids = len(o.rotations.targetpids)
+    ipids = len(o.rotations.inputpids)
     op_shape = (tpids, len(txs), ipids, len(ixs))
 
     # check output = input
-    np.testing.assert_allclose(
-        o["interpolation_xgrid"], operators_card["interpolation_xgrid"]
-    )
-    np.testing.assert_allclose(o["targetgrid"], txs)
-    np.testing.assert_allclose(o["inputgrid"], ixs)
+    np.testing.assert_allclose(o.xgrid, operators_card["xgrid"])
+    np.testing.assert_allclose(o.rotations.targetgrid, txs)
+    np.testing.assert_allclose(o.rotations.inputgrid, ixs)
     for k in ["interpolation_polynomial_degree", "interpolation_is_log"]:
-        assert o[k] == operators_card[k]
-    np.testing.assert_allclose(o["q2_ref"], theory_card["Q0"] ** 2)
+        assert getattr(o.configs, k) == operators_card["configs"][k]
+    np.testing.assert_allclose(o.Q02, theory_card["Q0"] ** 2)
     # check available operators
-    assert len(o["Q2grid"]) == len(operators_card["Q2grid"])
-    assert list(o["Q2grid"].keys()) == operators_card["Q2grid"]
-    for ops in o["Q2grid"].values():
-        assert "operators" in ops
-        assert "operator_errors" in ops
-        assert ops["operators"].shape == op_shape
-        assert ops["operator_errors"].shape == op_shape
+    assert len(o.Q2grid) == len(operators_card["Q2grid"])
+    assert list(o.Q2grid) == operators_card["Q2grid"]
+    for _, ops in o.items():
+        assert ops.operator.shape == op_shape
+        assert ops.error.shape == op_shape
 
 
 def test_vfns():
@@ -130,14 +108,8 @@ def test_vfns():
     tc["kcThr"] = 1.0
     tc["kbThr"] = 1.0
     tc["order"] = (3, 0)
-    oc["debug_skip_non_singlet"] = False
+    oc["debug"]["skip_non_singlet"] = False
     # tc,oc = compatibility.update(theory_card,operators_card)
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
-    check_shapes(
-        o,
-        o["interpolation_xgrid"],
-        o["interpolation_xgrid"],
-        tc,
-        oc,
-    )
+    check_shapes(o, o.xgrid, o.xgrid, tc, oc)

From 0ce9ead9d6c752b9aeda738855cfc1dec1f7ae68 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:53:19 +0200
Subject: [PATCH 014/148] Recover all tests

---
 tests/eko/test_ev_op_grid.py | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/tests/eko/test_ev_op_grid.py b/tests/eko/test_ev_op_grid.py
index 86913e6ac..0fee639e3 100644
--- a/tests/eko/test_ev_op_grid.py
+++ b/tests/eko/test_ev_op_grid.py
@@ -112,14 +112,10 @@ def test_compute_q2grid(self):
         # we can also pass a single number
         opg = opgrid.compute()
         assert len(opg) == 2
-        assert all(
-            k in op for k in ["operators", "operator_errors"] for op in opg.values()
-        )
+        assert all(k in op for k in ["operator", "error"] for op in opg.values())
         opg = opgrid.compute(3)
         assert len(opg) == 1
-        assert all(
-            k in op for k in ["operators", "operator_errors"] for op in opg.values()
-        )
+        assert all(k in op for k in ["operator", "error"] for op in opg.values())
 
     def test_grid_computation_VFNS(self):
         """Checks that the grid can be computed"""
@@ -144,5 +140,5 @@ def test_mod_expanded(self):
             )
             sv_opg = sv_opgrid.compute(3)
             np.testing.assert_allclose(
-                opg[3]["operators"], sv_opg[3]["operators"], atol=0.7 * epsilon
+                opg[3]["operator"], sv_opg[3]["operator"], atol=0.7 * epsilon
             )

From 42e1b90f0ea2fec075848a79250c8c6b07473db1 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 17:10:10 +0100
Subject: [PATCH 015/148] Move ekobox loading to legacy

---
 src/ekobox/evol_pdf.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index ca019c69b..af2e425fe 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -2,6 +2,7 @@
 import pathlib
 
 import eko
+import eko.output.legacy
 from eko import basis_rotation as br
 from ekomark import apply
 
@@ -60,9 +61,9 @@ def evolve_pdfs(
             ops_id = f"o{operators_card['hash'][:6]}_t{theory_card['hash'][:6]}.tar"
             ops_id_path = pathlib.Path(ops_id)
             outpath = my_path / ops_id_path.relative_to(ops_id_path.anchor)
-            eko_output = eko.output.Output.load_tar(outpath)
+            eko_output = eko.output.legacy.load_tar(outpath)
         else:
-            eko_output = eko.output.Output.load_tar(my_path)
+            eko_output = eko.output.legacy.load_tar(my_path)
     else:
         eko_output = eko.run_dglap(theory_card, operators_card)
         if store_path is not None:

From 47832326547a5f25560aec69ef9834772954bb54 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 17:19:10 +0100
Subject: [PATCH 016/148] Replace bleeding-edge syntax for dict union

---
 src/eko/runner.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/eko/runner.py b/src/eko/runner.py
index face895a8..1cd76e87a 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -80,7 +80,7 @@ def __init__(self, theory_card, operators_card):
         operators_card["rotations"]["inputgrid"] = bfd.xgrid_raw
         operators_card["rotations"]["targetgrid"] = bfd.xgrid_raw
 
-        self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref)) | operators_card)
+        self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref), **operators_card))
 
     def get_output(self):
         """

From fe2f5553a903f5366e5b493b5cd3d288fd8df0d2 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:54:14 +0200
Subject: [PATCH 017/148] Update ekobox benchmarks

---
 benchmarks/ekobox/benchmark_evol_pdf.py | 24 +++++++----------
 pyproject.toml                          |  2 +-
 src/ekobox/gen_op.py                    | 35 ++++++++++++++-----------
 src/ekomark/data/operators.py           | 26 ++++++++++--------
 4 files changed, 44 insertions(+), 43 deletions(-)

diff --git a/benchmarks/ekobox/benchmark_evol_pdf.py b/benchmarks/ekobox/benchmark_evol_pdf.py
index a4233171f..485b86618 100644
--- a/benchmarks/ekobox/benchmark_evol_pdf.py
+++ b/benchmarks/ekobox/benchmark_evol_pdf.py
@@ -5,8 +5,8 @@
 import numpy as np
 import pytest
 
+import eko.output.legacy
 from eko import basis_rotation as br
-from eko import output
 from ekobox import evol_pdf as ev_p
 from ekobox import gen_op as g_o
 from ekobox import gen_theory as g_t
@@ -56,11 +56,11 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
         all_blocks = (load.load_blocks_from_file("EvPDF", 0))[1]
         info = load.load_info_from_file("EvPDF")
         ev_pdf = lhapdf.mkPDF("EvPDF", 0)
-    assert info["XMin"] == op["interpolation_xgrid"][0]
+    assert info["XMin"] == op["xgrid"][0]
     assert info["SetDesc"] == "MyEvolvedPDF"
     assert info["MZ"] == theory["MZ"]
     assert info["Debug"] == "Debug"
-    xgrid = op["interpolation_xgrid"]
+    xgrid = op["xgrid"]
     for Q2 in [20.0, 100.0, 10000.0]:
         for x in xgrid[10:40]:
             for pid in [21, 1, -1, 2, -2, 3, -3]:
@@ -80,9 +80,7 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
 
 @pytest.mark.isolated
 def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
-    op = g_o.gen_op_card(
-        [10, 100], update={"interpolation_xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}
-    )
+    op = g_o.gen_op_card([10, 100], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
     theory = g_t.gen_theory_card(0, 1.0)
     with lhapdf_path(test_pdf):
         pdfs = lhapdf.mkPDFs("myMSTW2008nlo90cl")
@@ -96,7 +94,7 @@ def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
         new_pdf_1 = lhapdf.mkPDF("Debug", 0)
         new_pdf_2 = lhapdf.mkPDF("Debug", 1)
         info = load.load_info_from_file("Debug")
-    assert info["XMin"] == op["interpolation_xgrid"][0]
+    assert info["XMin"] == op["xgrid"][0]
     assert len(pdfs) == len(new_pdfs)
     for Q2 in [10, 100]:
         for x in [1e-7, 0.01, 0.1, 0.2, 0.3]:
@@ -106,22 +104,18 @@ def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
 
 @pytest.mark.isolated
 def benchmark_gen_and_dump_out(tmp_path):
-    op = g_o.gen_op_card(
-        [100.0], update={"interpolation_xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}
-    )
+    op = g_o.gen_op_card([100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
     theory = g_t.gen_theory_card(0, 1.0)
 
     out = ev_p.gen_out(theory, op, path=tmp_path)
 
     ops_id = f"o{op['hash'][:6]}_t{theory['hash'][:6]}"
     outpath = f"{tmp_path}/{ops_id}.tar"
-    loaded_out = output.Output.load_tar(outpath)
-    for el, load_el in zip(
-        out["interpolation_xgrid"], loaded_out["interpolation_xgrid"]
-    ):
+    loaded_out = eko.output.legacy.load_tar(outpath)
+    for el, load_el in zip(out["xgrid"], loaded_out.xgrid):
         assert el == load_el
     for el, load_el in zip(
-        out["Q2grid"][100.0]["operators"], loaded_out["Q2grid"][100.0]["operators"]
+        out["Q2grid"][100.0]["operators"], loaded_out[100.0].operator
     ):
         np.testing.assert_allclose(
             out["Q2grid"][100.0]["operators"],
diff --git a/pyproject.toml b/pyproject.toml
index ebcbe3e55..732eba80d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,7 @@ genpdf = "ekobox.genpdf.cli:cli"
 test = "pytest tests"
 coverage = "$BROWSER htmlcov/index.html"
 test-cov = ["test", "coverage"]
-bench = "pytest benchmarks"
+bench = ["bench-iso", "bench-run"]
 bench-iso.cmd = "pytest benchmarks -m isolated"
 bench-iso.env.NUMBA_DISABLE_JIT.default = "0"
 bench-run.cmd = "pytest benchmarks -m 'not isolated'"
diff --git a/src/ekobox/gen_op.py b/src/ekobox/gen_op.py
index 9193d2c15..5eba6ca35 100644
--- a/src/ekobox/gen_op.py
+++ b/src/ekobox/gen_op.py
@@ -8,23 +8,26 @@
 
 
 def gen_op_card(Q2grid, update=None, name=None):
-    """
+    """Generate operators card.
+
     Generates an operator card with some mandatory user choice
     (in this case only the Q2 grid) and some default values which
-    can be changed by the update input dict
+    can be changed by the update input dict.
 
     Parameters
     ----------
-        Q2grid : list(float)
-            grid for Q2
-        update : dict
-            dictionary of info to update in op. card
-        name : str
-            name of exported op.card (if name not None)
+    Q2grid : list(float)
+        grid for Q2
+    update : dict
+        dictionary of info to update in op. card
+    name : str
+        name of exported op.card (if name not None)
+
     Returns
     -------
-        : dict
-            operator card
+    dict
+        operator card
+
     """
     # Constructing the dictionary with some default value
     def_op = copy.deepcopy(operators.default_card)
@@ -43,16 +46,16 @@ def gen_op_card(Q2grid, update=None, name=None):
 
 
 def export_op_card(name, op):
-    """
-    Export the operators card in the current directory
+    """Export the operators card in the current directory
 
     Parameters
     ----------
-        name : str
-            name of the op. card to export
+    name : str
+        name of the op. card to export
+
+    op : dict
+        op card
 
-        op : dict
-            op card
     """
     target = f"{name}.yaml"
     with open(target, "w", encoding="utf-8") as out:
diff --git a/src/ekomark/data/operators.py b/src/ekomark/data/operators.py
index 1a532e5e5..146ed70c8 100644
--- a/src/ekomark/data/operators.py
+++ b/src/ekomark/data/operators.py
@@ -9,19 +9,23 @@
 from . import db
 
 default_card = dict(
-    interpolation_xgrid=interpolation.make_grid(30, 20).tolist(),
-    interpolation_polynomial_degree=4,
-    interpolation_is_log=True,
-    debug_skip_non_singlet=False,
-    debug_skip_singlet=False,
-    ev_op_max_order=10,
-    ev_op_iterations=10,
-    backward_inversion="expanded",
-    n_integration_cores=0,
-    Q2grid=[100],
+    sorted(
+        dict(
+            xgrid=interpolation.make_grid(30, 20).tolist(),
+            configs=dict(
+                interpolation_polynomial_degree=4,
+                interpolation_is_log=True,
+                ev_op_max_order=10,
+                ev_op_iterations=10,
+                backward_inversion="expanded",
+                n_integration_cores=0,
+            ),
+            debug=dict(skip_non_singlet=False, skip_singlet=False),
+            Q2grid=[100],
+        ).items()
+    )
 )
 
-default_card = dict(sorted(default_card.items()))
 
 lhapdf_config = {
     # "ev_op_max_order": [10],

From cfc2288e7b5d0fcce0d9e776ccdd241e2c5280b8 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 17 Mar 2022 18:49:10 +0100
Subject: [PATCH 018/148] Replace remaining interpolation_xgrids

---
 benchmarks/HERA20_bench.py                      |  2 +-
 benchmarks/ekobox/benchmark_gen_info.py         |  4 ++--
 benchmarks/ekobox/benchmark_utils.py            |  4 ++--
 benchmarks/lha_paper_bench.py                   |  4 ++--
 src/ekobox/evol_pdf.py                          |  2 +-
 src/ekobox/gen_info.py                          |  4 ++--
 src/ekomark/benchmark/external/apfel_utils.py   |  2 +-
 src/ekomark/benchmark/external/lhapdf_utils.py  |  2 +-
 src/ekomark/benchmark/external/pegasus_utils.py |  2 +-
 src/ekomark/data/db.py                          |  2 +-
 src/ekomark/navigator/navigator.py              |  2 +-
 src/ekomark/plots.py                            |  2 +-
 tests/conftest.py                               | 10 +++++-----
 tests/eko/test_output.py                        | 12 +++++-------
 14 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/benchmarks/HERA20_bench.py b/benchmarks/HERA20_bench.py
index a09d83f3d..79f17c92b 100644
--- a/benchmarks/HERA20_bench.py
+++ b/benchmarks/HERA20_bench.py
@@ -22,7 +22,7 @@
 }
 
 # LHAPDF x-range is smaller
-base_op = {"interpolation_xgrid": interpolation.make_lambert_grid(50, 1.0e-6)}
+base_op = {"xgrid": interpolation.make_lambert_grid(50, 1.0e-6)}
 
 
 class BenchmarkHERA20(Runner):
diff --git a/benchmarks/ekobox/benchmark_gen_info.py b/benchmarks/ekobox/benchmark_gen_info.py
index 8e8f65566..7eb10d3d3 100644
--- a/benchmarks/ekobox/benchmark_gen_info.py
+++ b/benchmarks/ekobox/benchmark_gen_info.py
@@ -22,5 +22,5 @@ def benchmark_create_info_file():
     assert info["NumMembers"] == 4
     assert info["MTop"] == theory["mt"]
     np.testing.assert_allclose(info["QMin"], math.sqrt(op["Q2grid"][0]), rtol=1e-5)
-    assert info["XMin"] == op["interpolation_xgrid"][0]
-    assert info["XMax"] == op["interpolation_xgrid"][-1] == 1.0
+    assert info["XMin"] == op["xgrid"][0]
+    assert info["XMax"] == op["xgrid"][-1] == 1.0
diff --git a/benchmarks/ekobox/benchmark_utils.py b/benchmarks/ekobox/benchmark_utils.py
index 0b8ac5664..d29986eb0 100644
--- a/benchmarks/ekobox/benchmark_utils.py
+++ b/benchmarks/ekobox/benchmark_utils.py
@@ -12,13 +12,13 @@
 def benchmark_ekos_product():
     # Generating two ekos
     op1 = g_o.gen_op_card(
-        [60.0, 80.0, 100.0], update={"interpolation_xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}
+        [60.0, 80.0, 100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}
     )
     theory1 = g_t.gen_theory_card(0, 5.0)
 
     op2 = g_o.gen_op_card(
         [80.0, 100.0, 120.0],
-        update={"interpolation_xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]},
+        update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]},
     )
     theory2 = g_t.gen_theory_card(0, 10.0)
     theory_err = g_t.gen_theory_card(0, 5.0)
diff --git a/benchmarks/lha_paper_bench.py b/benchmarks/lha_paper_bench.py
index 65bc64fb8..9d3bc36d1 100644
--- a/benchmarks/lha_paper_bench.py
+++ b/benchmarks/lha_paper_bench.py
@@ -112,8 +112,8 @@ def run_lha(self, theory_updates):
             [
                 {
                     "Q2grid": [1e4],
-                    "ev_op_iterations": 10,
-                    "interpolation_xgrid": make_lambert_grid(60).tolist(),
+                    "configs": {"ev_op_iterations": 10},
+                    "xgrid": make_lambert_grid(60).tolist(),
                 }
             ],
             ["ToyLH"],
diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index af2e425fe..28914b182 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -74,7 +74,7 @@ def evolve_pdfs(
         evolved_PDF_list.append(apply.apply_pdf(eko_output, initial_PDF, targetgrid))
 
     if targetgrid is None:
-        targetgrid = operators_card["interpolation_xgrid"]
+        targetgrid = operators_card["xgrid"]
     if info_update is None:
         info_update = {}
     info_update["XMin"] = targetgrid[0]
diff --git a/src/ekobox/gen_info.py b/src/ekobox/gen_info.py
index 7deab82e9..757ae4c7c 100644
--- a/src/ekobox/gen_info.py
+++ b/src/ekobox/gen_info.py
@@ -32,8 +32,8 @@ def create_info_file(theory_card, operators_card, num_members, info_update):
     template_info.update(info_update)
     template_info["NumFlavors"] = 14
     template_info["Flavors"] = [-6, -5, -4, -3, -2, -1, 1, 2, 3, 4, 5, 6, 21, 22]
-    template_info["XMin"] = operators_card["interpolation_xgrid"][0]
-    template_info["XMax"] = operators_card["interpolation_xgrid"][-1]
+    template_info["XMin"] = operators_card["xgrid"][0]
+    template_info["XMax"] = operators_card["xgrid"][-1]
     template_info["NumMembers"] = num_members
     template_info["OrderQCD"] = theory_card["PTO"]
     template_info["QMin"] = round(math.sqrt(operators_card["Q2grid"][0]), 4)
diff --git a/src/ekomark/benchmark/external/apfel_utils.py b/src/ekomark/benchmark/external/apfel_utils.py
index dbc94a9de..3bb1016c8 100644
--- a/src/ekomark/benchmark/external/apfel_utils.py
+++ b/src/ekomark/benchmark/external/apfel_utils.py
@@ -36,7 +36,7 @@ def compute_apfel_data(
             output containing: target_xgrid, values
     """
 
-    target_xgrid = operators["interpolation_xgrid"]
+    target_xgrid = operators["xgrid"]
     pdf_name = pdf.set().name
 
     # Load apfel
diff --git a/src/ekomark/benchmark/external/lhapdf_utils.py b/src/ekomark/benchmark/external/lhapdf_utils.py
index c3533cda6..c623070d2 100644
--- a/src/ekomark/benchmark/external/lhapdf_utils.py
+++ b/src/ekomark/benchmark/external/lhapdf_utils.py
@@ -28,7 +28,7 @@ def compute_LHAPDF_data(operators, pdf, skip_pdfs, rotate_to_evolution_basis=Fal
             output containing: target_xgrid, values
     """
 
-    target_xgrid = operators["interpolation_xgrid"]
+    target_xgrid = operators["xgrid"]
 
     out_tabs = {}
     for q2 in operators["Q2grid"]:
diff --git a/src/ekomark/benchmark/external/pegasus_utils.py b/src/ekomark/benchmark/external/pegasus_utils.py
index 07f145848..87fb2f807 100644
--- a/src/ekomark/benchmark/external/pegasus_utils.py
+++ b/src/ekomark/benchmark/external/pegasus_utils.py
@@ -29,7 +29,7 @@ def compute_pegasus_data(theory, operators, skip_pdfs, rotate_to_evolution_basis
     """
     import pegasus  # pylint:disable=import-error,import-outside-toplevel
 
-    target_xgrid = operators["interpolation_xgrid"]
+    target_xgrid = operators["xgrid"]
 
     # init pegasus
     nf = theory["NfFF"]
diff --git a/src/ekomark/data/db.py b/src/ekomark/data/db.py
index 67328c522..98d754751 100644
--- a/src/ekomark/data/db.py
+++ b/src/ekomark/data/db.py
@@ -16,7 +16,7 @@ class Operator(Base):  # pylint: disable=too-few-public-methods
 
     interpolation_is_log = Column(Text)
     interpolation_polynomial_degree = Column(Integer)
-    interpolation_xgrid = Column(Text)
+    xgrid = Column(Text)
     debug_skip_non_singlet = Column(Boolean)
     debug_skip_singlet = Column(Boolean)
     ev_op_max_order = Column(Integer)
diff --git a/src/ekomark/navigator/navigator.py b/src/ekomark/navigator/navigator.py
index 286e43f86..fca3b746a 100644
--- a/src/ekomark/navigator/navigator.py
+++ b/src/ekomark/navigator/navigator.py
@@ -71,7 +71,7 @@ def fill_operators(self, op, obj):
             obj : dict
                 to be updated pandas record
         """
-        xgrid = op["interpolation_xgrid"]
+        xgrid = op["xgrid"]
         obj["xgrid"] = (
             f"{len(xgrid)}pts: "
             + f"{'log' if op['interpolation_is_log'] else 'x'}"
diff --git a/src/ekomark/plots.py b/src/ekomark/plots.py
index d7612d014..2fcff96f8 100644
--- a/src/ekomark/plots.py
+++ b/src/ekomark/plots.py
@@ -253,7 +253,7 @@ def save_operators_to_pdf(path, theory, ops, me, skip_pdfs, change_lab=False):
                 new_op = {}
                 new_op_err = {}
                 # loop on xgrid point
-                for j in range(len(me["interpolation_xgrid"])):
+                for j in range(len(me["xgrid"])):
                     # loop on pid in
                     for label_in, val, val_err in zip(ops_names, res[j], res_err[j]):
                         if label_in in skip_pdfs:
diff --git a/tests/conftest.py b/tests/conftest.py
index 03f38fa79..35a8a9213 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -35,18 +35,18 @@ def mk_g(self, q2s, lpids, lx):
 
     def fake_output(self):
         # build data
-        interpolation_xgrid = np.array([0.5, 1.0])
+        xgrid = np.array([0.5, 1.0])
         interpolation_polynomial_degree = 1
         interpolation_is_log = False
         pids = [0, 1]
         q2_ref = 1
         q2_out = 2
-        Q2grid = self.mk_g([q2_out], len(pids), len(interpolation_xgrid))
+        Q2grid = self.mk_g([q2_out], len(pids), len(xgrid))
         d = dict(
-            xgrid=interpolation_xgrid,
+            xgrid=xgrid,
             rotations=dict(
-                targetgrid=interpolation_xgrid,
-                inputgrid=interpolation_xgrid,
+                targetgrid=xgrid,
+                inputgrid=xgrid,
                 inputpids=pids,
                 targetpids=pids,
             ),
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 138fd9248..f058551cb 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -225,21 +225,19 @@ def test_flavor_reshape(self, fake_output):
             manipulate.flavor_reshape(copy.deepcopy(o1))
 
     def test_to_evol(self, fake_factory):
-        interpolation_xgrid = np.array([0.5, 1.0])
+        xgrid = np.array([0.5, 1.0])
         interpolation_polynomial_degree = 1
         interpolation_is_log = False
         q2_ref = 1
         q2_out = 2
-        Q2grid = fake_factory.mk_g(
-            [q2_out], len(br.flavor_basis_pids), len(interpolation_xgrid)
-        )
+        Q2grid = fake_factory.mk_g([q2_out], len(br.flavor_basis_pids), len(xgrid))
         d = dict(
-            xgrid=interpolation_xgrid,
+            xgrid=xgrid,
             Q0=np.sqrt(q2_ref),
             Q2grid=Q2grid,
             rotations=dict(
-                targetgrid=interpolation_xgrid,
-                inputgrid=interpolation_xgrid,
+                targetgrid=xgrid,
+                inputgrid=xgrid,
                 inputpids=br.flavor_basis_pids,
                 targetpids=br.flavor_basis_pids,
             ),

From b8566825b4fb69857f138cba4dff7a6c095429f2 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:55:24 +0200
Subject: [PATCH 019/148] Recover ekobox but product

---
 benchmarks/ekobox/benchmark_evol_pdf.py | 11 ++++------
 benchmarks/ekobox/benchmark_gen_op.py   | 10 +++++----
 benchmarks/ekobox/benchmark_utils.py    | 22 ++++++++------------
 src/eko/output/legacy.py                |  6 +++++-
 src/ekobox/evol_pdf.py                  |  2 +-
 src/ekobox/gen_op.py                    |  7 ++++++-
 src/ekobox/utils.py                     | 27 +++++++++++++++----------
 7 files changed, 46 insertions(+), 39 deletions(-)

diff --git a/benchmarks/ekobox/benchmark_evol_pdf.py b/benchmarks/ekobox/benchmark_evol_pdf.py
index 485b86618..464416c38 100644
--- a/benchmarks/ekobox/benchmark_evol_pdf.py
+++ b/benchmarks/ekobox/benchmark_evol_pdf.py
@@ -112,12 +112,9 @@ def benchmark_gen_and_dump_out(tmp_path):
     ops_id = f"o{op['hash'][:6]}_t{theory['hash'][:6]}"
     outpath = f"{tmp_path}/{ops_id}.tar"
     loaded_out = eko.output.legacy.load_tar(outpath)
-    for el, load_el in zip(out["xgrid"], loaded_out.xgrid):
-        assert el == load_el
-    for el, load_el in zip(
-        out["Q2grid"][100.0]["operators"], loaded_out[100.0].operator
-    ):
+    assert list(out.xgrid) == list(loaded_out.xgrid)
+    for el, load_el in zip(out[100.0].operator, loaded_out[100.0].operator):
         np.testing.assert_allclose(
-            out["Q2grid"][100.0]["operators"],
-            loaded_out["Q2grid"][100.0]["operators"],
+            out[100.0].operator,
+            loaded_out[100.0].operator,
         )
diff --git a/benchmarks/ekobox/benchmark_gen_op.py b/benchmarks/ekobox/benchmark_gen_op.py
index cacc832cd..bd3b613ed 100644
--- a/benchmarks/ekobox/benchmark_gen_op.py
+++ b/benchmarks/ekobox/benchmark_gen_op.py
@@ -8,15 +8,17 @@
 def benchmark_gen_op_card():
     op = g_o.gen_op_card([10, 100])
     assert op["Q2grid"] == [10, 100]
-    assert op["interpolation_polynomial_degree"] == 4
+    assert op["configs"]["interpolation_polynomial_degree"] == 4
     up_err = {"Prova": "Prova"}
     with pytest.raises(ValueError):
         op = g_o.gen_op_card([10], update=up_err)
-    up = {"interpolation_polynomial_degree": 2, "interpolation_is_log": False}
+    up = {
+        "configs": {"interpolation_polynomial_degree": 2, "interpolation_is_log": False}
+    }
     op = g_o.gen_op_card([100], update=up)
     assert op["Q2grid"] == [100]
-    assert op["interpolation_polynomial_degree"] == 2
-    assert op["interpolation_is_log"] is False
+    assert op["configs"]["interpolation_polynomial_degree"] == 2
+    assert op["configs"]["interpolation_is_log"] is False
 
 
 @pytest.mark.isolated
diff --git a/benchmarks/ekobox/benchmark_utils.py b/benchmarks/ekobox/benchmark_utils.py
index d29986eb0..37a5661f0 100644
--- a/benchmarks/ekobox/benchmark_utils.py
+++ b/benchmarks/ekobox/benchmark_utils.py
@@ -31,20 +31,14 @@ def benchmark_ekos_product():
         _ = utils.ekos_product(eko_ini, eko_fin_err)
     # product is copied
     eko_res = utils.ekos_product(eko_ini, eko_fin, in_place=False)
+
+    assert eko_res.Q02 == eko_ini.Q02
+    np.testing.assert_allclose(eko_res.Q2grid[1:], eko_fin.Q2grid)
+    np.testing.assert_allclose(eko_ini[80.0].operator, eko_res[80.0].operator)
+
     # product overwrites initial
     eko_res2 = utils.ekos_product(eko_ini, eko_fin)
-    np.testing.assert_allclose(
-        eko_res["Q2grid"][80.0]["operators"], eko_res2["Q2grid"][80.0]["operators"]
-    )
-    np.testing.assert_allclose(eko_res2["q2_ref"], eko_ini["q2_ref"])
-    np.testing.assert_allclose(
-        list(eko_res2["Q2grid"].keys()), list(eko_fin["Q2grid"].keys())
-    )
 
-    np.testing.assert_allclose(
-        eko_ini["Q2grid"][80.0]["operators"], eko_res2["Q2grid"][80.0]["operators"]
-    )
-    np.testing.assert_allclose(eko_res["q2_ref"], eko_ini["q2_ref"])
-    np.testing.assert_allclose(
-        list(eko_res["Q2grid"].keys()), list(eko_fin["Q2grid"].keys())
-    )
+    assert eko_res2.Q02 == eko_ini.Q02
+    np.testing.assert_allclose(eko_res2.Q2grid[1:], eko_fin.Q2grid)
+    np.testing.assert_allclose(eko_res[80.0].operator, eko_res2[80.0].operator)
diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 44d03836c..deefa7fd7 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -259,4 +259,8 @@ def load_tar(tarname):
             operator_grid[q2] = dict(zip(grids.keys(), slices))
         metadata["Q2grid"] = operator_grid
 
-    return struct.EKO.from_dict(metadata)
+    eko = struct.EKO.from_dict(metadata)
+    for q2, op in metadata["Q2grid"].items():
+        eko[q2] = op
+
+    return eko
diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index 28914b182..60c4ed24c 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -129,5 +129,5 @@ def gen_out(theory_card, op_card, path=None):
     if path is not None:
         ops_id = f"o{op_card['hash'][:6]}_t{theory_card['hash'][:6]}"
         path = f"{path}/{ops_id}.tar"
-        eko_output.dump_tar(path)
+        eko.output.legacy.dump_tar(eko_output, path)
     return eko_output
diff --git a/src/ekobox/gen_op.py b/src/ekobox/gen_op.py
index 5eba6ca35..6ce7d9034 100644
--- a/src/ekobox/gen_op.py
+++ b/src/ekobox/gen_op.py
@@ -37,7 +37,12 @@ def gen_op_card(Q2grid, update=None, name=None):
         for k in update.keys():
             if k not in def_op.keys():
                 raise ValueError("Provided key not in operators card")
-        def_op.update(update)
+        for key, value in update.items():
+            # properly update sections
+            if isinstance(value, dict):
+                def_op[key].update(value)
+            else:
+                def_op[key] = value
     serialized = sql.serialize(def_op)
     def_op["hash"] = (sql.add_hash(serialized))[-1]
     if name is not None:
diff --git a/src/ekobox/utils.py b/src/ekobox/utils.py
index e228d7cc4..a5b759252 100644
--- a/src/ekobox/utils.py
+++ b/src/ekobox/utils.py
@@ -3,10 +3,12 @@
 
 import numpy as np
 
+from eko.output import EKO
+
 
 # TODO: add a control on the theory (but before we need to implement another
 # kind of output which includes the theory and operator runcards)
-def ekos_product(eko_ini, eko_fin, in_place=True):
+def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
     """Returns the product of two ekos
 
     Parameters
@@ -24,19 +26,20 @@ def ekos_product(eko_ini, eko_fin, in_place=True):
         eko operator
 
     """
-    if eko_fin["q2_ref"] not in eko_ini["Q2grid"].keys():
+    # TODO: check if it's close, instead of checking identity
+    if eko_fin.Q02 not in eko_ini.Q2grid:
         raise ValueError(
             "Initial Q2 of final eko operator does not match any final Q2 in"
             " the initial eko operator"
         )
-    ope1 = eko_ini["Q2grid"][eko_fin["q2_ref"]]["operators"]
-    ope1_error = eko_ini["Q2grid"][eko_fin["q2_ref"]]["operator_errors"]
+    ope1 = eko_ini[eko_fin.Q02].operator
+    ope1_error = eko_ini[eko_fin.Q02].error
 
     ope2_dict = {}
     ope2_error_dict = {}
-    for q2, op in eko_fin["Q2grid"].items():
-        ope2_dict[q2] = op["operators"]
-        ope2_error_dict[q2] = op["operator_errors"]
+    for q2, op in eko_fin.items():
+        ope2_dict[q2] = op.operator
+        ope2_error_dict[q2] = op.error
 
     final_op_dict = {}
     final_op_error_dict = {}
@@ -49,14 +52,16 @@ def ekos_product(eko_ini, eko_fin, in_place=True):
         ) + np.einsum("ajbk,bkcl -> ajcl", ope1_error, op2)
 
         final_dict[q2] = {
-            "operators": final_op_dict[q2],
-            "operator_errors": final_op_error_dict[q2],
+            "operator": final_op_dict[q2],
+            "error": final_op_error_dict[q2],
         }
 
-    final_eko = None
     if in_place is False:
         final_eko = copy.deepcopy(eko_ini)
     else:
         final_eko = eko_ini
-    final_eko["Q2grid"] = final_dict
+
+    for q2, op in final_dict.items():
+        final_eko[q2] = op
+
     return final_eko

From e36ccdb3dd0efe2c85f9728aa1b61c6f7301d149 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:56:07 +0200
Subject: [PATCH 020/148] Simplify ekobox product

---
 src/ekobox/utils.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/ekobox/utils.py b/src/ekobox/utils.py
index a5b759252..504cbb329 100644
--- a/src/ekobox/utils.py
+++ b/src/ekobox/utils.py
@@ -32,8 +32,8 @@ def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
             "Initial Q2 of final eko operator does not match any final Q2 in"
             " the initial eko operator"
         )
-    ope1 = eko_ini[eko_fin.Q02].operator
-    ope1_error = eko_ini[eko_fin.Q02].error
+    ope1 = eko_ini[eko_fin.Q02].operator.copy()
+    ope1_error = eko_ini[eko_fin.Q02].error.copy()
 
     ope2_dict = {}
     ope2_error_dict = {}
@@ -61,7 +61,14 @@ def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
     else:
         final_eko = eko_ini
 
-    for q2, op in final_dict.items():
-        final_eko[q2] = op
+    for q2, op2 in eko_fin.items():
+        op = np.einsum("ajbk,bkcl -> ajcl", ope1, op2.operator)
+
+        error = np.einsum("ajbk,bkcl -> ajcl", ope1, op2.error) + np.einsum(
+            "ajbk,bkcl -> ajcl", ope1_error, op2.operator
+        )
+
+        alphas = eko_fin[q2].alphas
+        final_eko[q2] = dict(operator=op, error=error, alphas=alphas)
 
     return final_eko

From 9bf11608b399d13bd04587f387392a510d747ed4 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 18 Mar 2022 09:29:11 +0100
Subject: [PATCH 021/148] Upgrade product: do not recompute existing operators

---
 src/ekobox/utils.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/ekobox/utils.py b/src/ekobox/utils.py
index 504cbb329..6538a59d1 100644
--- a/src/ekobox/utils.py
+++ b/src/ekobox/utils.py
@@ -62,6 +62,9 @@ def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
         final_eko = eko_ini
 
     for q2, op2 in eko_fin.items():
+        if q2 in eko_ini:
+            continue
+
         op = np.einsum("ajbk,bkcl -> ajcl", ope1, op2.operator)
 
         error = np.einsum("ajbk,bkcl -> ajcl", ope1, op2.error) + np.einsum(

From c72157c548bb04dd4ee8af7fa0c7e3c55b183d44 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:57:46 +0200
Subject: [PATCH 022/148] Introduce xgrid type

---
 src/eko/evolution_operator/__init__.py | 10 +---
 src/eko/interpolation.py               | 82 +++++++++++++++++---------
 src/eko/output/struct.py               |  5 +-
 src/eko/runner.py                      | 16 ++---
 4 files changed, 67 insertions(+), 46 deletions(-)

diff --git a/src/eko/evolution_operator/__init__.py b/src/eko/evolution_operator/__init__.py
index a03a27fa1..4d2a17678 100644
--- a/src/eko/evolution_operator/__init__.py
+++ b/src/eko/evolution_operator/__init__.py
@@ -435,13 +435,9 @@ def run_op_integration(
                 )
                 temp_dict[label] = res[:2]
             column.append(temp_dict)
-
         logger.info(
-            "%s: computing operators - %u/%u took: %6f s",
-            self.log_label,
-            k + 1,
-            self.grid_size,
-            (time.perf_counter() - start_time),
+            f"{self.log_label}: computing operators: - {k+1}/{self.grid_size}"
+            f" took: {(time.perf_counter() - start_time):6f} s"
         )
         return column
 
@@ -499,7 +495,7 @@ def integrate(
 
         # run integration in parallel for each grid point
         # or avoid opening a single pool
-        args = (self.run_op_integration, enumerate(np.log(self.int_disp.xgrid_raw)))
+        args = (self.run_op_integration, enumerate(np.log(self.int_disp.xgrid.raw)))
         if self.n_pools == 1:
             res = map(*args)
         else:
diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index 09f63f7dd..665a3bebe 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -414,6 +414,44 @@ def __call__(self, *args, **kwargs):
         return self.callable(*args, **kwargs)
 
 
+class XGrid:
+    def __init__(self, xgrid: np.ndarray, log: bool = True):
+        ugrid = np.array(np.unique(xgrid), np.float_)
+        if len(xgrid) != len(ugrid):
+            raise ValueError(f"xgrid is not unique: {xgrid}")
+        if len(xgrid) < 2:
+            raise ValueError(f"xgrid needs at least 2 points, received {len(xgrid)}")
+
+        self.log = log
+
+        # henceforth ugrid might no longer be the input!
+        # which is ok, because for most of the code this is all we need to do
+        # to distinguish log and non-log
+        if log:
+            self._raw = ugrid
+            ugrid = np.log(ugrid)
+
+        self.grid = ugrid
+
+    def __len__(self) -> int:
+        return len(self.grid)
+
+    def __eq__(self, other) -> bool:
+        """Checks equality"""
+        return all([len(self) == len(other), np.allclose(self.raw, other.raw)])
+
+    @property
+    def raw(self) -> np.ndarray:
+        return self.grid if not self.log else self._raw
+
+    @property
+    def size(self) -> int:
+        return self.grid.size
+
+    def tolist(self) -> list[float]:
+        return self.raw.tolist()
+
+
 class InterpolatorDispatcher:
     """
     Setups the interpolator.
@@ -426,7 +464,7 @@ class InterpolatorDispatcher:
 
     Parameters
     ----------
-        xgrid_in : numpy.ndarray
+        xgrid : numpy.ndarray
             Grid in x-space from which the interpolators are constructed
         polynomial_degree : int
             degree of the interpolation polynomial
@@ -437,30 +475,17 @@ class InterpolatorDispatcher:
     """
 
     def __init__(self, xgrid, polynomial_degree, log=True, mode_N=True):
+        xgrid = XGrid(xgrid, log=log)
         # sanity checks
-        xgrid_size = len(xgrid)
-        ugrid = np.array(np.unique(xgrid), np.float_)
-        if xgrid_size != len(ugrid):
-            raise ValueError(f"xgrid is not unique: {xgrid}")
-        xgrid = ugrid
-        if xgrid_size < 2:
-            raise ValueError(f"xgrid needs at least 2 points, received {xgrid_size}")
         if polynomial_degree < 1:
             raise ValueError(
                 f"need at least polynomial_degree 1, received {polynomial_degree}"
             )
-        if xgrid_size <= polynomial_degree:
+        if len(xgrid) <= polynomial_degree:
             raise ValueError(
                 f"to interpolate with degree {polynomial_degree} "
                 " we need at least that much points + 1"
             )
-        # keep a true copy of grid
-        self.xgrid_raw = xgrid
-        # henceforth xgrid might no longer be the input!
-        # which is ok, because for most of the code this is all we need to do
-        # to distinguish log and non-log
-        if log:
-            xgrid = np.log(xgrid)
 
         # Save the different variables
         self.xgrid = xgrid
@@ -468,7 +493,7 @@ def __init__(self, xgrid, polynomial_degree, log=True, mode_N=True):
         self.log = log
         logger.info(
             "Interpolation: number of points = %d, polynomial degree = %d, logarithmic = %s",
-            xgrid_size,
+            len(xgrid),
             polynomial_degree,
             log,
         )
@@ -482,20 +507,20 @@ def __init__(self, xgrid, polynomial_degree, log=True, mode_N=True):
         if polynomial_degree % 2 == 0:
             po2 -= 1
         # iterate areas: there is 1 less then number of points
-        for i in range(xgrid_size - 1):
+        for i in range(len(xgrid) - 1):
             kmin = max(0, i - po2)
             kmax = kmin + polynomial_degree
-            if kmax >= xgrid_size:
-                kmax = xgrid_size - 1
+            if kmax >= len(xgrid):
+                kmax = len(xgrid) - 1
                 kmin = kmax - polynomial_degree
             b = (kmin, kmax)
             list_of_blocks.append(b)
 
         # Generate the basis functions
         basis_functions = []
-        for i in range(xgrid_size):
+        for i in range(len(xgrid)):
             new_basis = BasisFunction(
-                xgrid, i, list_of_blocks, mode_log=log, mode_N=mode_N
+                xgrid.grid, i, list_of_blocks, mode_log=log, mode_N=mode_N
             )
             basis_functions.append(new_basis)
         self.basis = basis_functions
@@ -546,12 +571,11 @@ def from_dict(cls, operators_card, mode_N=True):
     def __eq__(self, other):
         """Checks equality"""
         checks = [
-            len(self.xgrid_raw) == len(other.xgrid_raw),
             self.log == other.log,
             self.polynomial_degree == other.polynomial_degree,
+            self.xgrid == other.xgrid,
         ]
-        # check elements after shape
-        return all(checks) and np.allclose(self.xgrid_raw, other.xgrid_raw)
+        return all(checks)
 
     def __iter__(self):
         # return iter(self.basis)
@@ -581,10 +605,10 @@ def get_interpolation(self, targetgrid):
 
         """
         # trivial?
-        if len(targetgrid) == len(self.xgrid_raw) and np.allclose(
-            targetgrid, self.xgrid_raw
+        if len(targetgrid) == len(self.xgrid) and np.allclose(
+            targetgrid, self.xgrid.raw
         ):
-            return np.eye(len(self.xgrid_raw))
+            return np.eye(len(self.xgrid))
         # compute map
         out = []
         for x in targetgrid:
@@ -607,7 +631,7 @@ def to_dict(self):
                 full grid configuration
         """
         ret = {
-            "xgrid": self.xgrid_raw,
+            "xgrid": self.xgrid.tolist(),
             "configs": {
                 "interpolation_polynomial_degree": self.polynomial_degree,
                 "interpolation_is_log": self.log,
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 5717e54b0..021344763 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -4,6 +4,7 @@
 
 import numpy as np
 
+from .. import interpolation
 from .. import version as vmod
 
 
@@ -71,7 +72,7 @@ class EKO:
     to PDFs and dumping to file.
     """
 
-    xgrid: np.ndarray
+    xgrid: interpolation.XGrid
     Q02: float
     _operators: Dict[float, Optional[Operator]]
     configs: Configs
@@ -108,7 +109,7 @@ def Q2grid(self):
     @classmethod
     def from_dict(cls, dictionary):
         return cls(
-            xgrid=np.array(dictionary["xgrid"]),
+            xgrid=interpolation.XGrid(dictionary["xgrid"]),
             Q02=dictionary["Q0"] ** 2,
             _operators={q2: None for q2 in dictionary["Q2grid"]},
             configs=Configs.from_dict(dictionary["configs"]),
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 1cd76e87a..7947eebea 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -69,16 +69,16 @@ def __init__(self, theory_card, operators_card):
 
         rot = operators_card.get("rotations", {})
         self.post_process = dict(
-            inputgrid=rot.get("inputgrid", bfd.xgrid_raw),
-            targetgrid=rot.get("targetgrid", bfd.xgrid_raw),
+            inputgrid=rot.get("inputgrid", bfd.xgrid.raw),
+            targetgrid=rot.get("targetgrid", bfd.xgrid.raw),
             inputbasis=rot.get("inputbasis"),
             targetbasis=rot.get("targetbasis"),
         )
 
         if "rotations" not in operators_card:
             operators_card["rotations"] = {}
-        operators_card["rotations"]["inputgrid"] = bfd.xgrid_raw
-        operators_card["rotations"]["targetgrid"] = bfd.xgrid_raw
+        operators_card["rotations"]["inputgrid"] = bfd.xgrid.raw
+        operators_card["rotations"]["targetgrid"] = bfd.xgrid.raw
 
         self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref), **operators_card))
 
@@ -94,20 +94,20 @@ def get_output(self):
         # add all operators
         self.out.rotations.inputpids = np.array(br.flavor_basis_pids)
         self.out.rotations.targetpids = np.array(br.flavor_basis_pids)
-        self.out.rotations.inputgrid = self.out.xgrid
-        self.out.rotations.targetgrid = self.out.xgrid
+        self.out.rotations.inputgrid = self.out.xgrid.grid
+        self.out.rotations.targetgrid = self.out.xgrid.grid
         for final_scale, op in self.op_grid.compute().items():
             self.out[float(final_scale)] = op
 
         # reshape xgrid
         inputgrid = (
             self.post_process["inputgrid"]
-            if self.post_process["inputgrid"] is not self.out.xgrid
+            if self.post_process["inputgrid"] is not self.out.xgrid.grid
             else None
         )
         targetgrid = (
             self.post_process["targetgrid"]
-            if self.post_process["targetgrid"] is not self.out.xgrid
+            if self.post_process["targetgrid"] is not self.out.xgrid.grid
             else None
         )
         if inputgrid is not None or targetgrid is not None:

From a2379713a56bd08c4ce1c17f7245ca96123924fd Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 12:58:56 +0200
Subject: [PATCH 023/148] Recover tests involving xgrid

---
 src/eko/interpolation.py        |  3 ++-
 tests/eko/test_ev_operator.py   |  2 +-
 tests/eko/test_interpolation.py |  4 ++--
 tests/eko/test_output.py        | 14 +++++++-------
 tests/eko/test_runner.py        |  9 +++++----
 5 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index 665a3bebe..f00909b70 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -438,7 +438,8 @@ def __len__(self) -> int:
 
     def __eq__(self, other) -> bool:
         """Checks equality"""
-        return all([len(self) == len(other), np.allclose(self.raw, other.raw)])
+        # check shape before comparing values
+        return len(self) == len(other) and np.allclose(self.raw, other.raw)
 
     @property
     def raw(self) -> np.ndarray:
diff --git a/tests/eko/test_ev_operator.py b/tests/eko/test_ev_operator.py
index 795712c6c..5fe5b3b68 100644
--- a/tests/eko/test_ev_operator.py
+++ b/tests/eko/test_ev_operator.py
@@ -337,7 +337,7 @@ def quad_ker_pegasus(
     mode0 = br.non_singlet_pids_map["ns+"]
     mode1 = 0
     method = ""
-    logxs = np.log(int_disp.xgrid_raw)
+    logxs = np.log(int_disp.xgrid.raw)
     a1 = 1
     a0 = 2
     nf = 3
diff --git a/tests/eko/test_interpolation.py b/tests/eko/test_interpolation.py
index 91e4905ad..3c377300f 100644
--- a/tests/eko/test_interpolation.py
+++ b/tests/eko/test_interpolation.py
@@ -24,7 +24,7 @@ def check_is_interpolator(interpolator):
         assert_almost_equal(one, 1.0)
 
     # polynoms need to be "orthogonal" at grid points
-    for j, (basis_j, xj) in enumerate(zip(interpolator, interpolator.xgrid_raw)):
+    for j, (basis_j, xj) in enumerate(zip(interpolator, interpolator.xgrid.raw)):
         one = basis_j(xj)
         assert_almost_equal(
             one,
@@ -110,7 +110,7 @@ def test_from_dict(self):
         }
         a = interpolation.InterpolatorDispatcher.from_dict(d)
         np.testing.assert_array_almost_equal(
-            a.xgrid, np.array([1e-7, 1e-4, 1e-1, 0.55, 1.0])
+            a.xgrid.grid, np.array([1e-7, 1e-4, 1e-1, 0.55, 1.0])
         )
         assert a.polynomial_degree == 1
         dd = {
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index f058551cb..cad0993ef 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -41,8 +41,8 @@ def test_io(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid, fake_output["xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid.raw, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid.raw, fake_output["xgrid"])
         # fake output files
         m_out = mock.mock_open(read_data="")
         with mock.patch("builtins.open", m_out) as mock_file:
@@ -56,14 +56,14 @@ def test_io(self, fake_output):
             fn = "test.yaml"
             o3 = legacy.load_yaml_from_file(fn)
             mock_file.assert_called_with(fn, encoding="utf-8")
-            np.testing.assert_almost_equal(o3.xgrid, fake_output["xgrid"])
+            np.testing.assert_almost_equal(o3.xgrid.raw, fake_output["xgrid"])
         # repeat for tar
         fn = "test.tar"
         with tempfile.TemporaryDirectory() as folder:
             fp = pathlib.Path(folder) / fn
             legacy.dump_tar(o1, fp)
             o4 = legacy.load_tar(fp)
-            np.testing.assert_almost_equal(o4.xgrid, fake_output["xgrid"])
+            np.testing.assert_almost_equal(o4.xgrid.raw, fake_output["xgrid"])
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
             legacy.dump_tar(o1, fn)
@@ -85,7 +85,7 @@ def test_rename_issue81(self, fake_output):
             shutil.move(fp1, fp2)
             # reload
             o4 = legacy.load_tar(fp2)
-            np.testing.assert_almost_equal(o4.xgrid, fake_output["xgrid"])
+            np.testing.assert_almost_equal(o4.xgrid.raw, fake_output["xgrid"])
 
     def test_io_bin(self, fake_output):
         # create object
@@ -98,8 +98,8 @@ def test_io_bin(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid, fake_output["xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid.raw, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid.raw, fake_output["xgrid"])
 
 
 class TestManipulate:
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 23ada38f6..c4e54c22f 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -4,6 +4,7 @@
 import numpy as np
 
 import eko
+import eko.interpolation
 from eko import compatibility
 
 theory_card = {
@@ -67,7 +68,7 @@ def test_targetgrid():
     oc["rotations"] = dict(targetgrid=tgrid)
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
-    check_shapes(o, tgrid, o.xgrid, tc, oc)
+    check_shapes(o, eko.interpolation.XGrid(np.array(tgrid)), o.xgrid, tc, oc)
 
 
 def test_targetbasis():
@@ -87,9 +88,9 @@ def check_shapes(o, txs, ixs, theory_card, operators_card):
     op_shape = (tpids, len(txs), ipids, len(ixs))
 
     # check output = input
-    np.testing.assert_allclose(o.xgrid, operators_card["xgrid"])
-    np.testing.assert_allclose(o.rotations.targetgrid, txs)
-    np.testing.assert_allclose(o.rotations.inputgrid, ixs)
+    np.testing.assert_allclose(o.xgrid.raw, operators_card["xgrid"])
+    np.testing.assert_allclose(o.rotations.targetgrid, txs.raw)
+    np.testing.assert_allclose(o.rotations.inputgrid, ixs.raw)
     for k in ["interpolation_polynomial_degree", "interpolation_is_log"]:
         assert getattr(o.configs, k) == operators_card["configs"][k]
     np.testing.assert_allclose(o.Q02, theory_card["Q0"] ** 2)

From 6b4b37d7690b2a22cf15ec7705e2b7762de18cea Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 18 Mar 2022 11:28:20 +0100
Subject: [PATCH 024/148] Remove bleeding edge syntax

---
 src/eko/interpolation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index f00909b70..afe56a458 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -449,7 +449,7 @@ def raw(self) -> np.ndarray:
     def size(self) -> int:
         return self.grid.size
 
-    def tolist(self) -> list[float]:
+    def tolist(self) -> list:
         return self.raw.tolist()
 
 

From cd557a19576ffadc386f74dcc3cc12ae5f81da81 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 25 Mar 2022 20:14:15 +0100
Subject: [PATCH 025/148] Add runcards classes

---
 src/eko/runcards.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 src/eko/runcards.py

diff --git a/src/eko/runcards.py b/src/eko/runcards.py
new file mode 100644
index 000000000..e93fecc89
--- /dev/null
+++ b/src/eko/runcards.py
@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+from dataclasses import dataclass
+
+
+@dataclass
+class TheoryCard:
+    pto: int
+
+
+@dataclass
+class OperatorCard:
+    xgrid: list[float]

From 148fcf0404b11fcd862404b3e3bf20158e3f1a30 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 13:01:23 +0200
Subject: [PATCH 026/148] Reshuffle files

---
 benchmarks/ekobox/benchmark_evol_pdf.py       | 21 +----
 benchmarks/ekobox/genpdf/benchmark_flavors.py | 88 -------------------
 benchmarks/ekobox/genpdf/benchmark_init.py    | 26 ------
 tests/ekobox/test_evol_pdf.py                 | 25 ++++++
 .../ekobox/test_gen_info.py                   |  2 -
 .../ekobox/test_gen_op.py                     |  2 -
 .../ekobox/test_gen_theory.py                 |  2 -
 tests/ekobox/test_genpdf.py                   | 30 +++++++
 tests/ekobox/test_genpdf_flavors.py           | 87 ++++++++++++++++++
 .../ekobox/test_utils.py                      |  3 +-
 10 files changed, 144 insertions(+), 142 deletions(-)
 rename benchmarks/ekobox/benchmark_gen_info.py => tests/ekobox/test_gen_info.py (95%)
 rename benchmarks/ekobox/benchmark_gen_op.py => tests/ekobox/test_gen_op.py (95%)
 rename benchmarks/ekobox/benchmark_gen_theory.py => tests/ekobox/test_gen_theory.py (95%)
 create mode 100644 tests/ekobox/test_genpdf.py
 create mode 100644 tests/ekobox/test_genpdf_flavors.py
 rename benchmarks/ekobox/benchmark_utils.py => tests/ekobox/test_utils.py (96%)

diff --git a/benchmarks/ekobox/benchmark_evol_pdf.py b/benchmarks/ekobox/benchmark_evol_pdf.py
index 464416c38..a3a4b16b7 100644
--- a/benchmarks/ekobox/benchmark_evol_pdf.py
+++ b/benchmarks/ekobox/benchmark_evol_pdf.py
@@ -1,11 +1,9 @@
 # -*- coding: utf-8 -*-
 import pathlib
 
-import lhapdf
 import numpy as np
 import pytest
 
-import eko.output.legacy
 from eko import basis_rotation as br
 from ekobox import evol_pdf as ev_p
 from ekobox import gen_op as g_o
@@ -13,6 +11,7 @@
 from ekobox.genpdf import load
 
 test_pdf = pathlib.Path(__file__).parent / "fakepdf"
+lhapdf = pytest.importorskip("lhapdf")
 
 
 @pytest.mark.isolated
@@ -100,21 +99,3 @@ def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
         for x in [1e-7, 0.01, 0.1, 0.2, 0.3]:
             for pid in [21, 1, 2]:
                 assert new_pdf_1.xfxQ2(pid, x, Q2) != new_pdf_2.xfxQ2(pid, x, Q2)
-
-
-@pytest.mark.isolated
-def benchmark_gen_and_dump_out(tmp_path):
-    op = g_o.gen_op_card([100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
-    theory = g_t.gen_theory_card(0, 1.0)
-
-    out = ev_p.gen_out(theory, op, path=tmp_path)
-
-    ops_id = f"o{op['hash'][:6]}_t{theory['hash'][:6]}"
-    outpath = f"{tmp_path}/{ops_id}.tar"
-    loaded_out = eko.output.legacy.load_tar(outpath)
-    assert list(out.xgrid) == list(loaded_out.xgrid)
-    for el, load_el in zip(out[100.0].operator, loaded_out[100.0].operator):
-        np.testing.assert_allclose(
-            out[100.0].operator,
-            loaded_out[100.0].operator,
-        )
diff --git a/benchmarks/ekobox/genpdf/benchmark_flavors.py b/benchmarks/ekobox/genpdf/benchmark_flavors.py
index 010dc7408..9dc6913f5 100644
--- a/benchmarks/ekobox/genpdf/benchmark_flavors.py
+++ b/benchmarks/ekobox/genpdf/benchmark_flavors.py
@@ -13,38 +13,6 @@
 lhapdf = pytest.importorskip("lhapdf")
 
 
-@pytest.mark.isolated
-def benchmark_is_evolution():
-    assert genpdf.flavors.is_evolution_labels(["V", "T3"])
-    assert not genpdf.flavors.is_evolution_labels(["21", "2"])
-
-
-@pytest.mark.isolated
-def benchmark_is_pids():
-    assert not genpdf.flavors.is_pid_labels(["V", "T3"])
-    assert not genpdf.flavors.is_pid_labels(["35", "9"])
-    assert not genpdf.flavors.is_pid_labels({})
-    assert genpdf.flavors.is_pid_labels([21, 2])
-
-
-@pytest.mark.isolated
-def benchmark_flavors_pid_to_flavor():
-    flavs = genpdf.flavors.pid_to_flavor([1, 2, 21, -3])
-    for f in flavs:
-        for g in flavs:
-            if not np.allclose(f, g):
-                assert f @ g == 0
-
-
-@pytest.mark.isolated
-def benchmark_flavors_evol_to_flavor():
-    flavs = genpdf.flavors.evol_to_flavor(["S", "g", "T3", "V8"])
-    for f in flavs:
-        for g in flavs:
-            if not np.allclose(f, g):
-                assert f @ g == 0
-
-
 @pytest.mark.isolated
 def benchmark_flavors_pids_ct14(tmp_path, cd):
     with cd(tmp_path):
@@ -101,59 +69,3 @@ def benchmark_flavors_evol_ct14(tmp_path, cd):
                     np.testing.assert_allclose(
                         pdf.xfxQ2(21, x, Q2), gonly.xfxQ2(21, x, Q2)
                     )
-
-
-@pytest.mark.isolated
-def benchmark_flavors_evol_raw():
-    blocks = [
-        {
-            "Q2grid": np.array([1, 2]),
-            "xgrid": np.array([0.1, 1.0]),
-            "pids": np.array([-1, 21, 1]),
-            "data": np.array([[0.1, 0.2, 0.1]] * 4),
-        }
-    ]
-    gonly = genpdf.flavors.project(blocks, genpdf.flavors.evol_to_flavor(["g"]))
-    assert len(gonly) == 1
-    np.testing.assert_allclose(
-        gonly[0]["data"],
-        np.array(
-            [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]] * 4
-        ),
-    )
-    Sonly = genpdf.flavors.project(blocks, genpdf.flavors.evol_to_flavor(["S"]))
-    assert len(Sonly) == 1
-    for i in [0, 1, 2, 3]:
-        # g and gamma are zero
-        np.testing.assert_allclose(Sonly[0]["data"][i][7], 0)
-        np.testing.assert_allclose(Sonly[0]["data"][i][0], 0)
-        # quark are all equal and equal to anti-quarks
-        for pid in [2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13]:
-            np.testing.assert_allclose(Sonly[0]["data"][i][pid], Sonly[0]["data"][i][1])
-
-
-@pytest.mark.isolated
-def benchmark_flavors_evol_nodata():
-    # try with a block without data
-    blocks = [
-        {
-            "Q2grid": np.array([1, 2]),
-            "xgrid": np.array([0.1, 1.0]),
-            "pids": np.array([-1, 21, 1]),
-            "data": np.array([]),
-        },
-        {
-            "Q2grid": np.array([1, 2]),
-            "xgrid": np.array([0.1, 1.0]),
-            "pids": np.array([-1, 21, 1]),
-            "data": np.array([[0.1, 0.2, 0.1]] * 4),
-        },
-    ]
-    gonly = genpdf.flavors.project(blocks, genpdf.flavors.evol_to_flavor(["g"]))
-    assert len(gonly) == 2
-    np.testing.assert_allclose(
-        gonly[1]["data"],
-        np.array(
-            [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]] * 4
-        ),
-    )
diff --git a/benchmarks/ekobox/genpdf/benchmark_init.py b/benchmarks/ekobox/genpdf/benchmark_init.py
index 3e23e8006..29a9b0b05 100644
--- a/benchmarks/ekobox/genpdf/benchmark_init.py
+++ b/benchmarks/ekobox/genpdf/benchmark_init.py
@@ -14,32 +14,6 @@
 lhapdf = pytest.importorskip("lhapdf")
 
 
-@pytest.mark.isolated
-def benchmark_genpdf_exceptions(tmp_path, cd):
-    # using a wrong label and then a wrong parent pdf
-    with cd(tmp_path):
-        with pytest.raises(TypeError):
-            genpdf.generate_pdf(
-                "test_genpdf_exceptions1",
-                ["f"],
-                {
-                    21: lambda x, Q2: 3.0 * x * (1.0 - x),
-                    2: lambda x, Q2: 4.0 * x * (1.0 - x),
-                },
-            )
-        with pytest.raises(ValueError):
-            genpdf.generate_pdf(
-                "test_genpdf_exceptions2",
-                ["g"],
-                10,
-            )
-        with pytest.raises(FileExistsError):
-            genpdf.install_pdf("foo")
-
-        with pytest.raises(TypeError):
-            genpdf.generate_pdf("debug", [21], info_update=(10, 15, 20))
-
-
 @pytest.mark.isolated
 def benchmark_genpdf_no_parent_and_install(tmp_path, cd):
     with cd(tmp_path):
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index e69de29bb..bf1f9b0ce 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+import eko.output.legacy
+from ekobox import evol_pdf as ev_p
+from ekobox import gen_op as g_o
+from ekobox import gen_theory as g_t
+
+
+def benchmark_gen_and_dump_out(tmp_path):
+    op = g_o.gen_op_card([100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
+    theory = g_t.gen_theory_card(0, 1.0)
+
+    out = ev_p.gen_out(theory, op, path=tmp_path)
+
+    ops_id = f"o{op['hash'][:6]}_t{theory['hash'][:6]}"
+    outpath = f"{tmp_path}/{ops_id}.tar"
+    loaded_out = eko.output.legacy.load_tar(outpath)
+    assert list(out.xgrid) == list(loaded_out.xgrid)
+    for el, load_el in zip(out[100.0].operator, loaded_out[100.0].operator):
+        np.testing.assert_allclose(
+            out[100.0].operator,
+            loaded_out[100.0].operator,
+        )
diff --git a/benchmarks/ekobox/benchmark_gen_info.py b/tests/ekobox/test_gen_info.py
similarity index 95%
rename from benchmarks/ekobox/benchmark_gen_info.py
rename to tests/ekobox/test_gen_info.py
index 7eb10d3d3..554fb7872 100644
--- a/benchmarks/ekobox/benchmark_gen_info.py
+++ b/tests/ekobox/test_gen_info.py
@@ -2,14 +2,12 @@
 import math
 
 import numpy as np
-import pytest
 
 from ekobox import gen_info as g_i
 from ekobox import gen_op as g_o
 from ekobox import gen_theory as g_t
 
 
-@pytest.mark.isolated
 def benchmark_create_info_file():
     op = g_o.gen_op_card([10, 100])
     theory = g_t.gen_theory_card(1, 10.0, update={"alphas": 0.2})
diff --git a/benchmarks/ekobox/benchmark_gen_op.py b/tests/ekobox/test_gen_op.py
similarity index 95%
rename from benchmarks/ekobox/benchmark_gen_op.py
rename to tests/ekobox/test_gen_op.py
index bd3b613ed..05fbbc389 100644
--- a/benchmarks/ekobox/benchmark_gen_op.py
+++ b/tests/ekobox/test_gen_op.py
@@ -4,7 +4,6 @@
 from ekobox import gen_op as g_o
 
 
-@pytest.mark.isolated
 def benchmark_gen_op_card():
     op = g_o.gen_op_card([10, 100])
     assert op["Q2grid"] == [10, 100]
@@ -21,7 +20,6 @@ def benchmark_gen_op_card():
     assert op["configs"]["interpolation_is_log"] is False
 
 
-@pytest.mark.isolated
 def benchmark_export_load_op_card(tmp_path, cd):
     with cd(tmp_path):
         op = g_o.gen_op_card([100], name="debug_op")
diff --git a/benchmarks/ekobox/benchmark_gen_theory.py b/tests/ekobox/test_gen_theory.py
similarity index 95%
rename from benchmarks/ekobox/benchmark_gen_theory.py
rename to tests/ekobox/test_gen_theory.py
index 07320fa5e..c353403eb 100644
--- a/benchmarks/ekobox/benchmark_gen_theory.py
+++ b/tests/ekobox/test_gen_theory.py
@@ -4,7 +4,6 @@
 from ekobox import gen_theory as g_t
 
 
-@pytest.mark.isolated
 def benchmark_gen_theory_card():
     theory = g_t.gen_theory_card(0, 1.0)
     assert theory["PTO"] == 0
@@ -19,7 +18,6 @@ def benchmark_gen_theory_card():
     assert theory["mb"] == 132.3
 
 
-@pytest.mark.isolated
 def benchmark_export_load_theory_card(tmp_path, cd):
     with cd(tmp_path):
         theory = g_t.gen_theory_card(2, 12.3, name="debug_theory")
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
new file mode 100644
index 000000000..f4881e9fc
--- /dev/null
+++ b/tests/ekobox/test_genpdf.py
@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+
+import pytest
+
+from ekobox import genpdf
+
+
+def benchmark_genpdf_exceptions(tmp_path, cd):
+    # using a wrong label and then a wrong parent pdf
+    with cd(tmp_path):
+        with pytest.raises(TypeError):
+            genpdf.generate_pdf(
+                "test_genpdf_exceptions1",
+                ["f"],
+                {
+                    21: lambda x, Q2: 3.0 * x * (1.0 - x),
+                    2: lambda x, Q2: 4.0 * x * (1.0 - x),
+                },
+            )
+        with pytest.raises(ValueError):
+            genpdf.generate_pdf(
+                "test_genpdf_exceptions2",
+                ["g"],
+                10,
+            )
+        with pytest.raises(FileExistsError):
+            genpdf.install_pdf("foo")
+
+        with pytest.raises(TypeError):
+            genpdf.generate_pdf("debug", [21], info_update=(10, 15, 20))
diff --git a/tests/ekobox/test_genpdf_flavors.py b/tests/ekobox/test_genpdf_flavors.py
new file mode 100644
index 000000000..adddce9fa
--- /dev/null
+++ b/tests/ekobox/test_genpdf_flavors.py
@@ -0,0 +1,87 @@
+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+from ekobox import genpdf
+
+
+def benchmark_is_evolution():
+    assert genpdf.flavors.is_evolution_labels(["V", "T3"])
+    assert not genpdf.flavors.is_evolution_labels(["21", "2"])
+
+
+def benchmark_is_pids():
+    assert not genpdf.flavors.is_pid_labels(["V", "T3"])
+    assert not genpdf.flavors.is_pid_labels(["35", "9"])
+    assert not genpdf.flavors.is_pid_labels({})
+    assert genpdf.flavors.is_pid_labels([21, 2])
+
+
+def benchmark_flavors_pid_to_flavor():
+    flavs = genpdf.flavors.pid_to_flavor([1, 2, 21, -3])
+    for f in flavs:
+        for g in flavs:
+            if not np.allclose(f, g):
+                assert f @ g == 0
+
+
+def benchmark_flavors_evol_to_flavor():
+    flavs = genpdf.flavors.evol_to_flavor(["S", "g", "T3", "V8"])
+    for f in flavs:
+        for g in flavs:
+            if not np.allclose(f, g):
+                assert f @ g == 0
+
+
+def benchmark_flavors_evol_raw():
+    blocks = [
+        {
+            "Q2grid": np.array([1, 2]),
+            "xgrid": np.array([0.1, 1.0]),
+            "pids": np.array([-1, 21, 1]),
+            "data": np.array([[0.1, 0.2, 0.1]] * 4),
+        }
+    ]
+    gonly = genpdf.flavors.project(blocks, genpdf.flavors.evol_to_flavor(["g"]))
+    assert len(gonly) == 1
+    np.testing.assert_allclose(
+        gonly[0]["data"],
+        np.array(
+            [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]] * 4
+        ),
+    )
+    Sonly = genpdf.flavors.project(blocks, genpdf.flavors.evol_to_flavor(["S"]))
+    assert len(Sonly) == 1
+    for i in [0, 1, 2, 3]:
+        # g and gamma are zero
+        np.testing.assert_allclose(Sonly[0]["data"][i][7], 0)
+        np.testing.assert_allclose(Sonly[0]["data"][i][0], 0)
+        # quark are all equal and equal to anti-quarks
+        for pid in [2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13]:
+            np.testing.assert_allclose(Sonly[0]["data"][i][pid], Sonly[0]["data"][i][1])
+
+
+def benchmark_flavors_evol_nodata():
+    # try with a block without data
+    blocks = [
+        {
+            "Q2grid": np.array([1, 2]),
+            "xgrid": np.array([0.1, 1.0]),
+            "pids": np.array([-1, 21, 1]),
+            "data": np.array([]),
+        },
+        {
+            "Q2grid": np.array([1, 2]),
+            "xgrid": np.array([0.1, 1.0]),
+            "pids": np.array([-1, 21, 1]),
+            "data": np.array([[0.1, 0.2, 0.1]] * 4),
+        },
+    ]
+    gonly = genpdf.flavors.project(blocks, genpdf.flavors.evol_to_flavor(["g"]))
+    assert len(gonly) == 2
+    np.testing.assert_allclose(
+        gonly[1]["data"],
+        np.array(
+            [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]] * 4
+        ),
+    )
diff --git a/benchmarks/ekobox/benchmark_utils.py b/tests/ekobox/test_utils.py
similarity index 96%
rename from benchmarks/ekobox/benchmark_utils.py
rename to tests/ekobox/test_utils.py
index 37a5661f0..69fd86d05 100644
--- a/benchmarks/ekobox/benchmark_utils.py
+++ b/tests/ekobox/test_utils.py
@@ -8,8 +8,7 @@
 from ekobox import utils
 
 
-@pytest.mark.isolated
-def benchmark_ekos_product():
+def test_ekos_product():
     # Generating two ekos
     op1 = g_o.gen_op_card(
         [60.0, 80.0, 100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}

From 442f3d796fdbf3749890c736a14f64c2af349bd3 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 21 Mar 2022 11:54:07 +0100
Subject: [PATCH 027/148] Fix tests to run

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 732eba80d..f6a03d93d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -130,7 +130,8 @@ markers = ["isolated: marks benchmarks as isolated"]
 # extensions not to check
 extension-pkg-whitelist = ["numpy", "numba", "lhapdf", "pegasus"]
 ignore-paths = ["benchmarks/", "doc/", "tests/"]
-jobs = 1                                                          # has to be 1 as pylint is NOT threadsafe
+# has to be 1 as pylint is NOT threadsafe
+jobs = 1
 [tool.pylint.messages_control]
 disable = ["invalid-name", "fixme"]
 [tool.pylint.reports]

From 039a055086cc5e1776c74a0072c493bf6febf054 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 21 Mar 2022 11:54:07 +0100
Subject: [PATCH 028/148] Fix tests to run

---
 pyproject.toml                      |  2 +-
 tests/conftest.py                   | 19 +++++++++++++++++++
 tests/ekobox/test_evol_pdf.py       | 10 +++++-----
 tests/ekobox/test_gen_info.py       |  2 +-
 tests/ekobox/test_gen_op.py         |  4 ++--
 tests/ekobox/test_gen_theory.py     |  4 ++--
 tests/ekobox/test_genpdf.py         |  2 +-
 tests/ekobox/test_genpdf_flavors.py | 12 ++++++------
 8 files changed, 37 insertions(+), 18 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f6a03d93d..4811a1c66 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -130,7 +130,7 @@ markers = ["isolated: marks benchmarks as isolated"]
 # extensions not to check
 extension-pkg-whitelist = ["numpy", "numba", "lhapdf", "pegasus"]
 ignore-paths = ["benchmarks/", "doc/", "tests/"]
-# has to be 1 as pylint is NOT threadsafe
+# jobs has to be 1 as pylint is NOT threadsafe
 jobs = 1
 [tool.pylint.messages_control]
 disable = ["invalid-name", "fixme"]
diff --git a/tests/conftest.py b/tests/conftest.py
index 35a8a9213..5d7b8b435 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,8 +1,27 @@
 # -*- coding: utf-8 -*-
+import os
+from contextlib import contextmanager
+
 import numpy as np
 import pytest
 
 
+@pytest.fixture
+def cd():
+    # thanks https://stackoverflow.com/questions/431684/
+    # how-do-i-change-the-working-directory-in-python/24176022#24176022
+    @contextmanager
+    def wrapped(newdir):
+        prevdir = os.getcwd()
+        os.chdir(os.path.expanduser(newdir))
+        try:
+            yield
+        finally:
+            os.chdir(prevdir)
+
+    return wrapped
+
+
 class FakePDF:
     def hasFlavor(self, pid):
         return pid == 1
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index bf1f9b0ce..dabb8616a 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -8,7 +8,7 @@
 from ekobox import gen_theory as g_t
 
 
-def benchmark_gen_and_dump_out(tmp_path):
+def test_gen_and_dump_out(tmp_path):
     op = g_o.gen_op_card([100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
     theory = g_t.gen_theory_card(0, 1.0)
 
@@ -17,9 +17,9 @@ def benchmark_gen_and_dump_out(tmp_path):
     ops_id = f"o{op['hash'][:6]}_t{theory['hash'][:6]}"
     outpath = f"{tmp_path}/{ops_id}.tar"
     loaded_out = eko.output.legacy.load_tar(outpath)
-    assert list(out.xgrid) == list(loaded_out.xgrid)
-    for el, load_el in zip(out[100.0].operator, loaded_out[100.0].operator):
+    assert out.xgrid.tolist() == loaded_out.xgrid.tolist()
+    for el, loaded_el in zip(out[100.0].operator, loaded_out[100.0].operator):
         np.testing.assert_allclose(
-            out[100.0].operator,
-            loaded_out[100.0].operator,
+            el,
+            loaded_el,
         )
diff --git a/tests/ekobox/test_gen_info.py b/tests/ekobox/test_gen_info.py
index 554fb7872..f82e76c76 100644
--- a/tests/ekobox/test_gen_info.py
+++ b/tests/ekobox/test_gen_info.py
@@ -8,7 +8,7 @@
 from ekobox import gen_theory as g_t
 
 
-def benchmark_create_info_file():
+def test_create_info_file():
     op = g_o.gen_op_card([10, 100])
     theory = g_t.gen_theory_card(1, 10.0, update={"alphas": 0.2})
     info = g_i.create_info_file(
diff --git a/tests/ekobox/test_gen_op.py b/tests/ekobox/test_gen_op.py
index 05fbbc389..bc0821d26 100644
--- a/tests/ekobox/test_gen_op.py
+++ b/tests/ekobox/test_gen_op.py
@@ -4,7 +4,7 @@
 from ekobox import gen_op as g_o
 
 
-def benchmark_gen_op_card():
+def test_gen_op_card():
     op = g_o.gen_op_card([10, 100])
     assert op["Q2grid"] == [10, 100]
     assert op["configs"]["interpolation_polynomial_degree"] == 4
@@ -20,7 +20,7 @@ def benchmark_gen_op_card():
     assert op["configs"]["interpolation_is_log"] is False
 
 
-def benchmark_export_load_op_card(tmp_path, cd):
+def test_export_load_op_card(tmp_path, cd):
     with cd(tmp_path):
         op = g_o.gen_op_card([100], name="debug_op")
         g_o.export_op_card("debug_op_two", op)
diff --git a/tests/ekobox/test_gen_theory.py b/tests/ekobox/test_gen_theory.py
index c353403eb..468b3c401 100644
--- a/tests/ekobox/test_gen_theory.py
+++ b/tests/ekobox/test_gen_theory.py
@@ -4,7 +4,7 @@
 from ekobox import gen_theory as g_t
 
 
-def benchmark_gen_theory_card():
+def test_gen_theory_card():
     theory = g_t.gen_theory_card(0, 1.0)
     assert theory["PTO"] == 0
     assert theory["Q0"] == 1.0
@@ -18,7 +18,7 @@ def benchmark_gen_theory_card():
     assert theory["mb"] == 132.3
 
 
-def benchmark_export_load_theory_card(tmp_path, cd):
+def test_export_load_theory_card(tmp_path, cd):
     with cd(tmp_path):
         theory = g_t.gen_theory_card(2, 12.3, name="debug_theory")
         g_t.export_theory_card("debug_theory_two", theory)
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index f4881e9fc..55837a928 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -5,7 +5,7 @@
 from ekobox import genpdf
 
 
-def benchmark_genpdf_exceptions(tmp_path, cd):
+def test_genpdf_exceptions(tmp_path, cd):
     # using a wrong label and then a wrong parent pdf
     with cd(tmp_path):
         with pytest.raises(TypeError):
diff --git a/tests/ekobox/test_genpdf_flavors.py b/tests/ekobox/test_genpdf_flavors.py
index adddce9fa..f6a767019 100644
--- a/tests/ekobox/test_genpdf_flavors.py
+++ b/tests/ekobox/test_genpdf_flavors.py
@@ -5,19 +5,19 @@
 from ekobox import genpdf
 
 
-def benchmark_is_evolution():
+def test_is_evolution():
     assert genpdf.flavors.is_evolution_labels(["V", "T3"])
     assert not genpdf.flavors.is_evolution_labels(["21", "2"])
 
 
-def benchmark_is_pids():
+def test_is_pids():
     assert not genpdf.flavors.is_pid_labels(["V", "T3"])
     assert not genpdf.flavors.is_pid_labels(["35", "9"])
     assert not genpdf.flavors.is_pid_labels({})
     assert genpdf.flavors.is_pid_labels([21, 2])
 
 
-def benchmark_flavors_pid_to_flavor():
+def test_flavors_pid_to_flavor():
     flavs = genpdf.flavors.pid_to_flavor([1, 2, 21, -3])
     for f in flavs:
         for g in flavs:
@@ -25,7 +25,7 @@ def benchmark_flavors_pid_to_flavor():
                 assert f @ g == 0
 
 
-def benchmark_flavors_evol_to_flavor():
+def test_flavors_evol_to_flavor():
     flavs = genpdf.flavors.evol_to_flavor(["S", "g", "T3", "V8"])
     for f in flavs:
         for g in flavs:
@@ -33,7 +33,7 @@ def benchmark_flavors_evol_to_flavor():
                 assert f @ g == 0
 
 
-def benchmark_flavors_evol_raw():
+def test_flavors_evol_raw():
     blocks = [
         {
             "Q2grid": np.array([1, 2]),
@@ -61,7 +61,7 @@ def benchmark_flavors_evol_raw():
             np.testing.assert_allclose(Sonly[0]["data"][i][pid], Sonly[0]["data"][i][1])
 
 
-def benchmark_flavors_evol_nodata():
+def test_flavors_evol_nodata():
     # try with a block without data
     blocks = [
         {

From 579dffce786f2a164b877fab39347fb0dc537ae9 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 21 Mar 2022 12:16:07 +0100
Subject: [PATCH 029/148] Remove unreachable code, improve tests

---
 src/ekobox/genpdf/flavors.py    |  2 --
 tests/ekobox/test_genpdf_cli.py | 21 +++++++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)
 create mode 100644 tests/ekobox/test_genpdf_cli.py

diff --git a/src/ekobox/genpdf/flavors.py b/src/ekobox/genpdf/flavors.py
index 116443419..b892deb99 100644
--- a/src/ekobox/genpdf/flavors.py
+++ b/src/ekobox/genpdf/flavors.py
@@ -129,8 +129,6 @@ def is_pid_labels(labels):
     except (ValueError, TypeError):
         return False
     for label in labels:
-        if not isinstance(label, np.int_):
-            return False
         if label not in br.flavor_basis_pids:
             return False
     return True
diff --git a/tests/ekobox/test_genpdf_cli.py b/tests/ekobox/test_genpdf_cli.py
new file mode 100644
index 000000000..25850c1d4
--- /dev/null
+++ b/tests/ekobox/test_genpdf_cli.py
@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+
+from click.testing import CliRunner
+
+from ekobox.genpdf.cli import cli
+
+
+def test_genpdf_CLI_messages():
+    runner = CliRunner()
+    result = runner.invoke(cli, ["generate"])
+    assert "Error: Missing argument 'NAME'." in result.output
+    result = runner.invoke(cli, ["install"])
+    assert "Error: Missing argument 'NAME'." in result.output
+    result = runner.invoke(cli, ["generate", "TestEmptyLabels"])
+    assert result.exception and "Labels must contain at least one element" in str(
+        result.exception
+    )
+    result = runner.invoke(cli, ["generate", "--help"])
+    assert "-p, --parent-pdf-set TEXT" in result.output
+    assert "-m, --members" in result.output
+    assert "-i, --install" in result.output

From eea43a2679dbc52f7bb7de499c52cb5f3b6ac201 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 21 Mar 2022 12:31:14 +0100
Subject: [PATCH 030/148] Add ekobox.mock test

---
 tests/ekobox/test_mock.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 tests/ekobox/test_mock.py

diff --git a/tests/ekobox/test_mock.py b/tests/ekobox/test_mock.py
new file mode 100644
index 000000000..0d9311086
--- /dev/null
+++ b/tests/ekobox/test_mock.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+import numpy as np
+
+from ekobox import mock
+
+
+def test_eko_identity():
+    for s in ((1, 2, 2, 2, 2), (1, 3, 3, 3, 3)):
+        i = mock.eko_identity(s)
+        assert s == i.shape
+        # is identity?
+        f = np.random.rand(*s[-2:])
+        g = np.einsum("qkbja,ja->qkb", i, f)
+        np.testing.assert_allclose(g[0], f)

From 406b2b4665898f0f6c67c50b60e893776de23330 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 21 Mar 2022 14:30:43 +0100
Subject: [PATCH 031/148] Start mocking lhapdf, revert flavors

---
 src/ekobox/genpdf/flavors.py     |  3 +++
 src/ekobox/genpdf/load.py        |  5 +----
 tests/conftest.py                | 17 +++++++++++++++++
 tests/ekobox/test_genpdf_load.py | 22 ++++++++++++++++++++++
 4 files changed, 43 insertions(+), 4 deletions(-)
 create mode 100644 tests/ekobox/test_genpdf_load.py

diff --git a/src/ekobox/genpdf/flavors.py b/src/ekobox/genpdf/flavors.py
index b892deb99..121d28c15 100644
--- a/src/ekobox/genpdf/flavors.py
+++ b/src/ekobox/genpdf/flavors.py
@@ -129,6 +129,9 @@ def is_pid_labels(labels):
     except (ValueError, TypeError):
         return False
     for label in labels:
+        # label might still be a list (for general projection)
+        if not isinstance(label, np.int_):
+            return False
         if label not in br.flavor_basis_pids:
             return False
     return True
diff --git a/src/ekobox/genpdf/load.py b/src/ekobox/genpdf/load.py
index 4c1112b2d..f52f8b0e3 100644
--- a/src/ekobox/genpdf/load.py
+++ b/src/ekobox/genpdf/load.py
@@ -55,13 +55,10 @@ def load_blocks_from_file(pdfset_name, member):
     """
     import lhapdf  # pylint: disable=import-error, import-outside-toplevel
 
-    pdf = lhapdf.mkPDF(pdfset_name, member)
     src = pathlib.Path(lhapdf.paths()[0]) / pdfset_name
     # read actual file
     cnt = []
-    with open(
-        src / f"{pdfset_name}_{pdf.memberID:04d}.dat", "r", encoding="utf-8"
-    ) as o:
+    with open(src / f"{pdfset_name}_{member:04d}.dat", "r", encoding="utf-8") as o:
         cnt = o.readlines()
     # file head
     head = cnt[0]
diff --git a/tests/conftest.py b/tests/conftest.py
index 5d7b8b435..0c91cb023 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 import os
+import pathlib
+import sys
 from contextlib import contextmanager
 
 import numpy as np
@@ -91,3 +93,18 @@ def fake_factory():
 @pytest.fixture
 def fake_output():
     return FakeOutput().fake_output()
+
+
+# Fake LHAPDF
+# Thanks https://stackoverflow.com/questions/43162722/mocking-a-module-import-in-pytest
+
+test_pdf = pathlib.Path(__file__).parents[1] / "benchmarks" / "ekobox" / "fakepdf"
+
+
+def lhapdf_paths():
+    return [test_pdf]
+
+
+module = type(sys)("lhapdf")
+module.paths = lhapdf_paths
+sys.modules["lhapdf"] = module
diff --git a/tests/ekobox/test_genpdf_load.py b/tests/ekobox/test_genpdf_load.py
new file mode 100644
index 000000000..d0e3e3555
--- /dev/null
+++ b/tests/ekobox/test_genpdf_load.py
@@ -0,0 +1,22 @@
+# -*- coding: utf-8 -*-
+import numpy as np
+
+from ekobox import genpdf
+
+
+def test_load_info():
+    info = genpdf.load.load_info_from_file("myCT14llo_NF3")
+    assert "SetDesc" in info
+    assert "fake" in info["SetDesc"]
+    assert sorted(info["Flavors"]) == sorted([-3, -2, -1, 21, 1, 2, 3])
+
+
+def test_load_data_ct14():
+    blocks = genpdf.load.load_blocks_from_file("myCT14llo_NF3", 0)[1]
+    assert len(blocks) == 1
+    b0 = blocks[0]
+    assert isinstance(b0, dict)
+    assert sorted(b0.keys()) == sorted(["pids", "xgrid", "Q2grid", "data"])
+    assert sorted(b0["pids"]) == sorted([-3, -2, -1, 21, 1, 2, 3])
+    assert len(b0["data"].T) == 7
+    np.testing.assert_allclose(b0["xgrid"][0], 1e-9)

From 9903dca14a261e5f3d306b46da0f24e5c3d472ca Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 22 Mar 2022 16:24:02 +0100
Subject: [PATCH 032/148] Add genpdf.export tests

---
 src/ekobox/genpdf/export.py         |  4 +-
 tests/ekobox/test_genpdf_export.py  | 92 +++++++++++++++++++++++++++++
 tests/ekobox/test_genpdf_flavors.py |  2 +
 3 files changed, 95 insertions(+), 3 deletions(-)
 create mode 100644 tests/ekobox/test_genpdf_export.py

diff --git a/src/ekobox/genpdf/export.py b/src/ekobox/genpdf/export.py
index 3a7a02de3..8f906513f 100644
--- a/src/ekobox/genpdf/export.py
+++ b/src/ekobox/genpdf/export.py
@@ -126,9 +126,7 @@ def dump_set(name, info, member_blocks, pdf_type_list=None):
     """
     dump_info(name, info)
     for mem, blocks in enumerate(member_blocks):
-        if not isinstance(pdf_type_list, list):
-            dump_blocks(name, mem, blocks)
-        elif len(pdf_type_list) == 0:
+        if not isinstance(pdf_type_list, list) or len(pdf_type_list) == 0:
             dump_blocks(name, mem, blocks)
         else:
             dump_blocks(name, mem, blocks, pdf_type=pdf_type_list[mem])
diff --git a/tests/ekobox/test_genpdf_export.py b/tests/ekobox/test_genpdf_export.py
new file mode 100644
index 000000000..578308136
--- /dev/null
+++ b/tests/ekobox/test_genpdf_export.py
@@ -0,0 +1,92 @@
+# -*- coding: utf-8 -*-
+import numpy as np
+import yaml
+
+from ekobox import genpdf
+
+
+def test_list_to_str():
+    a = genpdf.export.list_to_str([1, 2])
+    assert isinstance(a, str)
+    assert "1." in a
+    b = genpdf.export.list_to_str([1.0, 2.0])
+    assert isinstance(b, str)
+    assert "1." in a
+
+
+def test_array_to_str():
+    s = (2, 2)
+    a = genpdf.export.array_to_str(np.arange(4).reshape(s))
+    assert isinstance(a, str)
+    assert "1." in a
+    b = np.array([e.split() for e in a.splitlines()])
+    assert b.shape == s
+
+
+def test_dump_info(tmp_path):
+    n = "test"
+    p = tmp_path / n
+    f = p / f"{n}.info"
+    i = {"a": "b", "c": 2}
+    genpdf.export.dump_info(p, i)
+    assert p.exists()
+    assert f.exists()
+    # the files might not be perfect yaml, but should be yaml compatible
+    with open(f, "r", encoding="utf-8") as o:
+        ii = yaml.safe_load(o)
+    for k, v in i.items():
+        assert k in ii
+        assert ii[k] == v
+
+
+def fake_blocks(n_blocks, n_x, n_q2, n_pids):
+    bs = []
+    for _ in range(n_blocks):
+        bs.append(
+            {
+                "xgrid": np.linspace(0.0, 1.0, n_x),
+                "Q2grid": np.geomspace(1.0, 1e3, n_q2),
+                "pids": np.arange(n_pids),
+                "data": np.random.rand(n_x * n_q2, n_pids),
+            }
+        )
+    return bs
+
+
+def test_dump_blocks(tmp_path):
+    n = "test"
+    p = tmp_path / n
+    nb = 2
+    for m in range(3):
+        f = p / f"{n}_{m:04d}.dat"
+        is_my_type = m > 1
+        pdf_type = "Bla: blub" if is_my_type else None
+        genpdf.export.dump_blocks(p, m, fake_blocks(nb, 2, 2, 2), pdf_type=pdf_type)
+        assert p.exists()
+        assert f.exists()
+        cnt = f.read_text()
+        if is_my_type:
+            assert "Bla: blub" in cnt
+        else:
+            assert ("central" in cnt) == (m == 0)
+        assert "Format" in cnt
+        assert cnt.count("---") == nb + 1
+
+
+def test_dump_set(tmp_path):
+    n = "test"
+    p = tmp_path / n
+    i = {"a": "b", "c": 2}
+    nmem = 2
+    for pdf_type_list in (None, ["Bla: Blub"] * nmem):
+        genpdf.export.dump_set(
+            p, i, [fake_blocks(2, 2, 2, 2) for _ in range(nmem)], pdf_type_list
+        )
+        assert p.exists()
+        f = p / f"{n}.info"
+        assert f.exists()
+        for m in range(nmem):
+            f = p / f"{n}_{m:04d}.dat"
+            assert f.exists()
+            if pdf_type_list is not None:
+                assert "Bla: Blub" in f.read_text()
diff --git a/tests/ekobox/test_genpdf_flavors.py b/tests/ekobox/test_genpdf_flavors.py
index f6a767019..19013e2ce 100644
--- a/tests/ekobox/test_genpdf_flavors.py
+++ b/tests/ekobox/test_genpdf_flavors.py
@@ -7,6 +7,7 @@
 
 def test_is_evolution():
     assert genpdf.flavors.is_evolution_labels(["V", "T3"])
+    assert not genpdf.flavors.is_evolution_labels([[1, 2]])
     assert not genpdf.flavors.is_evolution_labels(["21", "2"])
 
 
@@ -14,6 +15,7 @@ def test_is_pids():
     assert not genpdf.flavors.is_pid_labels(["V", "T3"])
     assert not genpdf.flavors.is_pid_labels(["35", "9"])
     assert not genpdf.flavors.is_pid_labels({})
+    assert not genpdf.flavors.is_pid_labels([[1, 2]])
     assert genpdf.flavors.is_pid_labels([21, 2])
 
 

From 3b6717fed0817af7389c679630431fd453189480 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 22 Mar 2022 16:57:09 +0100
Subject: [PATCH 033/148] Improve lhapdf fixtures

---
 tests/conftest.py                | 28 ++++++++++++++++++++--------
 tests/ekobox/test_genpdf.py      | 13 ++++++++++++-
 tests/ekobox/test_genpdf_load.py |  8 ++++----
 3 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 0c91cb023..cee5c8df4 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 import os
 import pathlib
+import shutil
 import sys
 from contextlib import contextmanager
 
@@ -95,16 +96,27 @@ def fake_output():
     return FakeOutput().fake_output()
 
 
-# Fake LHAPDF
-# Thanks https://stackoverflow.com/questions/43162722/mocking-a-module-import-in-pytest
+@pytest.fixture
+def fake_lhapdf(tmp_path):
+    def lhapdf_paths():
+        return [tmp_path]
+
+    # Thanks https://stackoverflow.com/questions/43162722/mocking-a-module-import-in-pytest
+    module = type(sys)("lhapdf")
+    module.paths = lhapdf_paths
+    sys.modules["lhapdf"] = module
 
-test_pdf = pathlib.Path(__file__).parents[1] / "benchmarks" / "ekobox" / "fakepdf"
+    yield tmp_path
 
 
-def lhapdf_paths():
-    return [test_pdf]
+fakepdf = pathlib.Path(__file__).parents[1] / "benchmarks" / "ekobox" / "fakepdf"
 
 
-module = type(sys)("lhapdf")
-module.paths = lhapdf_paths
-sys.modules["lhapdf"] = module
+@pytest.fixture
+def fake_ct14(fake_lhapdf):
+    n = "myCT14llo_NF3"
+    src = fakepdf / n
+    dst = fake_lhapdf / n
+    shutil.copytree(src, dst)
+    yield n
+    shutil.rmtree(dst)
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 55837a928..5167595f3 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-
+import numpy as np
 import pytest
 
 from ekobox import genpdf
@@ -28,3 +28,14 @@ def test_genpdf_exceptions(tmp_path, cd):
 
         with pytest.raises(TypeError):
             genpdf.generate_pdf("debug", [21], info_update=(10, 15, 20))
+
+
+def test_generate_block():
+    xg = np.linspace(0.0, 1.0, 5)
+    q2s = np.geomspace(1.0, 1e3, 5)
+    pids = np.arange(3)
+    b = genpdf.generate_block(lambda pid, x, q2: pid * x * q2, xg, q2s, pids)
+    assert isinstance(b, dict)
+    assert sorted(b.keys()) == sorted(["data", "Q2grid", "xgrid", "pids"])
+    assert isinstance(b["data"], np.ndarray)
+    assert b["data"].shape == (len(xg) * len(q2s), len(pids))
diff --git a/tests/ekobox/test_genpdf_load.py b/tests/ekobox/test_genpdf_load.py
index d0e3e3555..00e823001 100644
--- a/tests/ekobox/test_genpdf_load.py
+++ b/tests/ekobox/test_genpdf_load.py
@@ -4,15 +4,15 @@
 from ekobox import genpdf
 
 
-def test_load_info():
-    info = genpdf.load.load_info_from_file("myCT14llo_NF3")
+def test_load_info(fake_ct14):
+    info = genpdf.load.load_info_from_file(fake_ct14)
     assert "SetDesc" in info
     assert "fake" in info["SetDesc"]
     assert sorted(info["Flavors"]) == sorted([-3, -2, -1, 21, 1, 2, 3])
 
 
-def test_load_data_ct14():
-    blocks = genpdf.load.load_blocks_from_file("myCT14llo_NF3", 0)[1]
+def test_load_data_ct14(fake_ct14):
+    blocks = genpdf.load.load_blocks_from_file(fake_ct14, 0)[1]
     assert len(blocks) == 1
     b0 = blocks[0]
     assert isinstance(b0, dict)

From 9cb64072481de64dba5abf0e1638ef2e18c56875 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 22 Mar 2022 17:21:28 +0100
Subject: [PATCH 034/148] Improve generate_pdf

---
 src/ekobox/genpdf/__init__.py | 52 +++++++++++++++++++++--------------
 tests/conftest.py             |  3 +-
 tests/ekobox/test_genpdf.py   | 26 ++++++++++++++++--
 3 files changed, 56 insertions(+), 25 deletions(-)

diff --git a/src/ekobox/genpdf/__init__.py b/src/ekobox/genpdf/__init__.py
index 496ef9d0b..c1cf515fb 100644
--- a/src/ekobox/genpdf/__init__.py
+++ b/src/ekobox/genpdf/__init__.py
@@ -11,20 +11,37 @@
 from . import export, flavors, load
 
 
-def take_data(parent_pdf_set=None, members=False):
+def take_data(parent_pdf_set=None, members=False, xgrid=None, Q2grid=None):
     """
-    Auxiliary function for generate_pdf. It provides the info, the heads
-    of the member files and the blocks to be generated to generate_pdf.
+    Auxiliary function for `generate_pdf`.
+
+    It provides the info, the heads of the member files and the blocks
+    to be generated to `generate_pdf`.
 
     Parameters
     ----------
-        parent_pdf_set :
-            the PDF set to be used as parent
+        parent_pdf_set : None or str or dict
+            the PDF set to be used as parent set
         members : bool
-            if true every member of the parent are loaded
+            if true every member of the parent is loaded
+        xgrid : list(float)
+            produced x grid if given
+        Q2grid : list(float)
+            produced Q2 grid if given
+
+    Returns
+    -------
+        info : dict
+            info dictionary
+        heads : list(str)
+            heads of member files if necessary
+        blocks : list(dict)
+            data blocks
     """
-    xgrid = np.geomspace(1e-9, 1, 240)
-    Q2grid = np.geomspace(1.3, 1e5, 35)
+    if xgrid is None:
+        xgrid = np.geomspace(1e-9, 1, 240)
+    if Q2grid is None:
+        Q2grid = np.geomspace(1.3, 1e5, 35)
     # collect blocks
     all_blocks = []
     info = None
@@ -44,9 +61,9 @@ def take_data(parent_pdf_set=None, members=False):
             info = load.load_info_from_file(parent_pdf_set)
             # iterate on members
             for m in range(int(info["NumMembers"])):
-                dat = load.load_blocks_from_file(parent_pdf_set, m)
-                heads.append(dat[0])
-                all_blocks.append(dat[1])
+                head, blocks = load.load_blocks_from_file(parent_pdf_set, m)
+                heads.append(head)
+                all_blocks.append(blocks)
                 if not members:
                     break
     elif isinstance(parent_pdf_set, dict):
@@ -65,7 +82,7 @@ def take_data(parent_pdf_set=None, members=False):
         )
     else:
         raise ValueError("Unknown parent pdf type")
-    return heads, info, all_blocks
+    return info, heads, all_blocks
 
 
 def generate_pdf(
@@ -147,7 +164,7 @@ def generate_pdf(
         flavor_combinations = flavors.pid_to_flavor(labels)
 
     # labels = verify_labels(args.labels)
-    heads, info, all_blocks = take_data(parent_pdf_set=parent_pdf_set, members=members)
+    info, heads, all_blocks = take_data(parent_pdf_set=parent_pdf_set, members=members)
 
     # filter the PDF
     new_all_blocks = []
@@ -156,10 +173,7 @@ def generate_pdf(
 
     # changing info file according to user choice
     if info_update is not None:
-        if isinstance(info_update, dict):
-            info.update(info_update)
-        else:
-            raise TypeError("Info to update are not in a dictionary format")
+        info.update(info_update)
     # write
     info["Flavors"] = [int(pid) for pid in br.flavor_basis_pids]
     info["NumFlavors"] = len(br.flavor_basis_pids)
@@ -190,9 +204,7 @@ def install_pdf(name):
     print(f"install_pdf {name}")
     target = pathlib.Path(lhapdf.paths()[0])
     src = pathlib.Path(name)
-    if not src.exists():
-        raise FileExistsError(src)
-    shutil.move(str(src), str(target))
+    shutil.move(src, target)
 
 
 def generate_block(xfxQ2, xgrid, Q2grid, pids):
diff --git a/tests/conftest.py b/tests/conftest.py
index cee5c8df4..e72161d1b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -11,8 +11,7 @@
 
 @pytest.fixture
 def cd():
-    # thanks https://stackoverflow.com/questions/431684/
-    # how-do-i-change-the-working-directory-in-python/24176022#24176022
+    # thanks https://stackoverflow.com/questions/431684/how-do-i-change-the-working-directory-in-python/24176022#24176022
     @contextmanager
     def wrapped(newdir):
         prevdir = os.getcwd()
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 5167595f3..27aa43463 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -6,8 +6,8 @@
 
 
 def test_genpdf_exceptions(tmp_path, cd):
-    # using a wrong label and then a wrong parent pdf
     with cd(tmp_path):
+        # wrong label
         with pytest.raises(TypeError):
             genpdf.generate_pdf(
                 "test_genpdf_exceptions1",
@@ -17,15 +17,16 @@ def test_genpdf_exceptions(tmp_path, cd):
                     2: lambda x, Q2: 4.0 * x * (1.0 - x),
                 },
             )
+        # wrong parent pdf
         with pytest.raises(ValueError):
             genpdf.generate_pdf(
                 "test_genpdf_exceptions2",
                 ["g"],
                 10,
             )
-        with pytest.raises(FileExistsError):
+        # non-existant PDF set
+        with pytest.raises(FileNotFoundError):
             genpdf.install_pdf("foo")
-
         with pytest.raises(TypeError):
             genpdf.generate_pdf("debug", [21], info_update=(10, 15, 20))
 
@@ -39,3 +40,22 @@ def test_generate_block():
     assert sorted(b.keys()) == sorted(["data", "Q2grid", "xgrid", "pids"])
     assert isinstance(b["data"], np.ndarray)
     assert b["data"].shape == (len(xg) * len(q2s), len(pids))
+
+
+def test_install_pdf(fake_lhapdf, tmp_path, cd):
+    mytmp = tmp_path / "install"
+    mytmp.mkdir()
+    n = "bla"
+    p = mytmp / n
+    i = "test.info"
+    with cd(mytmp):
+        with pytest.raises(FileNotFoundError):
+            genpdf.install_pdf(p)
+        p.mkdir()
+        (p / i).write_text("Bla")
+        genpdf.install_pdf(p)
+    pp = tmp_path / n
+    assert not p.exists()
+    assert pp.exists()
+    assert (pp / i).exists()
+    assert "Bla" == (pp / i).read_text()

From 65ab083ba0919b70e32123e443eaf8711bc91959 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 22 Mar 2022 18:04:48 +0100
Subject: [PATCH 035/148] Add first genpdf test and improve former

---
 src/ekobox/genpdf/__init__.py | 37 ++++++++++++++++--------
 tests/ekobox/test_genpdf.py   | 53 +++++++++++++++++++++++++++++++++--
 2 files changed, 75 insertions(+), 15 deletions(-)

diff --git a/src/ekobox/genpdf/__init__.py b/src/ekobox/genpdf/__init__.py
index c1cf515fb..f58687cea 100644
--- a/src/ekobox/genpdf/__init__.py
+++ b/src/ekobox/genpdf/__init__.py
@@ -86,33 +86,40 @@ def take_data(parent_pdf_set=None, members=False, xgrid=None, Q2grid=None):
 
 
 def generate_pdf(
-    name, labels, parent_pdf_set=None, members=False, info_update=None, install=False
+    name,
+    labels,
+    parent_pdf_set=None,
+    members=False,
+    info_update=None,
+    install=False,
+    xgrid=None,
+    Q2grid=None,
 ):
     """
     Generate a new PDF from a parent PDF with a set of flavors.
 
-    If parent_pdf_set is the name of an available PDF set,
+    If `parent_pdf_set` is the name of an available PDF set,
     it will be used as parent. In order to use the toy PDF
-    as parent, it is enough to set parent_pdf_set = "toy" or "toylh".
-    If parent_pdf_set is not specified, a debug PDF constructed as
-    x * (1-x) for every flavor will be usedas parent.
+    as parent, it is enough to set `parent_pdf_set` to "toy" or "toylh".
+    If `parent_pdf_set` is not specified, a debug PDF constructed as
+    x * (1-x) for every flavor will be used as parent.
     It is also possible to provide custom functions for each flavor
-    in the form of a dictionary: {pid: f(x,Q2)}.
+    in the form of a dictionary: `{pid: f(x,Q2)}`.
 
-    In labels it is possible to pass a list of PIDs or evolution basis
+    With `labels` it is possible to pass a list of PIDs or evolution basis
     combinations to keep in the generated PDF. In order to project
     on custom combinations of PIDs, it is also possible to pass a list
     containing the desired factors for each flavor.
 
     The default behaviour is to generate only one member for a PDF set
-    (the zero member) but it can be changed setting to True the member flag.
+    (the zero member) but it can be changed setting to True the `members` flag.
 
-    The info_update argument is a dictionary and provide to the user a way
-    to change the info file of the generated PDF set. If a key of info_update
+    The `info_update` argument is a dictionary and provide to the user as a way
+    to change the info file of the generated PDF set. If a key of `info_update`
     matches with one key of the standard info file, the information
     are updated, otherwise they are simply added.
 
-    Turning True the value of the install flag, it is possible to autmatically
+    Turning True the value of the `install` flag, it is possible to automatically
     install the generated PDF to the lhapdf directory. By default install is False.
 
     Parameters
@@ -127,6 +134,10 @@ def generate_pdf(
             iterate on members
         install : bool
             install on LHAPDF path
+        xgrid : list(float)
+            produced x grid if given
+        Q2grid : list(float)
+            produced Q2 grid if given
 
     Examples
     --------
@@ -164,7 +175,9 @@ def generate_pdf(
         flavor_combinations = flavors.pid_to_flavor(labels)
 
     # labels = verify_labels(args.labels)
-    info, heads, all_blocks = take_data(parent_pdf_set=parent_pdf_set, members=members)
+    info, heads, all_blocks = take_data(
+        parent_pdf_set, members, xgrid=xgrid, Q2grid=Q2grid
+    )
 
     # filter the PDF
     new_all_blocks = []
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 27aa43463..66b9d5861 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -45,7 +45,7 @@ def test_generate_block():
 def test_install_pdf(fake_lhapdf, tmp_path, cd):
     mytmp = tmp_path / "install"
     mytmp.mkdir()
-    n = "bla"
+    n = "test_install_pdf"
     p = mytmp / n
     i = "test.info"
     with cd(mytmp):
@@ -57,5 +57,52 @@ def test_install_pdf(fake_lhapdf, tmp_path, cd):
     pp = tmp_path / n
     assert not p.exists()
     assert pp.exists()
-    assert (pp / i).exists()
-    assert "Bla" == (pp / i).read_text()
+    ppi = pp / i
+    assert ppi.exists()
+    assert "Bla" == ppi.read_text()
+
+
+def test_generate_pdf_debug(fake_lhapdf, tmp_path, cd):
+    mytmp = tmp_path / "install"
+    mytmp.mkdir()
+    n = "test_generate_pdf_debug"
+    xg = np.linspace(0.0, 1.0, 5)
+    q2s = np.geomspace(1.0, 1e3, 5)
+    p = mytmp / n
+    i = f"{n}.info"
+    with cd(mytmp):
+        genpdf.generate_pdf(
+            n,
+            [21],
+            None,
+            info_update={"Debug": "debug"},
+            install=True,
+            xgrid=xg,
+            Q2grid=q2s,
+        )
+    pp = tmp_path / n
+    assert not p.exists()
+    assert pp.exists()
+    # check info file
+    ppi = pp / i
+    assert ppi.exists()
+    assert "Debug: debug" in ppi.read_text()
+    ii = genpdf.load.load_info_from_file(n)
+    assert "Debug" in ii
+    assert ii["Debug"] == "debug"
+    # check member file
+    ppm = pp / f"{n}_0000.dat"
+    assert ppm.exists()
+    assert "PdfType: central" in ppm.read_text()
+    head, blocks = genpdf.load.load_blocks_from_file(n, 0)
+    assert "PdfType: central" in head
+    assert len(blocks) == 1
+    b = blocks[0]
+    assert 21 in b["pids"]
+    for k, line in enumerate(b["data"]):
+        for pid, f in zip(b["pids"], line):
+            # the gluon is non-zero in the bulk
+            if pid == 21 and k > len(xg) - 1 and k < len(b["data"]) - len(xg):
+                assert not f == 0.0
+            else:
+                assert f == 0.0

From 726808febb0d3ac53a0df80fa60a88e37c134e5a Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 11:32:55 +0100
Subject: [PATCH 036/148] Recover shutil.move in py3.8 and lower

---
 src/ekobox/genpdf/__init__.py | 4 +++-
 tests/ekobox/test_genpdf.py   | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/ekobox/genpdf/__init__.py b/src/ekobox/genpdf/__init__.py
index f58687cea..3bb4e901e 100644
--- a/src/ekobox/genpdf/__init__.py
+++ b/src/ekobox/genpdf/__init__.py
@@ -217,7 +217,9 @@ def install_pdf(name):
     print(f"install_pdf {name}")
     target = pathlib.Path(lhapdf.paths()[0])
     src = pathlib.Path(name)
-    shutil.move(src, target)
+    # shutil.move only accepts paths since 3.9 so we need to cast
+    # https://docs.python.org/3/library/shutil.html?highlight=shutil#shutil.move
+    shutil.move(str(src), str(target))
 
 
 def generate_block(xfxQ2, xgrid, Q2grid, pids):
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 66b9d5861..3bf3cf639 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -43,6 +43,7 @@ def test_generate_block():
 
 
 def test_install_pdf(fake_lhapdf, tmp_path, cd):
+    # move into subdir to be able to move
     mytmp = tmp_path / "install"
     mytmp.mkdir()
     n = "test_install_pdf"

From 8f3c854a155846d9b1cd6ae49a0316398653aee8 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 12:33:49 +0100
Subject: [PATCH 037/148] Improve genpdf tests

---
 tests/conftest.py           | 19 ++++++++++--
 tests/ekobox/test_genpdf.py | 61 ++++++++++++++++++++++++++++++++-----
 2 files changed, 70 insertions(+), 10 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index e72161d1b..679284613 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -111,11 +111,24 @@ def lhapdf_paths():
 fakepdf = pathlib.Path(__file__).parents[1] / "benchmarks" / "ekobox" / "fakepdf"
 
 
-@pytest.fixture
-def fake_ct14(fake_lhapdf):
-    n = "myCT14llo_NF3"
+def fake_pdf(fake_lhapdf, n):
     src = fakepdf / n
     dst = fake_lhapdf / n
     shutil.copytree(src, dst)
     yield n
     shutil.rmtree(dst)
+
+
+@pytest.fixture
+def fake_ct14(fake_lhapdf):
+    yield from fake_pdf(fake_lhapdf, "myCT14llo_NF3")
+
+
+@pytest.fixture
+def fake_nn31(fake_lhapdf):
+    yield from fake_pdf(fake_lhapdf, "myNNPDF31_nlo_as_0118")
+
+
+@pytest.fixture
+def fake_mstw(fake_lhapdf):
+    yield from fake_pdf(fake_lhapdf, "myMSTW2008nlo90cl")
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 3bf3cf639..6a7cf80f9 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -63,12 +63,12 @@ def test_install_pdf(fake_lhapdf, tmp_path, cd):
     assert "Bla" == ppi.read_text()
 
 
-def test_generate_pdf_debug(fake_lhapdf, tmp_path, cd):
-    mytmp = tmp_path / "install"
+def test_generate_pdf_debug_pid(fake_lhapdf, cd):
+    mytmp = fake_lhapdf / "install"
     mytmp.mkdir()
-    n = "test_generate_pdf_debug"
+    n = "test_generate_pdf_debug_pid"
     xg = np.linspace(0.0, 1.0, 5)
-    q2s = np.geomspace(1.0, 1e3, 5)
+    q2s = np.geomspace(1.0, 1e3, 7)
     p = mytmp / n
     i = f"{n}.info"
     with cd(mytmp):
@@ -81,7 +81,7 @@ def test_generate_pdf_debug(fake_lhapdf, tmp_path, cd):
             xgrid=xg,
             Q2grid=q2s,
         )
-    pp = tmp_path / n
+    pp = fake_lhapdf / n
     assert not p.exists()
     assert pp.exists()
     # check info file
@@ -102,8 +102,55 @@ def test_generate_pdf_debug(fake_lhapdf, tmp_path, cd):
     assert 21 in b["pids"]
     for k, line in enumerate(b["data"]):
         for pid, f in zip(b["pids"], line):
-            # the gluon is non-zero in the bulk
-            if pid == 21 and k > len(xg) - 1 and k < len(b["data"]) - len(xg):
+            # the gluon is non-zero in the bulk - x=0 is included here
+            if (
+                pid == 21
+                and k > len(b["Q2grid"]) - 1
+                and k < len(b["data"]) - len(b["Q2grid"])
+            ):
                 assert not f == 0.0
             else:
                 assert f == 0.0
+
+
+def test_generate_pdf_pdf_evol(fake_lhapdf, fake_nn31, fake_mstw, cd):
+    # iterate pdfs with their error type and number of blocks
+    for fake_pdf, err_type, nb in ((fake_nn31, "replica", 2), (fake_mstw, "error", 3)):
+        n = f"test_generate_pdf_{err_type}_evol"
+        p = fake_lhapdf / n
+        i = f"{n}.info"
+        pi = p / i
+        with cd(fake_lhapdf):
+            genpdf.generate_pdf(
+                n,
+                ["S"],
+                fake_pdf,
+                members=True,
+            )
+        assert p.exists()
+        # check info file
+        assert pi.exists()
+        # check member file
+        for m in range(1 + 1):
+            pm = p / f"{n}_{m:04d}.dat"
+            assert pm.exists()
+            head, blocks = genpdf.load.load_blocks_from_file(n, m)
+            assert ("PdfType: central" if m == 0 else f"PdfType: {err_type}") in head
+            assert len(blocks) == nb
+            for b in blocks:
+                for k, line in enumerate(b["data"]):
+                    for pid, f in zip(b["pids"], line):
+                        # the singlet is non-zero in the bulk - x >= 0
+                        if abs(pid) in range(1, 6 + 1) and k < len(b["data"]) - len(
+                            b["Q2grid"]
+                        ):
+                            assert not f == 0.0
+                            assert not np.isclose(f, 0.0, atol=1e-15)
+                        else:
+                            # MSTW is not 0 at the end, but only almost
+                            if err_type == "error" and k >= len(b["data"]) - len(
+                                b["Q2grid"]
+                            ):
+                                np.testing.assert_allclose(f, 0.0, atol=1e-15)
+                            else:
+                                assert f == 0.0

From 275e0caa834e3cb6ced6620ec34e30576ecfbf8e Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 12:49:17 +0100
Subject: [PATCH 038/148] Complete genpdf.generate_pdf test

---
 src/ekobox/genpdf/__init__.py |  2 +-
 tests/ekobox/test_genpdf.py   | 56 +++++++++++++++++++++++++++++++----
 2 files changed, 52 insertions(+), 6 deletions(-)

diff --git a/src/ekobox/genpdf/__init__.py b/src/ekobox/genpdf/__init__.py
index 3bb4e901e..ebaf696b1 100644
--- a/src/ekobox/genpdf/__init__.py
+++ b/src/ekobox/genpdf/__init__.py
@@ -154,7 +154,7 @@ def generate_pdf(
         through the pure-singlet contributions (starting at |NNLO|)
 
         >>> from eko import basis_rotation as br
-        >>> from ekobox.tools import genpdf
+        >>> from ekobox import genpdf
         >>> import numpy as np
         >>> anti_qed_singlet = np.zeros_like(br.flavor_basis_pids, dtype=np.float_)
         >>> anti_qed_singlet[br.flavor_basis_pids.index(1)] = -4
diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 6a7cf80f9..76b9e7e1e 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -2,6 +2,7 @@
 import numpy as np
 import pytest
 
+from eko import basis_rotation as br
 from ekobox import genpdf
 
 
@@ -113,9 +114,13 @@ def test_generate_pdf_debug_pid(fake_lhapdf, cd):
                 assert f == 0.0
 
 
-def test_generate_pdf_pdf_evol(fake_lhapdf, fake_nn31, fake_mstw, cd):
+def test_generate_pdf_pdf_evol(fake_lhapdf, fake_nn31, fake_mstw, fake_ct14, cd):
     # iterate pdfs with their error type and number of blocks
-    for fake_pdf, err_type, nb in ((fake_nn31, "replica", 2), (fake_mstw, "error", 3)):
+    for fake_pdf, err_type, nmem, nb in (
+        (fake_nn31, "replica", 1, 2),
+        (fake_mstw, "error", 1, 3),
+        (fake_ct14, "", 0, 1),
+    ):
         n = f"test_generate_pdf_{err_type}_evol"
         p = fake_lhapdf / n
         i = f"{n}.info"
@@ -125,13 +130,13 @@ def test_generate_pdf_pdf_evol(fake_lhapdf, fake_nn31, fake_mstw, cd):
                 n,
                 ["S"],
                 fake_pdf,
-                members=True,
+                members=nmem > 0,
             )
         assert p.exists()
         # check info file
         assert pi.exists()
-        # check member file
-        for m in range(1 + 1):
+        # check member files
+        for m in range(nmem + 1):
             pm = p / f"{n}_{m:04d}.dat"
             assert pm.exists()
             head, blocks = genpdf.load.load_blocks_from_file(n, m)
@@ -154,3 +159,44 @@ def test_generate_pdf_pdf_evol(fake_lhapdf, fake_nn31, fake_mstw, cd):
                                 np.testing.assert_allclose(f, 0.0, atol=1e-15)
                             else:
                                 assert f == 0.0
+
+
+def test_generate_pdf_toy_antiqed(fake_lhapdf, cd):
+    # iterate pdfs with their error type and number of blocks
+    n = "test_generate_pdf_toy_antiqed"
+    xg = np.linspace(1e-5, 1.0, 5)
+    q2s = np.geomspace(1.0, 1e3, 7)
+    anti_qed_singlet = np.zeros_like(br.flavor_basis_pids, dtype=np.float_)
+    anti_qed_singlet[br.flavor_basis_pids.index(1)] = -4
+    anti_qed_singlet[br.flavor_basis_pids.index(-1)] = -4
+    anti_qed_singlet[br.flavor_basis_pids.index(2)] = 1
+    anti_qed_singlet[br.flavor_basis_pids.index(-2)] = 1
+    p = fake_lhapdf / n
+    i = f"{n}.info"
+    pi = p / i
+    with cd(fake_lhapdf):
+        genpdf.generate_pdf(
+            n,
+            [anti_qed_singlet],
+            "toy",
+            xgrid=xg,
+            Q2grid=q2s,
+        )
+    assert p.exists()
+    # check info file
+    assert pi.exists()
+    # check member files
+    pm = p / f"{n}_0000.dat"
+    assert pm.exists()
+    assert "PdfType: central" in pm.read_text()
+    head, blocks = genpdf.load.load_blocks_from_file(n, 0)
+    assert "PdfType: central" in head
+    assert len(blocks) == 1
+    b = blocks[0]
+    for k, line in enumerate(b["data"]):
+        for pid, f in zip(b["pids"], line):
+            # the u and d are non-zero in the bulk - x=0 is not included here
+            if abs(pid) in [1, 2] and k < len(b["data"]) - len(b["Q2grid"]):
+                assert not f == 0.0
+            else:
+                assert f == 0.0

From fbe9e9d057954daddc9af701467b227bbef294ab Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 12:52:59 +0100
Subject: [PATCH 039/148] Resolve fake_pdf name clash

---
 tests/conftest.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 679284613..4969506dd 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -111,7 +111,7 @@ def lhapdf_paths():
 fakepdf = pathlib.Path(__file__).parents[1] / "benchmarks" / "ekobox" / "fakepdf"
 
 
-def fake_pdf(fake_lhapdf, n):
+def copy_lhapdf(fake_lhapdf, n):
     src = fakepdf / n
     dst = fake_lhapdf / n
     shutil.copytree(src, dst)
@@ -121,14 +121,14 @@ def fake_pdf(fake_lhapdf, n):
 
 @pytest.fixture
 def fake_ct14(fake_lhapdf):
-    yield from fake_pdf(fake_lhapdf, "myCT14llo_NF3")
+    yield from copy_lhapdf(fake_lhapdf, "myCT14llo_NF3")
 
 
 @pytest.fixture
 def fake_nn31(fake_lhapdf):
-    yield from fake_pdf(fake_lhapdf, "myNNPDF31_nlo_as_0118")
+    yield from copy_lhapdf(fake_lhapdf, "myNNPDF31_nlo_as_0118")
 
 
 @pytest.fixture
 def fake_mstw(fake_lhapdf):
-    yield from fake_pdf(fake_lhapdf, "myMSTW2008nlo90cl")
+    yield from copy_lhapdf(fake_lhapdf, "myMSTW2008nlo90cl")

From d47788ce1ef52d982ddf3e95c059992238dd09cd Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 14:16:09 +0100
Subject: [PATCH 040/148] Complete genpdf.cli tests

---
 tests/ekobox/test_genpdf_cli.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tests/ekobox/test_genpdf_cli.py b/tests/ekobox/test_genpdf_cli.py
index 25850c1d4..c412bdb7a 100644
--- a/tests/ekobox/test_genpdf_cli.py
+++ b/tests/ekobox/test_genpdf_cli.py
@@ -19,3 +19,19 @@ def test_genpdf_CLI_messages():
     assert "-p, --parent-pdf-set TEXT" in result.output
     assert "-m, --members" in result.output
     assert "-i, --install" in result.output
+
+
+def test_genpdf_CLI(fake_lhapdf, cd):
+    n = "test_genpdf_CLI"
+    runner = CliRunner()
+    result = None
+    with cd(fake_lhapdf):
+        result = runner.invoke(cli, ["generate", n, "21"])
+    assert result is not None
+    assert result.exception is None
+    p = fake_lhapdf / n
+    assert p.exists()
+    pi = p / f"{n}.info"
+    assert pi.exists()
+    pm = p / f"{n}_0000.dat"
+    assert pm.exists()

From a96aca421a052bc0c988bf0d595f7d691d0748a4 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 15:08:25 +0100
Subject: [PATCH 041/148] Add ekobox install cli test

---
 tests/ekobox/test_genpdf.py     |  6 +++---
 tests/ekobox/test_genpdf_cli.py | 12 +++++++-----
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/tests/ekobox/test_genpdf.py b/tests/ekobox/test_genpdf.py
index 76b9e7e1e..3f68ae9b4 100644
--- a/tests/ekobox/test_genpdf.py
+++ b/tests/ekobox/test_genpdf.py
@@ -43,9 +43,9 @@ def test_generate_block():
     assert b["data"].shape == (len(xg) * len(q2s), len(pids))
 
 
-def test_install_pdf(fake_lhapdf, tmp_path, cd):
+def test_install_pdf(fake_lhapdf, cd):
     # move into subdir to be able to move
-    mytmp = tmp_path / "install"
+    mytmp = fake_lhapdf / "install"
     mytmp.mkdir()
     n = "test_install_pdf"
     p = mytmp / n
@@ -56,7 +56,7 @@ def test_install_pdf(fake_lhapdf, tmp_path, cd):
         p.mkdir()
         (p / i).write_text("Bla")
         genpdf.install_pdf(p)
-    pp = tmp_path / n
+    pp = fake_lhapdf / n
     assert not p.exists()
     assert pp.exists()
     ppi = pp / i
diff --git a/tests/ekobox/test_genpdf_cli.py b/tests/ekobox/test_genpdf_cli.py
index c412bdb7a..ec973140e 100644
--- a/tests/ekobox/test_genpdf_cli.py
+++ b/tests/ekobox/test_genpdf_cli.py
@@ -22,13 +22,15 @@ def test_genpdf_CLI_messages():
 
 
 def test_genpdf_CLI(fake_lhapdf, cd):
+    mytmp = fake_lhapdf / "install"
+    mytmp.mkdir()
     n = "test_genpdf_CLI"
     runner = CliRunner()
-    result = None
-    with cd(fake_lhapdf):
-        result = runner.invoke(cli, ["generate", n, "21"])
-    assert result is not None
-    assert result.exception is None
+    with cd(mytmp):
+        result_gen = runner.invoke(cli, ["generate", n, "21"])
+        assert result_gen.exception is None
+        result_inst = runner.invoke(cli, ["install", n])
+        assert result_inst.exception is None
     p = fake_lhapdf / n
     assert p.exists()
     pi = p / f"{n}.info"

From 2e19e5788fe03e147990e9814f8babd1cbb01877 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 23 Mar 2022 15:14:06 +0100
Subject: [PATCH 042/148] Rename ekobox info file

---
 src/ekobox/__init__.py                           |  2 +-
 src/ekobox/evol_pdf.py                           |  4 ++--
 src/ekobox/gen_theory.py                         | 16 ++++++----------
 src/ekobox/{gen_info.py => info_file.py}         |  6 +++---
 tests/ekobox/test_evol_pdf.py                    |  8 +++++++-
 .../{test_gen_info.py => test_info_file.py}      |  6 +++---
 6 files changed, 22 insertions(+), 20 deletions(-)
 rename src/ekobox/{gen_info.py => info_file.py} (92%)
 rename tests/ekobox/{test_gen_info.py => test_info_file.py} (87%)

diff --git a/src/ekobox/__init__.py b/src/ekobox/__init__.py
index 3ce63bd8f..085acddf2 100644
--- a/src/ekobox/__init__.py
+++ b/src/ekobox/__init__.py
@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 from ekomark import apply
 
-from . import evol_pdf, gen_info, gen_op, gen_theory
+from . import evol_pdf, gen_op, gen_theory, info_file
diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index 60c4ed24c..ea6c1eee6 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -6,7 +6,7 @@
 from eko import basis_rotation as br
 from ekomark import apply
 
-from . import gen_info, genpdf
+from . import genpdf, info_file
 
 
 def evolve_pdfs(
@@ -79,7 +79,7 @@ def evolve_pdfs(
         info_update = {}
     info_update["XMin"] = targetgrid[0]
     info_update["XMax"] = targetgrid[-1]
-    info = gen_info.create_info_file(
+    info = info_file.build(
         theory_card,
         operators_card,
         len(evolved_PDF_list),
diff --git a/src/ekobox/gen_theory.py b/src/ekobox/gen_theory.py
index 69fba7cdd..cbc2d8267 100644
--- a/src/ekobox/gen_theory.py
+++ b/src/ekobox/gen_theory.py
@@ -12,26 +12,22 @@ def gen_theory_card(pto, initial_scale, update=None, name=None):
 
     Parameters
     ----------
-
         pto : int
             perturbation theory order
         initial_scale: float
-            initial scale of evolution
+            initial scale of evolution [GeV]
         update : dict
             info to update to default theory card
         name : str
-            name of exported theory card (if name not None )
+            name of exported theory card (if name is not None )
 
     Returns
     -------
-
-        : dict
-        theory card
+        dict :
+            theory card
     """
     # Constructing the dictionary with some default values
     theory = copy.deepcopy(theories.default_card)
-    # delete unuseful member
-    del theory["FNS"]
     # Adding the mandatory inputs
     theory["PTO"] = pto
     theory["Q0"] = initial_scale
@@ -42,7 +38,7 @@ def gen_theory_card(pto, initial_scale, update=None, name=None):
                 raise ValueError("Provided key not in theory card")
         theory.update(update)
     serialized = sql.serialize(theory)
-    theory["hash"] = (sql.add_hash(serialized))[-1]
+    theory["hash"] = sql.add_hash(serialized)[-1]
     if name is not None:
         export_theory_card(name, theory)
     return theory
@@ -76,7 +72,7 @@ def import_theory_card(path):
 
     Returns
     -------
-        : dict
+        dict :
             theory card
     """
     with open(path, "r", encoding="utf-8") as o:
diff --git a/src/ekobox/gen_info.py b/src/ekobox/info_file.py
similarity index 92%
rename from src/ekobox/gen_info.py
rename to src/ekobox/info_file.py
index 757ae4c7c..626b52b67 100644
--- a/src/ekobox/gen_info.py
+++ b/src/ekobox/info_file.py
@@ -5,7 +5,7 @@
 from .genpdf import load
 
 
-def create_info_file(theory_card, operators_card, num_members, info_update):
+def build(theory_card, operators_card, num_members, info_update):
     """
     Generate a lhapdf info file from theory and operators card
 
@@ -22,8 +22,8 @@ def create_info_file(theory_card, operators_card, num_members, info_update):
 
     Returns
     -------
-        : dict
-        info file in lhapdf format
+        dict :
+            info file in lhapdf format
     """
     template_info = copy.deepcopy(load.template_info)
     template_info["SetDesc"] = "Evolved PDF from " + str(theory_card["Q0"]) + " GeV"
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index dabb8616a..c9d745309 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -9,7 +9,13 @@
 
 
 def test_gen_and_dump_out(tmp_path):
-    op = g_o.gen_op_card([100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
+    op = g_o.gen_op_card(
+        [100.0],
+        update={
+            "xgrid": [0.1, 0.5, 1.0],
+            "configs": {"interpolation_polynomial_degree": 1},
+        },
+    )
     theory = g_t.gen_theory_card(0, 1.0)
 
     out = ev_p.gen_out(theory, op, path=tmp_path)
diff --git a/tests/ekobox/test_gen_info.py b/tests/ekobox/test_info_file.py
similarity index 87%
rename from tests/ekobox/test_gen_info.py
rename to tests/ekobox/test_info_file.py
index f82e76c76..68d3e3dfc 100644
--- a/tests/ekobox/test_gen_info.py
+++ b/tests/ekobox/test_info_file.py
@@ -3,15 +3,15 @@
 
 import numpy as np
 
-from ekobox import gen_info as g_i
 from ekobox import gen_op as g_o
 from ekobox import gen_theory as g_t
+from ekobox import info_file
 
 
-def test_create_info_file():
+def test_build():
     op = g_o.gen_op_card([10, 100])
     theory = g_t.gen_theory_card(1, 10.0, update={"alphas": 0.2})
-    info = g_i.create_info_file(
+    info = info_file.build(
         theory, op, 4, info_update={"SetDesc": "Prova", "NewArg": 15.3, "MTop": 1.0}
     )
     assert info["AlphaS_MZ"] == 0.2

From 9ba039e7ef788bcfc82ef7d99c6255d352b8f065 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 13:02:10 +0200
Subject: [PATCH 043/148] Complete coverage

---
 pyproject.toml                |  2 +-
 src/ekobox/evol_pdf.py        | 40 ++-------------------
 tests/ekobox/test_evol_pdf.py | 65 ++++++++++++++++++++++-------------
 tests/ekobox/test_utils.py    | 19 ++++++----
 4 files changed, 59 insertions(+), 67 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4811a1c66..a2130c1f3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -118,7 +118,7 @@ python_classes = ['Test*', 'Benchmark*']
 python_functions = ['test_*', 'benchmark_*']
 addopts = [
   '--cov=eko',
-  # '--cov=ekobox',
+  '--cov=ekobox',
   '--cov-report=html',
   '--cov-report=xml',
   '--strict-markers',
diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index ea6c1eee6..55c622777 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -28,39 +28,28 @@ def evolve_pdfs(
     ----------
         initial_PDF_list : list(lhapdf object)
             list of PDF members to be evolved
-
         theory_card : dict
             theory card
-
         operators_card : dict
             operators card
-
         path : str
             path to cached eko output (if "None" it will be recomputed)
-
         store_path : str
             path where the eko is stored (if "None" will not be saved)
-
         targetgrid : list(float)
             target x-grid (if different from input x-grid)
-
         install : bool
             set whether to install evolved PDF to lhapdf directory
-
         name : str
             set name of evolved PDF
-
         info_update : dict
             dict of info to add or update to default info file
-
     """
     eko_output = None
     if path is not None:
         my_path = pathlib.Path(path)
         if my_path.is_dir():
-            ops_id = f"o{operators_card['hash'][:6]}_t{theory_card['hash'][:6]}.tar"
-            ops_id_path = pathlib.Path(ops_id)
-            outpath = my_path / ops_id_path.relative_to(ops_id_path.anchor)
+            outpath = my_path / ekofileid(theory_card, operators_card)
             eko_output = eko.output.legacy.load_tar(outpath)
         else:
             eko_output = eko.output.legacy.load_tar(my_path)
@@ -106,28 +95,5 @@ def evolve_pdfs(
         genpdf.install_pdf(name)
 
 
-def gen_out(theory_card, op_card, path=None):
-    """
-    Generates EKO output from theory and operators cards and, if requested,
-    dumps it in tar format
-
-    Parameters
-    ----------
-        theory_card : dict
-            theory card
-        op_card : dict
-            operators card
-        path : str
-            path of dumped output (if "None" output is not dumped)
-
-    Returns
-    -------
-        : eko.output.Output
-            eko output
-    """
-    eko_output = eko.run_dglap(theory_card, op_card)
-    if path is not None:
-        ops_id = f"o{op_card['hash'][:6]}_t{theory_card['hash'][:6]}"
-        path = f"{path}/{ops_id}.tar"
-        eko.output.legacy.dump_tar(eko_output, path)
-    return eko_output
+def ekofileid(theory_card, operators_card):
+    return f"o{operators_card['hash'][:6]}_t{theory_card['hash'][:6]}.tar"
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index c9d745309..ff9999e81 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -1,31 +1,50 @@
 # -*- coding: utf-8 -*-
 
-import numpy as np
+from banana import toy
 
-import eko.output.legacy
+import eko
+import eko.output.legacy as out
 from ekobox import evol_pdf as ev_p
 from ekobox import gen_op as g_o
 from ekobox import gen_theory as g_t
 
+op = g_o.gen_op_card(
+    [100.0],
+    update={
+        "xgrid": [0.1, 0.5, 1.0],
+        "configs": {"interpolation_polynomial_degree": 1},
+    },
+)
+theory = g_t.gen_theory_card(0, 1.65)
 
-def test_gen_and_dump_out(tmp_path):
-    op = g_o.gen_op_card(
-        [100.0],
-        update={
-            "xgrid": [0.1, 0.5, 1.0],
-            "configs": {"interpolation_polynomial_degree": 1},
-        },
-    )
-    theory = g_t.gen_theory_card(0, 1.0)
-
-    out = ev_p.gen_out(theory, op, path=tmp_path)
-
-    ops_id = f"o{op['hash'][:6]}_t{theory['hash'][:6]}"
-    outpath = f"{tmp_path}/{ops_id}.tar"
-    loaded_out = eko.output.legacy.load_tar(outpath)
-    assert out.xgrid.tolist() == loaded_out.xgrid.tolist()
-    for el, loaded_el in zip(out[100.0].operator, loaded_out[100.0].operator):
-        np.testing.assert_allclose(
-            el,
-            loaded_el,
-        )
+
+def test_evolve_pdfs_run(fake_lhapdf, cd):
+    n = "test_evolve_pdfs_run"
+    mytmp = fake_lhapdf / "install"
+    mytmp.mkdir()
+    with cd(mytmp):
+        ev_p.evolve_pdfs([toy.mkPDF("", 0)], theory, op, install=True, name=n)
+    p = fake_lhapdf / n
+    assert p.exists()
+
+
+def test_evolve_pdfs_dump_path(fake_lhapdf, cd):
+    n = "test_evolve_pdfs_dump_path"
+    peko = fake_lhapdf / ev_p.ekofileid(theory, op)
+    out.dump_tar(eko.run_dglap(theory, op), peko)
+    assert peko.exists()
+    with cd(fake_lhapdf):
+        ev_p.evolve_pdfs([toy.mkPDF("", 0)], theory, op, name=n, path=fake_lhapdf)
+    p = fake_lhapdf / n
+    assert p.exists()
+
+
+def test_evolve_pdfs_dump_file(fake_lhapdf, cd):
+    n = "test_evolve_pdfs_dump_file"
+    peko = fake_lhapdf / ev_p.ekofileid(theory, op)
+    out.dump_tar(eko.run_dglap(theory, op), peko)
+    assert peko.exists()
+    with cd(fake_lhapdf):
+        ev_p.evolve_pdfs([toy.mkPDF("", 0)], theory, op, name=n, path=peko)
+    p = fake_lhapdf / n
+    assert p.exists()
diff --git a/tests/ekobox/test_utils.py b/tests/ekobox/test_utils.py
index 69fd86d05..a85606da9 100644
--- a/tests/ekobox/test_utils.py
+++ b/tests/ekobox/test_utils.py
@@ -2,7 +2,7 @@
 import numpy as np
 import pytest
 
-from ekobox import evol_pdf as ev_p
+import eko
 from ekobox import gen_op as g_o
 from ekobox import gen_theory as g_t
 from ekobox import utils
@@ -11,21 +11,28 @@
 def test_ekos_product():
     # Generating two ekos
     op1 = g_o.gen_op_card(
-        [60.0, 80.0, 100.0], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}
+        [60.0, 80.0, 100.0],
+        update={
+            "xgrid": [0.1, 0.5, 1.0],
+            "configs": {"interpolation_polynomial_degree": 1},
+        },
     )
     theory1 = g_t.gen_theory_card(0, 5.0)
 
     op2 = g_o.gen_op_card(
         [80.0, 100.0, 120.0],
-        update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]},
+        update={
+            "xgrid": [0.1, 0.5, 1.0],
+            "configs": {"interpolation_polynomial_degree": 1},
+        },
     )
     theory2 = g_t.gen_theory_card(0, 10.0)
     theory_err = g_t.gen_theory_card(0, 5.0)
 
-    eko_ini = ev_p.gen_out(theory1, op1)
-    eko_fin = ev_p.gen_out(theory2, op2)
+    eko_ini = eko.run_dglap(theory1, op1)
+    eko_fin = eko.run_dglap(theory2, op2)
     # Test_error
-    eko_fin_err = ev_p.gen_out(theory_err, op2)
+    eko_fin_err = eko.run_dglap(theory_err, op2)
     with pytest.raises(ValueError):
         _ = utils.ekos_product(eko_ini, eko_fin_err)
     # product is copied

From 15a2161c85436a1826303fae6ec0b65e1f36247b Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 24 Mar 2022 11:02:49 +0100
Subject: [PATCH 044/148] Rename gen_theory

---
 benchmarks/ekobox/benchmark_evol_pdf.py          |  6 +++---
 src/ekobox/__init__.py                           |  2 +-
 src/ekobox/{gen_theory.py => theory_card.py}     |  8 ++++----
 tests/ekobox/test_evol_pdf.py                    |  4 ++--
 tests/ekobox/test_info_file.py                   |  4 ++--
 .../{test_gen_theory.py => test_theory_card.py}  | 16 ++++++++--------
 tests/ekobox/test_utils.py                       |  8 ++++----
 7 files changed, 24 insertions(+), 24 deletions(-)
 rename src/ekobox/{gen_theory.py => theory_card.py} (91%)
 rename tests/ekobox/{test_gen_theory.py => test_theory_card.py} (52%)

diff --git a/benchmarks/ekobox/benchmark_evol_pdf.py b/benchmarks/ekobox/benchmark_evol_pdf.py
index a3a4b16b7..d2b2cd724 100644
--- a/benchmarks/ekobox/benchmark_evol_pdf.py
+++ b/benchmarks/ekobox/benchmark_evol_pdf.py
@@ -7,7 +7,7 @@
 from eko import basis_rotation as br
 from ekobox import evol_pdf as ev_p
 from ekobox import gen_op as g_o
-from ekobox import gen_theory as g_t
+from ekobox import theory_card as tc
 from ekobox.genpdf import load
 
 test_pdf = pathlib.Path(__file__).parent / "fakepdf"
@@ -22,7 +22,7 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
         10000.0,
     ]
     op = g_o.gen_op_card(q2grid)
-    theory = g_t.gen_theory_card(
+    theory = tc.generate(
         0,
         5.0,
         update={
@@ -80,7 +80,7 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
 @pytest.mark.isolated
 def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
     op = g_o.gen_op_card([10, 100], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
-    theory = g_t.gen_theory_card(0, 1.0)
+    theory = tc.generate(0, 1.0)
     with lhapdf_path(test_pdf):
         pdfs = lhapdf.mkPDFs("myMSTW2008nlo90cl")
     d = tmp_path / "sub"
diff --git a/src/ekobox/__init__.py b/src/ekobox/__init__.py
index 085acddf2..93c2e4e73 100644
--- a/src/ekobox/__init__.py
+++ b/src/ekobox/__init__.py
@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 from ekomark import apply
 
-from . import evol_pdf, gen_op, gen_theory, info_file
+from . import evol_pdf, gen_op, info_file, theory_card
diff --git a/src/ekobox/gen_theory.py b/src/ekobox/theory_card.py
similarity index 91%
rename from src/ekobox/gen_theory.py
rename to src/ekobox/theory_card.py
index cbc2d8267..ee9c71c3c 100644
--- a/src/ekobox/gen_theory.py
+++ b/src/ekobox/theory_card.py
@@ -5,7 +5,7 @@
 from banana.data import sql, theories
 
 
-def gen_theory_card(pto, initial_scale, update=None, name=None):
+def generate(pto, initial_scale, update=None, name=None):
     """
     Generates a theory card with some mandatory user choice and some
     default values which can be changed by the update input dict
@@ -40,11 +40,11 @@ def gen_theory_card(pto, initial_scale, update=None, name=None):
     serialized = sql.serialize(theory)
     theory["hash"] = sql.add_hash(serialized)[-1]
     if name is not None:
-        export_theory_card(name, theory)
+        dump(name, theory)
     return theory
 
 
-def export_theory_card(name, theory):
+def dump(name, theory):
     """
     Export the theory card in the current directory
 
@@ -61,7 +61,7 @@ def export_theory_card(name, theory):
         yaml.safe_dump(theory, out)
 
 
-def import_theory_card(path):
+def load(path):
     """
     Import the theory card specified by path
 
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index ff9999e81..f69ef5258 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -6,7 +6,7 @@
 import eko.output.legacy as out
 from ekobox import evol_pdf as ev_p
 from ekobox import gen_op as g_o
-from ekobox import gen_theory as g_t
+from ekobox import theory_card as tc
 
 op = g_o.gen_op_card(
     [100.0],
@@ -15,7 +15,7 @@
         "configs": {"interpolation_polynomial_degree": 1},
     },
 )
-theory = g_t.gen_theory_card(0, 1.65)
+theory = tc.generate(0, 1.65)
 
 
 def test_evolve_pdfs_run(fake_lhapdf, cd):
diff --git a/tests/ekobox/test_info_file.py b/tests/ekobox/test_info_file.py
index 68d3e3dfc..109983af4 100644
--- a/tests/ekobox/test_info_file.py
+++ b/tests/ekobox/test_info_file.py
@@ -4,13 +4,13 @@
 import numpy as np
 
 from ekobox import gen_op as g_o
-from ekobox import gen_theory as g_t
 from ekobox import info_file
+from ekobox import theory_card as tc
 
 
 def test_build():
     op = g_o.gen_op_card([10, 100])
-    theory = g_t.gen_theory_card(1, 10.0, update={"alphas": 0.2})
+    theory = tc.generate(1, 10.0, update={"alphas": 0.2})
     info = info_file.build(
         theory, op, 4, info_update={"SetDesc": "Prova", "NewArg": 15.3, "MTop": 1.0}
     )
diff --git a/tests/ekobox/test_gen_theory.py b/tests/ekobox/test_theory_card.py
similarity index 52%
rename from tests/ekobox/test_gen_theory.py
rename to tests/ekobox/test_theory_card.py
index 468b3c401..322a01e95 100644
--- a/tests/ekobox/test_gen_theory.py
+++ b/tests/ekobox/test_theory_card.py
@@ -1,28 +1,28 @@
 # -*- coding: utf-8 -*-
 import pytest
 
-from ekobox import gen_theory as g_t
+from ekobox import theory_card as tc
 
 
 def test_gen_theory_card():
-    theory = g_t.gen_theory_card(0, 1.0)
+    theory = tc.generate(0, 1.0)
     assert theory["PTO"] == 0
     assert theory["Q0"] == 1.0
     assert theory["mt"] == 173.07
     up_err = {"Prova": "Prova"}
     with pytest.raises(ValueError):
-        theory = g_t.gen_theory_card(0, 1.0, update=up_err)
+        theory = tc.generate(0, 1.0, update=up_err)
     up = {"mb": 132.3, "PTO": 2}
-    theory = g_t.gen_theory_card(0, 1.0, update=up)
+    theory = tc.generate(0, 1.0, update=up)
     assert theory["PTO"] == 2
     assert theory["mb"] == 132.3
 
 
 def test_export_load_theory_card(tmp_path, cd):
     with cd(tmp_path):
-        theory = g_t.gen_theory_card(2, 12.3, name="debug_theory")
-        g_t.export_theory_card("debug_theory_two", theory)
-        theory_loaded = g_t.import_theory_card("debug_theory.yaml")
-        theory_two_loaded = g_t.import_theory_card("debug_theory_two.yaml")
+        theory = tc.generate(2, 12.3, name="debug_theory")
+        tc.dump("debug_theory_two", theory)
+        theory_loaded = tc.load("debug_theory.yaml")
+        theory_two_loaded = tc.load("debug_theory_two.yaml")
         for key in theory.keys():
             assert theory[key] == theory_loaded[key] == theory_two_loaded[key]
diff --git a/tests/ekobox/test_utils.py b/tests/ekobox/test_utils.py
index a85606da9..001ec0c68 100644
--- a/tests/ekobox/test_utils.py
+++ b/tests/ekobox/test_utils.py
@@ -4,7 +4,7 @@
 
 import eko
 from ekobox import gen_op as g_o
-from ekobox import gen_theory as g_t
+from ekobox import theory_card as tc
 from ekobox import utils
 
 
@@ -17,7 +17,7 @@ def test_ekos_product():
             "configs": {"interpolation_polynomial_degree": 1},
         },
     )
-    theory1 = g_t.gen_theory_card(0, 5.0)
+    theory1 = tc.generate(0, 5.0)
 
     op2 = g_o.gen_op_card(
         [80.0, 100.0, 120.0],
@@ -26,8 +26,8 @@ def test_ekos_product():
             "configs": {"interpolation_polynomial_degree": 1},
         },
     )
-    theory2 = g_t.gen_theory_card(0, 10.0)
-    theory_err = g_t.gen_theory_card(0, 5.0)
+    theory2 = tc.generate(0, 10.0)
+    theory_err = tc.generate(0, 5.0)
 
     eko_ini = eko.run_dglap(theory1, op1)
     eko_fin = eko.run_dglap(theory2, op2)

From dcf29c99379fbb14f89f38b09d0640efe7c26051 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 24 Mar 2022 11:08:55 +0100
Subject: [PATCH 045/148] Rename gen_op

---
 benchmarks/ekobox/benchmark_evol_pdf.py       |  6 +--
 src/ekobox/__init__.py                        |  2 +-
 src/ekobox/{gen_op.py => operators_card.py}   | 49 +++++++++----------
 tests/ekobox/test_evol_pdf.py                 |  4 +-
 tests/ekobox/test_info_file.py                |  4 +-
 ...{test_gen_op.py => test_operators_card.py} | 20 ++++----
 tests/ekobox/test_theory_card.py              |  4 +-
 tests/ekobox/test_utils.py                    |  6 +--
 8 files changed, 47 insertions(+), 48 deletions(-)
 rename src/ekobox/{gen_op.py => operators_card.py} (65%)
 rename tests/ekobox/{test_gen_op.py => test_operators_card.py} (56%)

diff --git a/benchmarks/ekobox/benchmark_evol_pdf.py b/benchmarks/ekobox/benchmark_evol_pdf.py
index d2b2cd724..1b0c13d26 100644
--- a/benchmarks/ekobox/benchmark_evol_pdf.py
+++ b/benchmarks/ekobox/benchmark_evol_pdf.py
@@ -6,7 +6,7 @@
 
 from eko import basis_rotation as br
 from ekobox import evol_pdf as ev_p
-from ekobox import gen_op as g_o
+from ekobox import operators_card as oc
 from ekobox import theory_card as tc
 from ekobox.genpdf import load
 
@@ -21,7 +21,7 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
         100.0,
         10000.0,
     ]
-    op = g_o.gen_op_card(q2grid)
+    op = oc.generate(q2grid)
     theory = tc.generate(
         0,
         5.0,
@@ -79,7 +79,7 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
 
 @pytest.mark.isolated
 def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
-    op = g_o.gen_op_card([10, 100], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
+    op = oc.generate([10, 100], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
     theory = tc.generate(0, 1.0)
     with lhapdf_path(test_pdf):
         pdfs = lhapdf.mkPDFs("myMSTW2008nlo90cl")
diff --git a/src/ekobox/__init__.py b/src/ekobox/__init__.py
index 93c2e4e73..3a140e99a 100644
--- a/src/ekobox/__init__.py
+++ b/src/ekobox/__init__.py
@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 from ekomark import apply
 
-from . import evol_pdf, gen_op, info_file, theory_card
+from . import evol_pdf, info_file, operators_card, theory_card
diff --git a/src/ekobox/gen_op.py b/src/ekobox/operators_card.py
similarity index 65%
rename from src/ekobox/gen_op.py
rename to src/ekobox/operators_card.py
index 6ce7d9034..b11b1f455 100644
--- a/src/ekobox/gen_op.py
+++ b/src/ekobox/operators_card.py
@@ -7,27 +7,27 @@
 from ekomark.data import operators
 
 
-def gen_op_card(Q2grid, update=None, name=None):
-    """Generate operators card.
+def generate(Q2grid, update=None, name=None):
+    """
+    Generate operators card.
 
-    Generates an operator card with some mandatory user choice
+    Generates an operators card with some mandatory user choice
     (in this case only the Q2 grid) and some default values which
     can be changed by the update input dict.
 
     Parameters
     ----------
-    Q2grid : list(float)
-        grid for Q2
-    update : dict
-        dictionary of info to update in op. card
-    name : str
-        name of exported op.card (if name not None)
+        Q2grid : list(float)
+            grid for Q2
+        update : dict
+            dictionary of info to update in op. card
+        name : str
+            name of exported op.card (if name not None)
 
     Returns
     -------
-    dict
-        operator card
-
+        dict :
+            operators card
     """
     # Constructing the dictionary with some default value
     def_op = copy.deepcopy(operators.default_card)
@@ -46,40 +46,39 @@ def gen_op_card(Q2grid, update=None, name=None):
     serialized = sql.serialize(def_op)
     def_op["hash"] = (sql.add_hash(serialized))[-1]
     if name is not None:
-        export_op_card(name, def_op)
+        dump(name, def_op)
     return def_op
 
 
-def export_op_card(name, op):
-    """Export the operators card in the current directory
+def dump(name, op):
+    """
+    Export the operators card in the current directory
 
     Parameters
     ----------
-    name : str
-        name of the op. card to export
-
-    op : dict
-        op card
-
+        name : str
+            name of the operators card to export
+        op : dict
+            operators card
     """
     target = f"{name}.yaml"
     with open(target, "w", encoding="utf-8") as out:
         yaml.safe_dump(op, out)
 
 
-def import_op_card(path):
+def load(path):
     """
     Import the operators card specified by path
 
     Parameters
     ----------
         path : str
-            path to op. card in yaml format
+            path to operators card in yaml format
 
     Returns
     -------
-        : dict
-            op card
+        dict :
+            operators card
     """
     with open(path, "r", encoding="utf-8") as o:
         op = yaml.safe_load(o)
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index f69ef5258..fc833cd90 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -5,10 +5,10 @@
 import eko
 import eko.output.legacy as out
 from ekobox import evol_pdf as ev_p
-from ekobox import gen_op as g_o
+from ekobox import operators_card as oc
 from ekobox import theory_card as tc
 
-op = g_o.gen_op_card(
+op = oc.generate(
     [100.0],
     update={
         "xgrid": [0.1, 0.5, 1.0],
diff --git a/tests/ekobox/test_info_file.py b/tests/ekobox/test_info_file.py
index 109983af4..643d02745 100644
--- a/tests/ekobox/test_info_file.py
+++ b/tests/ekobox/test_info_file.py
@@ -3,13 +3,13 @@
 
 import numpy as np
 
-from ekobox import gen_op as g_o
 from ekobox import info_file
+from ekobox import operators_card as oc
 from ekobox import theory_card as tc
 
 
 def test_build():
-    op = g_o.gen_op_card([10, 100])
+    op = oc.generate([10, 100])
     theory = tc.generate(1, 10.0, update={"alphas": 0.2})
     info = info_file.build(
         theory, op, 4, info_update={"SetDesc": "Prova", "NewArg": 15.3, "MTop": 1.0}
diff --git a/tests/ekobox/test_gen_op.py b/tests/ekobox/test_operators_card.py
similarity index 56%
rename from tests/ekobox/test_gen_op.py
rename to tests/ekobox/test_operators_card.py
index bc0821d26..de196191c 100644
--- a/tests/ekobox/test_gen_op.py
+++ b/tests/ekobox/test_operators_card.py
@@ -1,30 +1,30 @@
 # -*- coding: utf-8 -*-
 import pytest
 
-from ekobox import gen_op as g_o
+from ekobox import operators_card as oc
 
 
-def test_gen_op_card():
-    op = g_o.gen_op_card([10, 100])
+def test_generate_ocard():
+    op = oc.generate([10, 100])
     assert op["Q2grid"] == [10, 100]
     assert op["configs"]["interpolation_polynomial_degree"] == 4
     up_err = {"Prova": "Prova"}
     with pytest.raises(ValueError):
-        op = g_o.gen_op_card([10], update=up_err)
+        op = oc.generate([10], update=up_err)
     up = {
         "configs": {"interpolation_polynomial_degree": 2, "interpolation_is_log": False}
     }
-    op = g_o.gen_op_card([100], update=up)
+    op = oc.generate([100], update=up)
     assert op["Q2grid"] == [100]
     assert op["configs"]["interpolation_polynomial_degree"] == 2
     assert op["configs"]["interpolation_is_log"] is False
 
 
-def test_export_load_op_card(tmp_path, cd):
+def test_dump_load_op_card(tmp_path, cd):
     with cd(tmp_path):
-        op = g_o.gen_op_card([100], name="debug_op")
-        g_o.export_op_card("debug_op_two", op)
-        op_loaded = g_o.import_op_card("debug_op.yaml")
-        op_two_loaded = g_o.import_op_card("debug_op_two.yaml")
+        op = oc.generate([100], name="debug_op")
+        oc.dump("debug_op_two", op)
+        op_loaded = oc.load("debug_op.yaml")
+        op_two_loaded = oc.load("debug_op_two.yaml")
         for key in op.keys():
             assert op[key] == op_loaded[key] == op_two_loaded[key]
diff --git a/tests/ekobox/test_theory_card.py b/tests/ekobox/test_theory_card.py
index 322a01e95..7b1f55ead 100644
--- a/tests/ekobox/test_theory_card.py
+++ b/tests/ekobox/test_theory_card.py
@@ -4,7 +4,7 @@
 from ekobox import theory_card as tc
 
 
-def test_gen_theory_card():
+def test_generate_theory_card():
     theory = tc.generate(0, 1.0)
     assert theory["PTO"] == 0
     assert theory["Q0"] == 1.0
@@ -18,7 +18,7 @@ def test_gen_theory_card():
     assert theory["mb"] == 132.3
 
 
-def test_export_load_theory_card(tmp_path, cd):
+def test_dump_load_theory_card(tmp_path, cd):
     with cd(tmp_path):
         theory = tc.generate(2, 12.3, name="debug_theory")
         tc.dump("debug_theory_two", theory)
diff --git a/tests/ekobox/test_utils.py b/tests/ekobox/test_utils.py
index 001ec0c68..ccf6198be 100644
--- a/tests/ekobox/test_utils.py
+++ b/tests/ekobox/test_utils.py
@@ -3,14 +3,14 @@
 import pytest
 
 import eko
-from ekobox import gen_op as g_o
+from ekobox import operators_card as oc
 from ekobox import theory_card as tc
 from ekobox import utils
 
 
 def test_ekos_product():
     # Generating two ekos
-    op1 = g_o.gen_op_card(
+    op1 = oc.generate(
         [60.0, 80.0, 100.0],
         update={
             "xgrid": [0.1, 0.5, 1.0],
@@ -19,7 +19,7 @@ def test_ekos_product():
     )
     theory1 = tc.generate(0, 5.0)
 
-    op2 = g_o.gen_op_card(
+    op2 = oc.generate(
         [80.0, 100.0, 120.0],
         update={
             "xgrid": [0.1, 0.5, 1.0],

From 0d7c49181feaf69f6f0429aca2f8f4b841f64108 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 25 Mar 2022 14:52:09 +0100
Subject: [PATCH 046/148] Apply some review suggestions

---
 src/eko/member.py             |  2 +-
 src/ekobox/evol_pdf.py        | 15 +++++++++++++++
 src/ekobox/genpdf/__init__.py |  2 +-
 src/ekobox/genpdf/load.py     |  2 +-
 src/ekobox/info_file.py       |  2 +-
 src/ekobox/operators_card.py  |  4 ++--
 src/ekobox/theory_card.py     |  4 ++--
 7 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/src/eko/member.py b/src/eko/member.py
index e9f3b4576..f97c8cca1 100644
--- a/src/eko/member.py
+++ b/src/eko/member.py
@@ -243,7 +243,7 @@ def operator_multiply(left, right, operation):
 
         Returns
         -------
-            dict :
+            dict
                 new operator members dictionary
         """
         # prepare paths
diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index 55c622777..8504c2462 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -96,4 +96,19 @@ def evolve_pdfs(
 
 
 def ekofileid(theory_card, operators_card):
+    """
+    Return a common filename composed by the hashes.
+
+    Parameters
+    ----------
+    theory_card : dict
+        theory card
+    operators_card : dict
+        operators card
+
+    Returns
+    -------
+    str
+        file name
+    """
     return f"o{operators_card['hash'][:6]}_t{theory_card['hash'][:6]}.tar"
diff --git a/src/ekobox/genpdf/__init__.py b/src/ekobox/genpdf/__init__.py
index ebaf696b1..4df6caf96 100644
--- a/src/ekobox/genpdf/__init__.py
+++ b/src/ekobox/genpdf/__init__.py
@@ -239,7 +239,7 @@ def generate_block(xfxQ2, xgrid, Q2grid, pids):
 
     Returns
     -------
-        dict :
+        dict
             PDF block
     """
     block = dict(Q2grid=Q2grid, pids=pids, xgrid=xgrid)
diff --git a/src/ekobox/genpdf/load.py b/src/ekobox/genpdf/load.py
index f52f8b0e3..de5322288 100644
--- a/src/ekobox/genpdf/load.py
+++ b/src/ekobox/genpdf/load.py
@@ -23,7 +23,7 @@ def load_info_from_file(pdfset_name):
 
     Returns
     -------
-        dict :
+        dict
             info dictionary
     """
     import lhapdf  # pylint: disable=import-error, import-outside-toplevel
diff --git a/src/ekobox/info_file.py b/src/ekobox/info_file.py
index 626b52b67..668ffdd5c 100644
--- a/src/ekobox/info_file.py
+++ b/src/ekobox/info_file.py
@@ -22,7 +22,7 @@ def build(theory_card, operators_card, num_members, info_update):
 
     Returns
     -------
-        dict :
+        dict
             info file in lhapdf format
     """
     template_info = copy.deepcopy(load.template_info)
diff --git a/src/ekobox/operators_card.py b/src/ekobox/operators_card.py
index b11b1f455..49de99240 100644
--- a/src/ekobox/operators_card.py
+++ b/src/ekobox/operators_card.py
@@ -26,7 +26,7 @@ def generate(Q2grid, update=None, name=None):
 
     Returns
     -------
-        dict :
+        dict
             operators card
     """
     # Constructing the dictionary with some default value
@@ -77,7 +77,7 @@ def load(path):
 
     Returns
     -------
-        dict :
+        dict
             operators card
     """
     with open(path, "r", encoding="utf-8") as o:
diff --git a/src/ekobox/theory_card.py b/src/ekobox/theory_card.py
index ee9c71c3c..76118a3c9 100644
--- a/src/ekobox/theory_card.py
+++ b/src/ekobox/theory_card.py
@@ -23,7 +23,7 @@ def generate(pto, initial_scale, update=None, name=None):
 
     Returns
     -------
-        dict :
+        dict
             theory card
     """
     # Constructing the dictionary with some default values
@@ -72,7 +72,7 @@ def load(path):
 
     Returns
     -------
-        dict :
+        dict
             theory card
     """
     with open(path, "r", encoding="utf-8") as o:

From 0b1be6d9c7f08d934777d573a49e0b03fdd2754b Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 1 Apr 2022 11:31:40 +0200
Subject: [PATCH 047/148] Remove bleeding edge type declaration syntax

---
 src/eko/runcards.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/eko/runcards.py b/src/eko/runcards.py
index e93fecc89..b9be63c4c 100644
--- a/src/eko/runcards.py
+++ b/src/eko/runcards.py
@@ -9,4 +9,4 @@ class TheoryCard:
 
 @dataclass
 class OperatorCard:
-    xgrid: list[float]
+    xgrid: list

From f2f12b81a7a417df48745e1b3f0954e1ad082970 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 5 Apr 2022 19:01:19 +0200
Subject: [PATCH 048/148] Add typing, progress on benchmark failure

---
 src/eko/output/legacy.py     | 87 +++++++++++++++++++++---------------
 src/eko/output/manipulate.py |  1 +
 src/eko/runner.py            |  3 +-
 3 files changed, 53 insertions(+), 38 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index deefa7fd7..ec3cc9418 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -1,9 +1,11 @@
 # -*- coding: utf-8 -*-
 import dataclasses
 import io
+import os
 import pathlib
 import tarfile
 import tempfile
+from typing import Optional, TextIO, Union
 
 import lz4.frame
 import numpy as np
@@ -13,9 +15,8 @@
 from . import struct
 
 
-def get_raw(eko, binarize=True, skip_q2_grid=False):
-    """
-    Serialize result as dict/YAML.
+def get_raw(eko: struct.EKO, binarize: bool = True, skip_q2_grid: bool = False):
+    """Serialize result as dict/YAML.
 
     This maps the original numpy matrices to lists.
 
@@ -56,66 +57,76 @@ def get_raw(eko, binarize=True, skip_q2_grid=False):
     return out
 
 
-def dump_yaml(obj, stream=None, binarize=True, skip_q2_grid=False):
-    """
-    Serialize result as YAML.
+def dump_yaml(
+    obj: struct.EKO,
+    stream: Optional[TextIO] = None,
+    binarize: bool = True,
+    skip_q2_grid: bool = False,
+):
+    """Serialize result as YAML.
 
     Parameters
     ----------
-        stream : None or stream
-            if given, dump is written on it
-        binarize : bool
-            dump in binary format (instead of list format)
-        skip_q2_grid : bool
-            avoid dumping Q2grid (i.e. the actual operators) into the yaml
-            file (default: ``False``)
+    stream : None or stream
+        if given, dump is written on it
+    binarize : bool
+        dump in binary format (instead of list format)
+    skip_q2_grid : bool
+        avoid dumping Q2grid (i.e. the actual operators) into the yaml
+        file (default: ``False``)
 
     Returns
     -------
-        dump : any
-            result of dump(output, stream), i.e. a string, if no stream is given or
-            Null, if written successfully to stream
+    dump : any
+        result of dump(output, stream), i.e. a string, if no stream is given or
+        Null, if written successfully to stream
+
     """
     # TODO explicitly silence yaml
     out = get_raw(obj, binarize, skip_q2_grid=skip_q2_grid)
     return yaml.dump(out, stream)
 
 
-def dump_yaml_to_file(obj, filename, binarize=True, skip_q2_grid=False):
-    """
-    Writes YAML representation to a file.
+def dump_yaml_to_file(
+    obj: struct.EKO,
+    filename: Union[str, os.PathLike],
+    binarize: bool = True,
+    skip_q2_grid: bool = False,
+):
+    """Writes YAML representation to a file.
 
     Parameters
     ----------
-        filename : str
-            target file name
-        binarize : bool
-            dump in binary format (instead of list format)
-        skip_q2_grid : bool
-            avoid dumping Q2grid (i.e. the actual operators) into the yaml
-            file (default: ``False``)
+    filename : str
+        target file name
+    binarize : bool
+        dump in binary format (instead of list format)
+    skip_q2_grid : bool
+        avoid dumping Q2grid (i.e. the actual operators) into the yaml
+        file (default: ``False``)
 
     Returns
     -------
-        ret : any
-            result of dump(output, stream), i.e. Null if written successfully
+    ret : any
+        result of dump(output, stream), i.e. Null if written successfully
+
     """
     with open(filename, "w", encoding="utf-8") as f:
         ret = dump_yaml(obj, f, binarize, skip_q2_grid=skip_q2_grid)
     return ret
 
 
-def dump_tar(obj, tarname):
-    """
-    Writes representation into a tar archive containing:
+def dump_tar(obj: struct.EKO, tarname: Union[str, os.PathLike]):
+    """Writes representation into a tar archive containing:
 
     - metadata (in YAML)
     - operator (in numpy ``.npy`` format)
 
     Parameters
     ----------
-        tarname : str
-            target file name
+    tarname : str
+        target file name
+
     """
     tarpath = pathlib.Path(tarname)
     if tarpath.suffix != ".tar":
@@ -150,13 +161,13 @@ def dump_tar(obj, tarname):
             tar.add(tmpdir, arcname=tarpath.stem)
 
 
-def load_yaml(stream, skip_q2_grid=False):
+def load_yaml(stream: TextIO, skip_q2_grid=False) -> struct.EKO:
     """
     Load YAML representation from stream
 
     Parameters
     ----------
-        stream : any
+        stream : TextIO
             source stream
         skip_q2_grid : bool
             avoid loading Q2grid (i.e. the actual operators) from the yaml
@@ -190,7 +201,9 @@ def load_yaml(stream, skip_q2_grid=False):
     return struct.EKO.from_dict(obj)
 
 
-def load_yaml_from_file(filename, skip_q2_grid=False):
+def load_yaml_from_file(
+    filename: Union[str, os.PathLike], skip_q2_grid: bool = False
+) -> struct.EKO:
     """
     Load YAML representation from file
 
@@ -213,7 +226,7 @@ def load_yaml_from_file(filename, skip_q2_grid=False):
     return obj
 
 
-def load_tar(tarname):
+def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
     """
     Load tar representation from file (compliant with :meth:`dump_tar`
     output).
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index f9e8b14cb..0f78496e9 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -23,6 +23,7 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
         inputgrid : None or list
             xgrid for the input
     """
+    __import__("pdb").set_trace()
     # calling with no arguments is an error
     if targetgrid is None and inputgrid is None:
         raise ValueError("Nor inputgrid nor targetgrid was given")
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 7947eebea..76f2fec8a 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -82,7 +82,7 @@ def __init__(self, theory_card, operators_card):
 
         self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref), **operators_card))
 
-    def get_output(self):
+    def get_output(self) -> EKO:
         """
         Collects all data for output (to run the evolution)
 
@@ -97,6 +97,7 @@ def get_output(self):
         self.out.rotations.inputgrid = self.out.xgrid.grid
         self.out.rotations.targetgrid = self.out.xgrid.grid
         for final_scale, op in self.op_grid.compute().items():
+            __import__("pdb").set_trace()
             self.out[float(final_scale)] = op
 
         # reshape xgrid

From 5d4aab21f23724526d92c109edccabf551fdbc33 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 13:04:57 +0200
Subject: [PATCH 049/148] Simplify and update runner layout

---
 src/eko/output/manipulate.py | 19 +++++++--
 src/eko/output/struct.py     | 50 ++++++++++++++++++----
 src/eko/runner.py            | 81 +++++++++++++++---------------------
 tests/conftest.py            |  1 +
 4 files changed, 93 insertions(+), 58 deletions(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 0f78496e9..cba8409fb 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -1,16 +1,23 @@
 # -*- coding: utf-8 -*-
 import logging
 import warnings
+from typing import Optional
 
 import numpy as np
 
 from .. import basis_rotation as br
 from .. import interpolation
+from .struct import EKO
 
 logger = logging.getLogger(__name__)
 
 
-def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
+def xgrid_reshape(
+    eko: EKO,
+    targetgrid: Optional[np.ndarray] = None,
+    inputgrid: Optional[np.ndarray] = None,
+    inplace: bool = True,
+):
     """
     Changes the operators to have in the output targetgrid and/or in the input inputgrid.
 
@@ -23,7 +30,6 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
         inputgrid : None or list
             xgrid for the input
     """
-    __import__("pdb").set_trace()
     # calling with no arguments is an error
     if targetgrid is None and inputgrid is None:
         raise ValueError("Nor inputgrid nor targetgrid was given")
@@ -86,7 +92,12 @@ def xgrid_reshape(eko, targetgrid=None, inputgrid=None, inplace=True):
         elem.error = errs
 
 
-def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
+def flavor_reshape(
+    eko: EKO,
+    targetbasis: Optional[np.ndarray] = None,
+    inputbasis: Optional[np.ndarray] = None,
+    inplace: bool = True,
+):
     """
     Changes the operators to have in the output targetbasis and/or in the input inputbasis.
 
@@ -147,7 +158,7 @@ def flavor_reshape(eko, targetbasis=None, inputbasis=None, inplace=True):
         eko.rotations.targetpids = [0] * len(eko.rotations.targetpids)
 
 
-def to_evol(eko, source=True, target=False, inplace=True):
+def to_evol(eko: EKO, source: bool = True, target: bool = False, inplace: bool = True):
     """
     Rotate the operator into evolution basis.
 
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 021344763..b6db7ff0b 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -4,6 +4,7 @@
 
 import numpy as np
 
+from .. import basis_rotation as br
 from .. import interpolation
 from .. import version as vmod
 
@@ -64,6 +65,12 @@ class Rotations(DictLike):
     targetpids: Optional[np.ndarray] = None
     inputpids: Optional[np.ndarray] = None
 
+    @classmethod
+    def default(cls, xgrid: interpolation.XGrid, pids: np.ndarray):
+        return cls(
+            targetgrid=xgrid.raw, inputgrid=xgrid.raw, targetpids=pids, inputpids=pids
+        )
+
 
 @dataclass
 class EKO:
@@ -78,6 +85,7 @@ class EKO:
     configs: Configs
     rotations: Rotations
     debug: Debug
+    pids: np.ndarray = np.array(br.flavor_basis_pids)
     version: str = vmod.__version__
     data_version: str = vmod.__data_version__
 
@@ -107,14 +115,42 @@ def Q2grid(self):
         return np.array(list(self._operators))
 
     @classmethod
-    def from_dict(cls, dictionary):
+    def from_dict(cls, runcard: dict):
+        """Make structure from runcard-like dictionary.
+
+        This constructor is made to be used with loaded runcards, in order to
+        minimize the amount of code needed to init a new object (you just to
+        load the runcard and call this function).
+
+        Note
+        ----
+        An object is initialized with no rotations, since the role of rotations
+        is to keep the current state of the output object after manipulations
+        happened.
+        Since a new object is here in the process of being created, no rotation
+        has to be logged.
+
+        Parameters
+        ----------
+        runcard : dict
+            a dictionary containing the runcard's content
+
+        Returns
+        -------
+        EKO
+            the generated structure
+
+        """
+        xgrid = interpolation.XGrid(runcard["xgrid"])
+        pids = runcard.get("pids", cls.pids)
         return cls(
-            xgrid=interpolation.XGrid(dictionary["xgrid"]),
-            Q02=dictionary["Q0"] ** 2,
-            _operators={q2: None for q2 in dictionary["Q2grid"]},
-            configs=Configs.from_dict(dictionary["configs"]),
-            rotations=Rotations.from_dict(dictionary.get("rotations", {})),
-            debug=Debug.from_dict(dictionary.get("debug", {})),
+            xgrid=xgrid,
+            pids=pids,
+            Q02=runcard["Q0"] ** 2,
+            _operators={q2: None for q2 in runcard["Q2grid"]},
+            configs=Configs.from_dict(runcard["configs"]),
+            rotations=Rotations.default(xgrid, pids),
+            debug=Debug.from_dict(runcard.get("debug", {})),
         )
 
     @classmethod
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 76f2fec8a..69128b578 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -4,14 +4,15 @@
 """
 import copy
 import logging
+from typing import Optional
 
 import numpy as np
 
-from . import basis_rotation as br
 from . import compatibility, interpolation, msbar_masses
 from .couplings import Couplings
 from .evolution_operator.grid import OperatorGrid
 from .output import EKO, manipulate
+from .output.struct import Rotations
 from .thresholds import ThresholdsAtlas
 
 logger = logging.getLogger(__name__)
@@ -39,7 +40,7 @@ class Runner:
 o888ooooood8 o888o  o888o     `Y8bood8P'
 """
 
-    def __init__(self, theory_card, operators_card):
+    def __init__(self, theory_card: dict, operators_card: dict):
         self.out = EKO()
 
         new_theory, new_operators = compatibility.update(theory_card, operators_card)
@@ -59,72 +60,58 @@ def __init__(self, theory_card, operators_card):
         # strong coupling
         sc = Couplings.from_dict(new_theory, masses=masses)
         # setup operator grid
-        self.op_grid = OperatorGrid.from_dict(
-            new_theory,
-            new_operators,
-            tc,
-            sc,
-            bfd,
-        )
+        self.op_grid = OperatorGrid.from_dict(new_theory, new_operators, tc, sc, bfd)
 
+        # save bases manipulations for a post processing step
         rot = operators_card.get("rotations", {})
-        self.post_process = dict(
-            inputgrid=rot.get("inputgrid", bfd.xgrid.raw),
-            targetgrid=rot.get("targetgrid", bfd.xgrid.raw),
-            inputbasis=rot.get("inputbasis"),
-            targetbasis=rot.get("targetbasis"),
-        )
-
-        if "rotations" not in operators_card:
-            operators_card["rotations"] = {}
-        operators_card["rotations"]["inputgrid"] = bfd.xgrid.raw
-        operators_card["rotations"]["targetgrid"] = bfd.xgrid.raw
+        self.post_process = {
+            key: rot.get(key, None)
+            for key in ("inputgrid", "targetgrid", "inputpids", "targetpids")
+        }
 
         self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref), **operators_card))
 
     def get_output(self) -> EKO:
-        """
-        Collects all data for output (to run the evolution)
+        """Run evolution and generate output operator.
+
+        Two steps are applied sequentially:
+
+        1. evolution is performed, computing the evolution operator in an
+           internal flavor and x-space basis
+        2. bases manipulations specified in the runcard are applied
 
         Returns
         -------
-            ret : eko.output.EKO
-                output instance
+        EKO
+            output instance
+
         """
         # add all operators
-        self.out.rotations.inputpids = np.array(br.flavor_basis_pids)
-        self.out.rotations.targetpids = np.array(br.flavor_basis_pids)
-        self.out.rotations.inputgrid = self.out.xgrid.grid
-        self.out.rotations.targetgrid = self.out.xgrid.grid
         for final_scale, op in self.op_grid.compute().items():
-            __import__("pdb").set_trace()
             self.out[float(final_scale)] = op
 
+        def similar_to_none(name: str) -> Optional[np.ndarray]:
+            grid = self.post_process[name]
+
+            if grid is None or np.allclose(grid, getattr(Rotations, name), atol=1e-12):
+                return None
+
+            return np.array(grid)
+
         # reshape xgrid
-        inputgrid = (
-            self.post_process["inputgrid"]
-            if self.post_process["inputgrid"] is not self.out.xgrid.grid
-            else None
-        )
-        targetgrid = (
-            self.post_process["targetgrid"]
-            if self.post_process["targetgrid"] is not self.out.xgrid.grid
-            else None
-        )
+        inputgrid = similar_to_none("inputgrid")
+        targetgrid = similar_to_none("targetgrid")
         if inputgrid is not None or targetgrid is not None:
             manipulate.xgrid_reshape(
                 self.out, targetgrid=targetgrid, inputgrid=inputgrid
             )
 
         # reshape flavors
-        inputbasis = self.post_process["inputbasis"]
-        if inputbasis is not None:
-            inputbasis = np.array(inputbasis)
-        targetbasis = self.post_process["targetbasis"]
-        if targetbasis is not None:
-            targetbasis = np.array(targetbasis)
-        if inputbasis is not None or targetbasis is not None:
+        inputpids = similar_to_none("inputpids")
+        targetpids = similar_to_none("targetpids")
+        if inputpids is not None or targetpids is not None:
             manipulate.flavor_reshape(
-                self.out, targetbasis=targetbasis, inputbasis=inputbasis
+                self.out, targetbasis=targetpids, inputbasis=inputpids
             )
+
         return copy.deepcopy(self.out)
diff --git a/tests/conftest.py b/tests/conftest.py
index 4969506dd..37fb098b2 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -65,6 +65,7 @@ def fake_output(self):
         Q2grid = self.mk_g([q2_out], len(pids), len(xgrid))
         d = dict(
             xgrid=xgrid,
+            pids=pids,
             rotations=dict(
                 targetgrid=xgrid,
                 inputgrid=xgrid,

From ad6366f8d9f063845ee246f28c448729d0b34fbf Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 18 Jul 2022 13:05:40 +0200
Subject: [PATCH 050/148] Check grids sizes before comparison

---
 src/eko/runner.py | 6 ++++--
 tests/conftest.py | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/eko/runner.py b/src/eko/runner.py
index 69128b578..ac3483eef 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -12,7 +12,6 @@
 from .couplings import Couplings
 from .evolution_operator.grid import OperatorGrid
 from .output import EKO, manipulate
-from .output.struct import Rotations
 from .thresholds import ThresholdsAtlas
 
 logger = logging.getLogger(__name__)
@@ -93,7 +92,10 @@ def get_output(self) -> EKO:
         def similar_to_none(name: str) -> Optional[np.ndarray]:
             grid = self.post_process[name]
 
-            if grid is None or np.allclose(grid, getattr(Rotations, name), atol=1e-12):
+            default = self.out.xgrid.grid if "grid" in name else self.out.pids
+            if grid is None or (
+                len(grid) == default.size and np.allclose(grid, default, atol=1e-12)
+            ):
                 return None
 
             return np.array(grid)
diff --git a/tests/conftest.py b/tests/conftest.py
index 37fb098b2..70c08000c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -11,7 +11,7 @@
 
 @pytest.fixture
 def cd():
-    # thanks https://stackoverflow.com/questions/431684/how-do-i-change-the-working-directory-in-python/24176022#24176022
+    # thanks https://stackoverflow.com/a/24176022/8653979
     @contextmanager
     def wrapped(newdir):
         prevdir = os.getcwd()

From 976faefc245ce1fbb519a59d4f75676dfcccd071 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 7 Apr 2022 17:59:02 +0200
Subject: [PATCH 051/148] Combine ekos with chosen precision

---
 src/eko/output/struct.py | 10 ++++++++++
 src/ekobox/utils.py      | 16 +++++++++++-----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index b6db7ff0b..f1578bf95 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -114,6 +114,16 @@ def items(self):
     def Q2grid(self):
         return np.array(list(self._operators))
 
+    def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
+        q2s = self.Q2grid
+        close = q2s[np.isclose(q2, q2s, rtol=rtol, atol=atol)]
+
+        if close.size == 1:
+            return close[0]
+        if close.size == 0:
+            return None
+        raise ValueError(f"Multiple values of Q2 have been found close to {q2}")
+
     @classmethod
     def from_dict(cls, runcard: dict):
         """Make structure from runcard-like dictionary.
diff --git a/src/ekobox/utils.py b/src/ekobox/utils.py
index 6538a59d1..9fb66d3a9 100644
--- a/src/ekobox/utils.py
+++ b/src/ekobox/utils.py
@@ -8,7 +8,9 @@
 
 # TODO: add a control on the theory (but before we need to implement another
 # kind of output which includes the theory and operator runcards)
-def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
+def ekos_product(
+    eko_ini: EKO, eko_fin: EKO, rtol: float = 1e-6, atol: float = 1e-10, in_place=True
+) -> EKO:
     """Returns the product of two ekos
 
     Parameters
@@ -17,6 +19,10 @@ def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
         initial eko operator
     eko_fin : eko.output.Output
         final eko operator
+    rtol : float
+        relative tolerance on Q2, used to check compatibility
+    atol : float
+        absolute tolerance on Q2, used to check compatibility
     in_place : bool
         do operation in place, modifying input arrays
 
@@ -26,14 +32,14 @@ def ekos_product(eko_ini: EKO, eko_fin: EKO, in_place=True) -> EKO:
         eko operator
 
     """
-    # TODO: check if it's close, instead of checking identity
-    if eko_fin.Q02 not in eko_ini.Q2grid:
+    q2match = eko_ini.approx(eko_fin.Q02, rtol=rtol, atol=atol)
+    if q2match is None:
         raise ValueError(
             "Initial Q2 of final eko operator does not match any final Q2 in"
             " the initial eko operator"
         )
-    ope1 = eko_ini[eko_fin.Q02].operator.copy()
-    ope1_error = eko_ini[eko_fin.Q02].error.copy()
+    ope1 = eko_ini[q2match].operator.copy()
+    ope1_error = eko_ini[q2match].error.copy()
 
     ope2_dict = {}
     ope2_error_dict = {}

From 8157ea86f427a624cda3b62b428e035d26be5a4e Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 7 Apr 2022 17:59:40 +0200
Subject: [PATCH 052/148] Remove annotation about improving deprecated
 interface

---
 src/eko/output/legacy.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index ec3cc9418..28eae1895 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -82,7 +82,6 @@ def dump_yaml(
         Null, if written successfully to stream
 
     """
-    # TODO explicitly silence yaml
     out = get_raw(obj, binarize, skip_q2_grid=skip_q2_grid)
     return yaml.dump(out, stream)
 

From 59f37b24b1d693947841c209a0fb4f0bc00f7bc2 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 7 Apr 2022 19:23:23 +0200
Subject: [PATCH 053/148] Add loading semantics to operator objects

---
 src/eko/output/struct.py | 69 +++++++++++++++++++++++++++++++++++++---
 1 file changed, 65 insertions(+), 4 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index f1578bf95..7338d40ff 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,4 +1,9 @@
 # -*- coding: utf-8 -*-
+import logging
+import os
+import pathlib
+import tempfile
+import typing
 from dataclasses import dataclass, fields
 from typing import Dict, Literal, Optional
 
@@ -8,6 +13,8 @@
 from .. import interpolation
 from .. import version as vmod
 
+logger = logging.getLogger(__name__)
+
 
 class DictLike:
     def __init__(self, **kwargs):
@@ -90,16 +97,36 @@ class EKO:
     data_version: str = vmod.__data_version__
 
     def __iter__(self):
-        return iter(self._operators)
+        """Iterate operators, with minimal load.
+
+        Pay attention, this iterator:
+
+        - is similar to ``dict.items()``, since it returns tuples of ``(q2,
+          operator)``
+        - is not a read-only operation from the point of view of the in-memory
+          object (since the final result after iteration is no operator loaded)
+        - but it is a read-only operation from the point of view of the
+          permanent object on-disk
+
+        Yields
+        ------
+        tuple
+            couples of ``(q2, operator)``, loaded immediately before, unloaded
+            immediately after
+
+        """
+        for q2 in self.Q2grid:
+            yield q2, self[q2]
+            del self[q2]
 
-    def __contains__(self, q2):
+    def __contains__(self, q2: float) -> bool:
         return q2 in self._operators
 
-    def __getitem__(self, q2):
+    def __getitem__(self, q2: float):
         # TODO: autoload
         return self._operators[q2]
 
-    def __setitem__(self, q2, op):
+    def __setitem__(self, q2: float, op: Operator):
         # TODO: autodump
         if isinstance(op, dict):
             op = Operator.from_dict(op)
@@ -107,6 +134,33 @@ def __setitem__(self, q2, op):
             raise ValueError("Only operators can be stored.")
         self._operators[q2] = op
 
+    def __delitem__(self, q2: float):
+        """Drop operator from memory.
+
+        This method only drops the operator from memory, and it's not expected
+        to do anything else.
+
+        Autosave is done on set, and explicit saves are performed by the
+        computation functions.
+
+        If a further explicit save is required, repeat explicit assignment::
+
+            eko[q2] = eko[q2]
+
+        This is only useful if the operator has been mutated in place, that in
+        general should be avoided, since the operator should only be the result
+        of a full computation or a library manipulation.
+
+
+        Parameters
+        ----------
+        q2 : float
+            the value of :math:`Q^2` for which the corresponding operator
+            should be dropped
+
+        """
+        self._operators[q2] = None
+
     def items(self):
         return self._operators.items()
 
@@ -184,3 +238,10 @@ def raw(self):
             rotations=self.rotations.raw,
             debug=self.debug.raw,
         )
+
+    def close(self):
+        for q2 in self.Q2grid:
+            del self[q2]
+
+    def __del__(self):
+        self.close()

From b5ff85a0ef4573664106f9636b785e0875478bc3 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 7 Apr 2022 19:23:37 +0200
Subject: [PATCH 054/148] Bind operator object to a given path

---
 src/eko/output/struct.py | 47 +++++++++++++++++++++++++++++++++++-----
 1 file changed, 42 insertions(+), 5 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 7338d40ff..154bb9fc5 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -81,14 +81,41 @@ def default(cls, xgrid: interpolation.XGrid, pids: np.ndarray):
 
 @dataclass
 class EKO:
-    """
-    Wrapper for the output to help with application
-    to PDFs and dumping to file.
+    """Operator interface.
+
+    This class offers an interface to an abstract operator, between memory and
+    disk.
+
+    An actual operator might be arbitrarily huge, and in particular size
+    limitations in memory are far more strict than on disk.
+    Since manually managing, for each application, the burden of off-loading
+    part of the operator might be hard and occasionally not possible (without a
+    clear picture of the internals), the library itself offers this facility.
+
+    In particular, the data format on disk has a complete specification, and
+    can hold a full operator independently of the loading procedure.
+    In order to accomplish the former goal, the remaining task of partial
+    loading is done by this class (for the Python library, other
+    implementations are possible and encouraged).
+
+    For this reason, a core component of an :cls:`EKO` object is a path,
+    referring to the location on disk of the corresponding operator.
+    Any :cls:`EKO` has an associated path:
+
+    - for the computed object, it corresponds to the path where the actual
+    result of the computation is already saved
+    - for a new object, it is the path at which any result of final or
+    intermediate computation is stored, as soon as it is produced
+
+    The computation can be stopped at any time, without the loss of any of the
+    intermediate results.
+
     """
 
+    path: pathlib.Path
+    _operators: Dict[float, Optional[Operator]]
     xgrid: interpolation.XGrid
     Q02: float
-    _operators: Dict[float, Optional[Operator]]
     configs: Configs
     rotations: Rotations
     debug: Debug
@@ -96,6 +123,10 @@ class EKO:
     version: str = vmod.__version__
     data_version: str = vmod.__data_version__
 
+    def __post_init__(self):
+        if self.path.suffix != ".tar":
+            raise ValueError("Not a valid path")
+
     def __iter__(self):
         """Iterate operators, with minimal load.
 
@@ -205,9 +236,14 @@ def from_dict(cls, runcard: dict):
             the generated structure
 
         """
+        path = pathlib.Path(runcard.get("path", tempfile.mkstemp(suffix=".tar")[1]))
         xgrid = interpolation.XGrid(runcard["xgrid"])
         pids = runcard.get("pids", cls.pids)
+
+        logger.info(f"New operator created at path '{path}'")
+
         return cls(
+            path=path,
             xgrid=xgrid,
             pids=pids,
             Q02=runcard["Q0"] ** 2,
@@ -218,8 +254,9 @@ def from_dict(cls, runcard: dict):
         )
 
     @classmethod
-    def load(cls, path):
+    def load(cls, path: typing.Union[str, os.PathLike]):
         return cls(
+            path=pathlib.Path(path),
             xgrid=None,
             Q02=None,
             _operators={q2: None for q2 in ()},

From 0718d15488b769c69326b1a9ee879925fb5b8bc3 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 7 Apr 2022 19:57:53 +0200
Subject: [PATCH 055/148] Attempt valid tarfile creation... fail

---
 src/eko/output/struct.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 154bb9fc5..c695c4e3e 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -2,6 +2,7 @@
 import logging
 import os
 import pathlib
+import tarfile
 import tempfile
 import typing
 from dataclasses import dataclass, fields
@@ -125,7 +126,9 @@ class EKO:
 
     def __post_init__(self):
         if self.path.suffix != ".tar":
-            raise ValueError("Not a valid path")
+            raise ValueError("Not a valid path for an EKO")
+        if not tarfile.is_tarfile(self.path):
+            raise ValueError("EKO: the corresponding file is not a valid tar archive")
 
     def __iter__(self):
         """Iterate operators, with minimal load.
@@ -237,6 +240,10 @@ def from_dict(cls, runcard: dict):
 
         """
         path = pathlib.Path(runcard.get("path", tempfile.mkstemp(suffix=".tar")[1]))
+        path.unlink()
+        with tarfile.open(path, mode="x") as tar:
+            tar.addfile(tarfile.TarInfo("metadata.yaml"))
+
         xgrid = interpolation.XGrid(runcard["xgrid"])
         pids = runcard.get("pids", cls.pids)
 

From d3efb9eeb003788e699fa31d34dbad9006355739 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 14:09:13 +0200
Subject: [PATCH 056/148] Simplify output tests, removing unittest framework

---
 tests/eko/test_output.py | 29 +++++++++--------------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index cad0993ef..980aa5bcd 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -4,7 +4,6 @@
 import pathlib
 import shutil
 import tempfile
-from unittest import mock
 
 import numpy as np
 import pytest
@@ -30,7 +29,7 @@ def chk_keys(a, b):
 
 
 class TestLegacy:
-    def test_io(self, fake_output):
+    def test_io(self, fake_output, tmp_path):
         # create object
         o1 = output.EKO.from_dict(fake_output)
         for q2, op in fake_output["Q2grid"].items():
@@ -44,26 +43,16 @@ def test_io(self, fake_output):
         np.testing.assert_almost_equal(o1.xgrid.raw, fake_output["xgrid"])
         np.testing.assert_almost_equal(o2.xgrid.raw, fake_output["xgrid"])
         # fake output files
-        m_out = mock.mock_open(read_data="")
-        with mock.patch("builtins.open", m_out) as mock_file:
-            fn = "test.yaml"
-            legacy.dump_yaml_to_file(o1, fn)
-            mock_file.assert_called_with(fn, "w", encoding="utf-8")
+        fpyaml = tmp_path / "test.yaml"
+        legacy.dump_yaml_to_file(o1, fpyaml)
         # fake input file
-        stream.seek(0)
-        m_in = mock.mock_open(read_data=stream.getvalue())
-        with mock.patch("builtins.open", m_in) as mock_file:
-            fn = "test.yaml"
-            o3 = legacy.load_yaml_from_file(fn)
-            mock_file.assert_called_with(fn, encoding="utf-8")
-            np.testing.assert_almost_equal(o3.xgrid.raw, fake_output["xgrid"])
+        o3 = legacy.load_yaml_from_file(fpyaml)
+        np.testing.assert_almost_equal(o3.xgrid.raw, fake_output["xgrid"])
         # repeat for tar
-        fn = "test.tar"
-        with tempfile.TemporaryDirectory() as folder:
-            fp = pathlib.Path(folder) / fn
-            legacy.dump_tar(o1, fp)
-            o4 = legacy.load_tar(fp)
-            np.testing.assert_almost_equal(o4.xgrid.raw, fake_output["xgrid"])
+        fptar = tmp_path / "test.tar"
+        legacy.dump_tar(o1, fptar)
+        o4 = legacy.load_tar(fptar)
+        np.testing.assert_almost_equal(o4.xgrid.raw, fake_output["xgrid"])
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
             legacy.dump_tar(o1, fn)

From b7ff70712d8de037780733c44009e2283f750f0d Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 14:09:38 +0200
Subject: [PATCH 057/148] Bootstrap new directory layout

---
 src/eko/output/struct.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index c695c4e3e..072ad2f05 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -2,6 +2,7 @@
 import logging
 import os
 import pathlib
+import shutil
 import tarfile
 import tempfile
 import typing
@@ -9,6 +10,7 @@
 from typing import Dict, Literal, Optional
 
 import numpy as np
+import yaml
 
 from .. import basis_rotation as br
 from .. import interpolation
@@ -241,8 +243,19 @@ def from_dict(cls, runcard: dict):
         """
         path = pathlib.Path(runcard.get("path", tempfile.mkstemp(suffix=".tar")[1]))
         path.unlink()
-        with tarfile.open(path, mode="x") as tar:
-            tar.addfile(tarfile.TarInfo("metadata.yaml"))
+        with tempfile.TemporaryDirectory() as td:
+            td = pathlib.Path(td)
+            # TODO: replace with actual runcards
+            (td / "metadata.yaml").write_text(yaml.dump(runcard), encoding="utf-8")
+            (td / "recipes").mkdir()
+            (td / "parts").mkdir()
+            (td / "operators").mkdir()
+
+            with tarfile.open(path, mode="w") as tar:
+                for element in td.glob("*"):
+                    tar.add(element, arcname=element.name)
+
+            shutil.rmtree(td)
 
         xgrid = interpolation.XGrid(runcard["xgrid"])
         pids = runcard.get("pids", cls.pids)

From 3a15ea322a5e3769ba1cbd0d38b02d0c6352f8c0 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 15:33:39 +0200
Subject: [PATCH 058/148] Split operator file bootstraping in separate function

---
 src/eko/output/struct.py | 25 +++++++++++++++++++++----
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 072ad2f05..cd4a6222c 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -214,6 +214,26 @@ def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
             return None
         raise ValueError(f"Multiple values of Q2 have been found close to {q2}")
 
+    @staticmethod
+    def bootstrap(tdir: typing.Union[str, os.PathLike], theory: dict, operator: dict):
+        tdir = pathlib.Path(tdir)
+        (tdir / "theory.yaml").write_text(yaml.dump(theory), encoding="utf-8")
+        (tdir / "operator.yaml").write_text(yaml.dump(operator), encoding="utf-8")
+        (tdir / "recipes").mkdir()
+        (tdir / "parts").mkdir()
+        (tdir / "operators").mkdir()
+
+    def update_runcard(self, runcard: dict, which: str = "theory"):
+        names = ("theory", "operator")
+        if which not in names:
+            raise ValueError(f"Runcard '{which}' not available, choose in {names}.")
+
+        with tarfile.open(self.path, mode="w") as tar:
+            with tempfile.NamedTemporaryFile() as tmp:
+                tmppath = pathlib.Path(tmp.name)
+                tmppath.write_text(yaml.dump(runcard), encoding="utf-8")
+                tar.add(tmppath, arcname=f"{which}.yaml")
+
     @classmethod
     def from_dict(cls, runcard: dict):
         """Make structure from runcard-like dictionary.
@@ -246,10 +266,7 @@ def from_dict(cls, runcard: dict):
         with tempfile.TemporaryDirectory() as td:
             td = pathlib.Path(td)
             # TODO: replace with actual runcards
-            (td / "metadata.yaml").write_text(yaml.dump(runcard), encoding="utf-8")
-            (td / "recipes").mkdir()
-            (td / "parts").mkdir()
-            (td / "operators").mkdir()
+            cls.bootstrap(td, theory={}, operator=runcard)
 
             with tarfile.open(path, mode="w") as tar:
                 for element in td.glob("*"):

From 33b70d07e4aebdc4ebc3769d189284562063214a Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 15:51:56 +0200
Subject: [PATCH 059/148] Add methods to retrieve runcards

---
 src/eko/output/struct.py | 32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index cd4a6222c..a3576f6a3 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -223,16 +223,28 @@ def bootstrap(tdir: typing.Union[str, os.PathLike], theory: dict, operator: dict
         (tdir / "parts").mkdir()
         (tdir / "operators").mkdir()
 
-    def update_runcard(self, runcard: dict, which: str = "theory"):
-        names = ("theory", "operator")
-        if which not in names:
-            raise ValueError(f"Runcard '{which}' not available, choose in {names}.")
-
-        with tarfile.open(self.path, mode="w") as tar:
-            with tempfile.NamedTemporaryFile() as tmp:
-                tmppath = pathlib.Path(tmp.name)
-                tmppath.write_text(yaml.dump(runcard), encoding="utf-8")
-                tar.add(tmppath, arcname=f"{which}.yaml")
+    def extract(self, filename: str) -> str:
+        with tarfile.open(self.path, "r") as tar:
+            fd = tar.extractfile(filename)
+            if fd is None:
+                raise ValueError(
+                    f"The member '{filename}' is not a readable file inside EKO tar"
+                )
+            content = fd.read().decode()
+
+        return content
+
+    @property
+    def theory(self) -> dict:
+        return yaml.safe_load(self.extract("theory.yaml"))
+
+    @property
+    def theory_card(self) -> dict:
+        return self.theory
+
+    @property
+    def operator_card(self) -> dict:
+        return yaml.safe_load(self.extract("theory.yaml"))
 
     @classmethod
     def from_dict(cls, runcard: dict):

From a186b7fb5fe4111ea0bc333bb68678ede52fd0ba Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 16:37:47 +0200
Subject: [PATCH 060/148] Rename from_dict constructor

---
 src/eko/output/legacy.py    |   4 +-
 src/eko/output/struct.py    | 114 +++++++++++++++++++++++++-----------
 src/eko/runner.py           |   4 +-
 tests/eko/test_output.py    |  14 ++---
 tests/ekomark/test_apply.py |   4 +-
 5 files changed, 93 insertions(+), 47 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 28eae1895..536142f94 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -197,7 +197,7 @@ def load_yaml(stream: TextIO, skip_q2_grid=False) -> struct.EKO:
                     v = np.frombuffer(lz4.frame.decompress(v))
                     v = v.reshape(len_tpids, len_tgrid, len_ipids, len_igrid)
                 op[k] = v
-    return struct.EKO.from_dict(obj)
+    return struct.EKO.new(theory={}, operator=obj)
 
 
 def load_yaml_from_file(
@@ -271,7 +271,7 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
             operator_grid[q2] = dict(zip(grids.keys(), slices))
         metadata["Q2grid"] = operator_grid
 
-    eko = struct.EKO.from_dict(metadata)
+    eko = struct.EKO.new(theory={}, operator=metadata)
     for q2, op in metadata["Q2grid"].items():
         eko[q2] = op
 
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index a3576f6a3..618ca8906 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -18,6 +18,8 @@
 
 logger = logging.getLogger(__name__)
 
+PathLike = typing.Union[str, os.PathLike]
+
 
 class DictLike:
     def __init__(self, **kwargs):
@@ -215,7 +217,7 @@ def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
         raise ValueError(f"Multiple values of Q2 have been found close to {q2}")
 
     @staticmethod
-    def bootstrap(tdir: typing.Union[str, os.PathLike], theory: dict, operator: dict):
+    def bootstrap(tdir: PathLike, theory: dict, operator: dict):
         tdir = pathlib.Path(tdir)
         (tdir / "theory.yaml").write_text(yaml.dump(theory), encoding="utf-8")
         (tdir / "operator.yaml").write_text(yaml.dump(operator), encoding="utf-8")
@@ -223,8 +225,11 @@ def bootstrap(tdir: typing.Union[str, os.PathLike], theory: dict, operator: dict
         (tdir / "parts").mkdir()
         (tdir / "operators").mkdir()
 
-    def extract(self, filename: str) -> str:
-        with tarfile.open(self.path, "r") as tar:
+    @staticmethod
+    def extract(path: PathLike, filename: str) -> str:
+        path = pathlib.Path(path)
+
+        with tarfile.open(path, "r") as tar:
             fd = tar.extractfile(filename)
             if fd is None:
                 raise ValueError(
@@ -232,11 +237,12 @@ def extract(self, filename: str) -> str:
                 )
             content = fd.read().decode()
 
+        __import__("pdb").set_trace()
         return content
 
     @property
     def theory(self) -> dict:
-        return yaml.safe_load(self.extract("theory.yaml"))
+        return yaml.safe_load(self.extract(self.path, "theory.yaml"))
 
     @property
     def theory_card(self) -> dict:
@@ -244,10 +250,51 @@ def theory_card(self) -> dict:
 
     @property
     def operator_card(self) -> dict:
-        return yaml.safe_load(self.extract("theory.yaml"))
+        return yaml.safe_load(self.extract(self.path, "operator.yaml"))
 
     @classmethod
-    def from_dict(cls, runcard: dict):
+    def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
+        """Build the in-memory object alone.
+
+        Note
+        ----
+        This constructor is meant for internal use, backing the usual ones (like
+        :meth:`new` or :meth:`load`), but it should not be used directly, since
+        it has no guarantee that the underlying path is valid, breaking the
+        object semantic.
+
+        Parameters
+        ----------
+        theory : dict
+            the theory card
+        operator : dict
+            the operator card
+        path : str or os.PathLike
+            the underlying path (it has to be a valid object, but it is not
+            guaranteed, see the note)
+
+        Returns
+        -------
+        EKO
+            the generated structure
+
+        """
+        xgrid = interpolation.XGrid(operator["xgrid"])
+        pids = np.array(operator.get("pids", cls.pids))
+
+        return cls(
+            path=path,
+            xgrid=xgrid,
+            pids=pids,
+            Q02=operator["Q0"] ** 2,
+            _operators={q2: None for q2 in operator["Q2grid"]},
+            configs=Configs.from_dict(operator["configs"]),
+            rotations=Rotations.default(xgrid, pids),
+            debug=Debug.from_dict(operator.get("debug", {})),
+        )
+
+    @classmethod
+    def new(cls, theory: dict, operator: dict, path: Optional[PathLike] = None):
         """Make structure from runcard-like dictionary.
 
         This constructor is made to be used with loaded runcards, in order to
@@ -264,8 +311,13 @@ def from_dict(cls, runcard: dict):
 
         Parameters
         ----------
-        runcard : dict
-            a dictionary containing the runcard's content
+        theory : dict
+            the theory card
+        operator : dict
+            the operator card
+        path : str or os.PathLike
+            the underlying path (if not provided, it is created in a temporary
+            path)
 
         Returns
         -------
@@ -273,12 +325,13 @@ def from_dict(cls, runcard: dict):
             the generated structure
 
         """
-        path = pathlib.Path(runcard.get("path", tempfile.mkstemp(suffix=".tar")[1]))
+        path = pathlib.Path(
+            path if path is not None else tempfile.mkstemp(suffix=".tar")[1]
+        )
         path.unlink()
         with tempfile.TemporaryDirectory() as td:
             td = pathlib.Path(td)
-            # TODO: replace with actual runcards
-            cls.bootstrap(td, theory={}, operator=runcard)
+            cls.bootstrap(td, theory=theory, operator=operator)
 
             with tarfile.open(path, mode="w") as tar:
                 for element in td.glob("*"):
@@ -286,38 +339,29 @@ def from_dict(cls, runcard: dict):
 
             shutil.rmtree(td)
 
-        xgrid = interpolation.XGrid(runcard["xgrid"])
-        pids = runcard.get("pids", cls.pids)
-
+        eko = cls.detached(theory, operator, path=path)
         logger.info(f"New operator created at path '{path}'")
-
-        return cls(
-            path=path,
-            xgrid=xgrid,
-            pids=pids,
-            Q02=runcard["Q0"] ** 2,
-            _operators={q2: None for q2 in runcard["Q2grid"]},
-            configs=Configs.from_dict(runcard["configs"]),
-            rotations=Rotations.default(xgrid, pids),
-            debug=Debug.from_dict(runcard.get("debug", {})),
-        )
+        return eko
 
     @classmethod
-    def load(cls, path: typing.Union[str, os.PathLike]):
-        return cls(
-            path=pathlib.Path(path),
-            xgrid=None,
-            Q02=None,
-            _operators={q2: None for q2 in ()},
-            configs=None,
-            rotations=None,
-            debug=None,
-        )
+    def load(cls, path: PathLike):
+        path = pathlib.Path(path)
+        if not tarfile.is_tarfile(path):
+            raise ValueError("EKO: the corresponding file is not a valid tar archive")
+
+        theory = yaml.safe_load(cls.extract(path, "theory.yaml"))
+        operator = yaml.safe_load(cls.extract(path, "operator.yaml"))
+
+        eko = cls.detached(theory, operator, path=path)
+        logger.info(f"Operator loaded from path '{path}'")
+        return eko
 
     @property
     def raw(self):
         return dict(
+            path=str(self.path),
             xgrid=self.xgrid.tolist(),
+            pids=self.pids.tolist(),
             Q0=float(np.sqrt(self.Q02)),
             Q2grid=self.Q2grid,
             configs=self.configs.raw,
diff --git a/src/eko/runner.py b/src/eko/runner.py
index ac3483eef..7ad960b3e 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -68,7 +68,9 @@ def __init__(self, theory_card: dict, operators_card: dict):
             for key in ("inputgrid", "targetgrid", "inputpids", "targetpids")
         }
 
-        self.out = EKO.from_dict(dict(Q0=np.sqrt(tc.q2_ref), **operators_card))
+        self.out = EKO.new(
+            theory=theory_card, operator=dict(Q0=np.sqrt(tc.q2_ref), **operators_card)
+        )
 
     def get_output(self) -> EKO:
         """Run evolution and generate output operator.
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 980aa5bcd..6e0d9853c 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -31,7 +31,7 @@ def chk_keys(a, b):
 class TestLegacy:
     def test_io(self, fake_output, tmp_path):
         # create object
-        o1 = output.EKO.from_dict(fake_output)
+        o1 = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         # test streams
@@ -60,7 +60,7 @@ def test_io(self, fake_output, tmp_path):
     def test_rename_issue81(self, fake_output):
         # https://github.com/N3PDF/eko/issues/81
         # create object
-        o1 = output.EKO.from_dict(fake_output)
+        o1 = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
 
@@ -78,7 +78,7 @@ def test_rename_issue81(self, fake_output):
 
     def test_io_bin(self, fake_output):
         # create object
-        o1 = output.EKO.from_dict(fake_output)
+        o1 = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         # test streams
@@ -95,7 +95,7 @@ class TestManipulate:
     def test_xgrid_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
-        o1 = output.EKO.from_dict(fake_output)
+        o1 = output.EKO.new(theory={}, operator=fake_output)
         o1.xgrid = xg
         o1.rotations.targetgrid = xg
         o1.rotations.inputgrid = xg
@@ -143,7 +143,7 @@ def test_xgrid_reshape(self, fake_output):
 
     def test_reshape_io(self, fake_output):
         # create object
-        o1 = output.EKO.from_dict(fake_output)
+        o1 = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         o2 = copy.deepcopy(o1)
@@ -160,7 +160,7 @@ def test_reshape_io(self, fake_output):
     def test_flavor_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
-        o1 = output.EKO.from_dict(fake_output)
+        o1 = output.EKO.new(theory={}, operator=fake_output)
         o1.xgrid = xg
         o1.rotations.targetgrid = xg
         o1.rotations.inputgrid = xg
@@ -238,7 +238,7 @@ def test_to_evol(self, fake_factory):
                 backward_inversion="exact",
             ),
         )
-        o00 = output.EKO.from_dict(d)
+        o00 = output.EKO.new(theory={}, operator=d)
         o00[q2_out] = Q2grid[q2_out]
         o01 = copy.deepcopy(o00)
         manipulate.to_evol(o01)
diff --git a/tests/ekomark/test_apply.py b/tests/ekomark/test_apply.py
index 47b342bdf..1f048322a 100644
--- a/tests/ekomark/test_apply.py
+++ b/tests/ekomark/test_apply.py
@@ -9,7 +9,7 @@ class TestApply:
     def test_apply(self, fake_output, fake_pdf):
         q2_out = list(fake_output["Q2grid"].keys())[0]
         # create object
-        o = output.EKO.from_dict(fake_output)
+        o = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o[q2] = output.Operator.from_dict(op)
         # fake pdfs
@@ -35,7 +35,7 @@ def test_apply(self, fake_output, fake_pdf):
     def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
         q2_out = list(fake_output["Q2grid"].keys())[0]
         # create object
-        o = output.EKO.from_dict(fake_output)
+        o = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o[q2] = output.Operator.from_dict(op)
         # fake pdfs

From 8093d99da6758ae61913eff179bca26f628adeea Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 17:05:22 +0200
Subject: [PATCH 061/148] Init eko CLI

---
 pyproject.toml             |  1 +
 src/ekobox/cli/__init__.py |  3 +++
 src/ekobox/cli/_base.py    |  7 +++++++
 src/ekobox/cli/run.py      | 18 ++++++++++++++++++
 4 files changed, 29 insertions(+)
 create mode 100644 src/ekobox/cli/__init__.py
 create mode 100644 src/ekobox/cli/_base.py
 create mode 100644 src/ekobox/cli/run.py

diff --git a/pyproject.toml b/pyproject.toml
index a2130c1f3..875eacb4c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -82,6 +82,7 @@ files = ["src/eko/version.py"]
 [tool.poetry.scripts]
 ekonav = "ekomark.navigator:launch_navigator"
 genpdf = "ekobox.genpdf.cli:cli"
+eko = "ekobox.cli:command"
 
 [tool.poe.tasks]
 test = "pytest tests"
diff --git a/src/ekobox/cli/__init__.py b/src/ekobox/cli/__init__.py
new file mode 100644
index 000000000..95fbff988
--- /dev/null
+++ b/src/ekobox/cli/__init__.py
@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+from . import run
+from ._base import command
diff --git a/src/ekobox/cli/_base.py b/src/ekobox/cli/_base.py
new file mode 100644
index 000000000..b53d3aff2
--- /dev/null
+++ b/src/ekobox/cli/_base.py
@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+import click
+
+
+@click.group()
+def command():
+    pass
diff --git a/src/ekobox/cli/run.py b/src/ekobox/cli/run.py
new file mode 100644
index 000000000..0afd90bf3
--- /dev/null
+++ b/src/ekobox/cli/run.py
@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+import click
+
+from ._base import command
+
+
+@command.command("run")
+@click.argument("q2")
+def subcommand(q2):
+    """Launch EKO computation.
+
+    Parameters
+    ----------
+    q2: sequence[float]
+        sequnce of q2 to compute
+
+    """
+    print(f"Running EKO for {q2}")

From 159b541c85d24b15a1af7d209a6926b694c74655 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 19:39:22 +0200
Subject: [PATCH 062/148] Add self managed item retrieval, through context

---
 src/eko/output/struct.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 618ca8906..a0ca766da 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import contextlib
 import logging
 import os
 import pathlib
@@ -199,6 +200,13 @@ def __delitem__(self, q2: float):
         """
         self._operators[q2] = None
 
+    @contextlib.contextmanager
+    def operator(self, q2: float):
+        try:
+            yield self[q2]
+        finally:
+            del self[q2]
+
     def items(self):
         return self._operators.items()
 

From ad6dd31adcdd6705e195afa666abb2371e727e52 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 8 Apr 2022 19:40:18 +0200
Subject: [PATCH 063/148] Test items self mnagement, not yet fully implemented

---
 tests/eko/test_output_struct.py | 47 +++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 tests/eko/test_output_struct.py

diff --git a/tests/eko/test_output_struct.py b/tests/eko/test_output_struct.py
new file mode 100644
index 000000000..4b9cffb77
--- /dev/null
+++ b/tests/eko/test_output_struct.py
@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*-
+from eko import output
+from eko.output import struct
+
+
+class TestLegacy:
+    def test_items(self, fake_output):
+        """Test autodump, autoload, and manual unload."""
+        eko = output.EKO.new(theory={}, operator=fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            eko[q2] = output.Operator.from_dict(op)
+
+        q2 = next(iter(fake_output["Q2grid"]))
+
+        eko._operators[q2] = None
+        assert isinstance(eko[q2], struct.Operator)
+        assert isinstance(eko._operators[q2], struct.Operator)
+
+        del eko[q2]
+
+        assert eko._operators[q2] is None
+
+    def test_iter(self, fake_output):
+        """Test managed iteration."""
+        eko = output.EKO.new(theory={}, operator=fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            eko[q2] = output.Operator.from_dict(op)
+
+        q2prev = None
+        for q2, op in eko:
+            if q2prev is not None:
+                assert eko._operators[q2prev] is None
+            assert isinstance(op, struct.Operator)
+            q2prev = q2
+
+    def test_context_operator(self, fake_output):
+        """Test automated handling through context."""
+        eko = output.EKO.new(theory={}, operator=fake_output)
+        for q2, op in fake_output["Q2grid"].items():
+            eko[q2] = output.Operator.from_dict(op)
+
+        q2 = next(iter(fake_output["Q2grid"]))
+
+        with eko.operator(q2) as op:
+            assert isinstance(op, struct.Operator)
+
+        assert eko._operators[q2] is None

From 8b71862b2ec40dfbe0dbe3209d1d249e769a1e77 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sat, 9 Apr 2022 09:26:49 +0200
Subject: [PATCH 064/148] Add IO methods for Operator

---
 src/eko/output/struct.py | 42 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index a0ca766da..2b823209b 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import contextlib
+import io
 import logging
 import os
 import pathlib
@@ -8,9 +9,11 @@
 import tempfile
 import typing
 from dataclasses import dataclass, fields
-from typing import Dict, Literal, Optional
+from typing import BinaryIO, Dict, Literal, Optional, Tuple
 
+import lz4.frame
 import numpy as np
+import numpy.lib.npyio as npyio
 import yaml
 
 from .. import basis_rotation as br
@@ -54,6 +57,42 @@ class Operator(DictLike):
     operator: np.ndarray
     error: Optional[np.ndarray] = None
 
+    # IO works with streams in memory, in order to avoid intermediate write on
+    # disk (keep read from and write to tar file only)
+
+    def save(self, compress: bool = True) -> Tuple[BinaryIO, bool]:
+        stream = io.BytesIO()
+        if self.error is None:
+            np.save(stream, self.operator)
+        else:
+            np.savez(stream, operator=self.operator, error=self.error)
+        stream.seek(0)
+
+        # compress if requested
+        if compress:
+            stream = io.BytesIO(lz4.frame.compress(stream.read()))
+
+        # return the stream ready to be read, and the type of array dumped (i.e.
+        # 'npy' or 'npz')
+        return stream, self.error is None
+
+    @classmethod
+    def load(cls, stream: BinaryIO):
+        content = np.load(stream)
+
+        if isinstance(content, np.ndarray):
+            op = content
+            err = None
+        elif isinstance(content, npyio.NpzFile):
+            op = content["operator"]
+            err = content["error"]
+        else:
+            raise ValueError(
+                "Not possible to load operator, content format not recognized"
+            )
+
+        return cls(alphas=0.0, operator=op, error=err)
+
 
 @dataclass
 class Debug(DictLike):
@@ -171,6 +210,7 @@ def __setitem__(self, q2: float, op: Operator):
             op = Operator.from_dict(op)
         if not isinstance(op, Operator):
             raise ValueError("Only operators can be stored.")
+
         self._operators[q2] = op
 
     def __delitem__(self, q2: float):

From 08cfeb9b826678cd02465c129391f32c64887be4 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sat, 9 Apr 2022 11:34:55 +0200
Subject: [PATCH 065/148] Extend EKO documentation

---
 src/eko/output/struct.py | 36 +++++++++++++++++++++++++++++++++---
 1 file changed, 33 insertions(+), 3 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 2b823209b..a109a4a12 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -155,16 +155,46 @@ class EKO:
     The computation can be stopped at any time, without the loss of any of the
     intermediate results.
 
+    Attributes
+    ----------
+    path : pathlib.Path
+        path on disk, to which this object is linked (and for which it is
+        essentially an interface)
+    Q02 : float
+        inital scale
+    xgrid : interpolation.XGrid
+        momentum fraction internal grid
+    pids : np.ndarray
+        array of integers, corresponding to internal PIDs
+    configs : Configs
+        specific configuration to be used during the calculation of these
+        operators
+    rotations : Rotations
+        manipulation information, describing the current status of the EKO (e.g.
+        `inputgrid` and `targetgrid`)
+    debug : Debug
+        debug configurations
+    version : str
+        library version used to create the corresponding file
+    data_version : str
+        specs version, to which the file adheres
+
     """
 
-    path: pathlib.Path
+    # operators cache, contains the Q2 grid information
     _operators: Dict[float, Optional[Operator]]
-    xgrid: interpolation.XGrid
+    # public attributes
+    # -----------------
+    # mandatory, identifying features
+    path: pathlib.Path
     Q02: float
+    xgrid: interpolation.XGrid
+    pids: np.ndarray
+    # collections
     configs: Configs
     rotations: Rotations
     debug: Debug
-    pids: np.ndarray = np.array(br.flavor_basis_pids)
+    # tagging information
     version: str = vmod.__version__
     data_version: str = vmod.__data_version__
 

From dedd220e26d9220213e3fe1e8c2139fa24177526 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sat, 9 Apr 2022 11:35:13 +0200
Subject: [PATCH 066/148] Rearrange EKO iterators

---
 src/eko/output/struct.py | 67 ++++++++++++++++++++++------------------
 1 file changed, 37 insertions(+), 30 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index a109a4a12..eba4a2fbb 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -204,32 +204,6 @@ def __post_init__(self):
         if not tarfile.is_tarfile(self.path):
             raise ValueError("EKO: the corresponding file is not a valid tar archive")
 
-    def __iter__(self):
-        """Iterate operators, with minimal load.
-
-        Pay attention, this iterator:
-
-        - is similar to ``dict.items()``, since it returns tuples of ``(q2,
-          operator)``
-        - is not a read-only operation from the point of view of the in-memory
-          object (since the final result after iteration is no operator loaded)
-        - but it is a read-only operation from the point of view of the
-          permanent object on-disk
-
-        Yields
-        ------
-        tuple
-            couples of ``(q2, operator)``, loaded immediately before, unloaded
-            immediately after
-
-        """
-        for q2 in self.Q2grid:
-            yield q2, self[q2]
-            del self[q2]
-
-    def __contains__(self, q2: float) -> bool:
-        return q2 in self._operators
-
     def __getitem__(self, q2: float):
         # TODO: autoload
         return self._operators[q2]
@@ -277,13 +251,46 @@ def operator(self, q2: float):
         finally:
             del self[q2]
 
-    def items(self):
-        return self._operators.items()
-
     @property
     def Q2grid(self):
         return np.array(list(self._operators))
 
+    def __iter__(self):
+        """Iterate over keys (i.e. Q2 values)
+
+        Yields
+        ------
+        float
+            q2 values
+
+        """
+        for q2 in self._operators:
+            yield q2
+
+    def items(self):
+        """Iterate operators, with minimal load.
+
+        Pay attention, this iterator:
+
+        - is not a read-only operation from the point of view of the in-memory
+          object (since the final result after iteration is no operator loaded)
+        - but it is a read-only operation from the point of view of the
+          permanent object on-disk
+
+        Yields
+        ------
+        tuple
+            couples of ``(q2, operator)``, loaded immediately before, unloaded
+            immediately after
+
+        """
+        for q2 in self.Q2grid:
+            yield q2, self[q2]
+            del self[q2]
+
+    def __contains__(self, q2: float) -> bool:
+        return q2 in self._operators
+
     def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
         q2s = self.Q2grid
         close = q2s[np.isclose(q2, q2s, rtol=rtol, atol=atol)]
@@ -358,7 +365,7 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
 
         """
         xgrid = interpolation.XGrid(operator["xgrid"])
-        pids = np.array(operator.get("pids", cls.pids))
+        pids = np.array(operator.get("pids", np.array(br.flavor_basis_pids)))
 
         return cls(
             path=path,

From 80e95006aa192da3a4ce7afb11aeecd45dce2ea3 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sun, 10 Apr 2022 12:14:55 +0200
Subject: [PATCH 067/148] Add autoload and autodump

---
 src/eko/output/struct.py        | 60 +++++++++++++++++++++++++++------
 tests/eko/test_output_struct.py |  2 +-
 2 files changed, 51 insertions(+), 11 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index eba4a2fbb..e5e61cb90 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -7,6 +7,7 @@
 import shutil
 import tarfile
 import tempfile
+import time
 import typing
 from dataclasses import dataclass, fields
 from typing import BinaryIO, Dict, Literal, Optional, Tuple
@@ -60,7 +61,7 @@ class Operator(DictLike):
     # IO works with streams in memory, in order to avoid intermediate write on
     # disk (keep read from and write to tar file only)
 
-    def save(self, compress: bool = True) -> Tuple[BinaryIO, bool]:
+    def save(self, compress: bool = True) -> Tuple[io.BytesIO, bool]:
         stream = io.BytesIO()
         if self.error is None:
             np.save(stream, self.operator)
@@ -77,7 +78,9 @@ def save(self, compress: bool = True) -> Tuple[BinaryIO, bool]:
         return stream, self.error is None
 
     @classmethod
-    def load(cls, stream: BinaryIO):
+    def load(cls, stream: BinaryIO, compressed: bool = True):
+        if compressed:
+            stream = io.BytesIO(lz4.frame.decompress(stream.read()))
         content = np.load(stream)
 
         if isinstance(content, np.ndarray):
@@ -206,14 +209,51 @@ def __post_init__(self):
 
     def __getitem__(self, q2: float):
         # TODO: autoload
-        return self._operators[q2]
-
-    def __setitem__(self, q2: float, op: Operator):
-        # TODO: autodump
-        if isinstance(op, dict):
-            op = Operator.from_dict(op)
-        if not isinstance(op, Operator):
-            raise ValueError("Only operators can be stored.")
+        op = self._operators[q2]
+        if op is not None:
+            return op
+
+        start = f"operators/{q2:8.2f}"
+
+        with tarfile.open(self.path) as tar:
+            names = list(filter(lambda n: n.startswith(start), tar.getnames()))
+
+            if len(names) == 0:
+                raise ValueError(f"Q2 value '{q2}' not available in '{self.path}'")
+            if len(names) > 1:
+                raise ValueError(
+                    f"Q2 value '{q2}' occurs multiple times in '{self.path}'"
+                )
+
+            name = names[0]
+            compressed = name.endswith(".lz4")
+            stream = tar.extractfile(name)
+
+            if stream is None:
+                raise ValueError
+
+            op = Operator.load(stream, compressed=compressed)
+
+        self._operators[q2] = op
+        return op
+
+    def __setitem__(self, q2: float, op: Optional[Operator], compress: bool = True):
+        if op is not None:
+            stream, without_err = op.save(compress)
+
+            suffix = "npy" if without_err else "npz"
+            if compress:
+                suffix += ".lz4"
+
+            info = tarfile.TarInfo(name=f"operators/{q2:8.2f}.{suffix}")
+            info.size = len(stream.getbuffer())
+            info.mtime = time.time()
+            info.mode = 436
+            info.uname = os.getlogin()
+            info.gname = os.getlogin()
+
+            with tarfile.open(self.path, "a") as tar:
+                tar.addfile(info, fileobj=stream)
 
         self._operators[q2] = op
 
diff --git a/tests/eko/test_output_struct.py b/tests/eko/test_output_struct.py
index 4b9cffb77..01bbe4456 100644
--- a/tests/eko/test_output_struct.py
+++ b/tests/eko/test_output_struct.py
@@ -27,7 +27,7 @@ def test_iter(self, fake_output):
             eko[q2] = output.Operator.from_dict(op)
 
         q2prev = None
-        for q2, op in eko:
+        for q2, op in eko.items():
             if q2prev is not None:
                 assert eko._operators[q2prev] is None
             assert isinstance(op, struct.Operator)

From 2673d1d4cf7e21f55491d2865883a28b0ef27f92 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sun, 10 Apr 2022 12:19:37 +0200
Subject: [PATCH 068/148] Remove user and group info from tar elements

---
 src/eko/output/struct.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index e5e61cb90..09487ebbe 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -249,8 +249,8 @@ def __setitem__(self, q2: float, op: Optional[Operator], compress: bool = True):
             info.size = len(stream.getbuffer())
             info.mtime = time.time()
             info.mode = 436
-            info.uname = os.getlogin()
-            info.gname = os.getlogin()
+            #  info.uname = os.getlogin()
+            #  info.gname = os.getlogin()
 
             with tarfile.open(self.path, "a") as tar:
                 tar.addfile(info, fileobj=stream)

From 54edfbca675007fc6ece056e6b5a8f0b4f553ca6 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 19 Jul 2022 11:15:50 +0200
Subject: [PATCH 069/148] Fix compatibility layer to use subsections

---
 benchmarks/eko/benchmark_evol_to_unity.py |  2 +-
 src/eko/compatibility.py                  | 15 ++++++++++++---
 tests/eko/test_ev_op_grid.py              |  2 +-
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/benchmarks/eko/benchmark_evol_to_unity.py b/benchmarks/eko/benchmark_evol_to_unity.py
index e0d38dd70..eb2e9d07d 100644
--- a/benchmarks/eko/benchmark_evol_to_unity.py
+++ b/benchmarks/eko/benchmark_evol_to_unity.py
@@ -48,7 +48,7 @@ class BenchmarkBackwardForward:
         "configs": {
             "interpolation_polynomial_degree": 1,
             "interpolation_is_log": True,
-            "ev_op_max_order": 1,
+            "ev_op_max_order": (2, 0),
             "ev_op_iterations": 1,
             "backward_inversion": "exact",
             "n_integration_cores": 1,
diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index a41ce4d91..34d44b4f1 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -1,4 +1,9 @@
 # -*- coding: utf-8 -*-
+"""Compatibility functions.
+
+Upgrade old input (NNPDF jargon compatible) to the native one.
+
+"""
 import copy
 
 
@@ -27,9 +32,13 @@ def update(theory, operators):
     if "QED" in new_theory:
         new_theory["order"] = (new_theory.pop("PTO") + 1, new_theory.pop("QED"))
     if operators is not None:
-        if isinstance(new_operators["ev_op_max_order"], int):
-            new_operators["ev_op_max_order"] = (
-                new_operators["ev_op_max_order"],
+        if "configs" not in operators:
+            raise ValueError("No subsections, old format.")
+
+        max_order = new_operators["configs"]["ev_op_max_order"]
+        if isinstance(max_order, int):
+            new_operators["configs"]["ev_op_max_order"] = (
+                max_order,
                 new_theory["order"][1],
             )
     return new_theory, new_operators
diff --git a/tests/eko/test_ev_op_grid.py b/tests/eko/test_ev_op_grid.py
index 0fee639e3..017176d85 100644
--- a/tests/eko/test_ev_op_grid.py
+++ b/tests/eko/test_ev_op_grid.py
@@ -140,5 +140,5 @@ def test_mod_expanded(self):
             )
             sv_opg = sv_opgrid.compute(3)
             np.testing.assert_allclose(
-                opg[3]["operator"], sv_opg[3]["operator"], atol=0.7 * epsilon
+                opg[3]["operators"], sv_opg[3]["operators"], atol=0.7 * epsilon
             )

From 2fb64a635853d1cf6c882b8d85a9543f8c6bfd17 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 19 Jul 2022 11:18:59 +0200
Subject: [PATCH 070/148] Update compatibility tests as well

---
 tests/eko/test_compatibility.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/eko/test_compatibility.py b/tests/eko/test_compatibility.py
index 5e09d6673..4fc08c6a9 100644
--- a/tests/eko/test_compatibility.py
+++ b/tests/eko/test_compatibility.py
@@ -1,5 +1,4 @@
 # -*- coding: utf-8 -*-
-import pytest
 
 from eko import compatibility
 
@@ -14,9 +13,13 @@
 def test_compatibility():
     new_theory = compatibility.update_theory(theory1)
 
+    assert new_theory["order"][0] == theory1["PTO"] + 1
 
-operator_dict = {"ev_op_max_order": 2}
+
+operator_dict = {"configs": {"ev_op_max_order": 2}}
 
 
 def test_compatibility_operators():
-    new_theory, new_operator = compatibility.update(theory1, operator_dict)
+    _, new_operator = compatibility.update(theory1, operator_dict)
+
+    assert not isinstance(new_operator["configs"]["ev_op_max_order"], int)

From 425485e0a7420eb46e439825fa46bbb156bb6290 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 19 Jul 2022 11:23:52 +0200
Subject: [PATCH 071/148] Disable workflows run on WIP branch

---
 .github/workflows/isobench.yml  | 5 ++++-
 .github/workflows/unittests.yml | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/isobench.yml b/.github/workflows/isobench.yml
index bd0cbd4e2..74cdaa96d 100644
--- a/.github/workflows/isobench.yml
+++ b/.github/workflows/isobench.yml
@@ -1,6 +1,9 @@
 name: isolated benchmarks
 
-on: push
+on:
+  push:
+    branches-ignore:
+      - feature/composite-output
 
 jobs:
   isobench:
diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index a7dd8eaa7..2e8da37f4 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -1,6 +1,9 @@
 name: tests
 
-on: push
+on:
+  push:
+    branches-ignore:
+      - feature/composite-output
 
 jobs:
   py38:

From 5b74d3662bc2fc519ed04e7b619ecace2675d77f Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 19 Jul 2022 11:54:22 +0200
Subject: [PATCH 072/148] Update operator card example

---
 tests/eko/test_ev_operator.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/tests/eko/test_ev_operator.py b/tests/eko/test_ev_operator.py
index 5fe5b3b68..60ddd6355 100644
--- a/tests/eko/test_ev_operator.py
+++ b/tests/eko/test_ev_operator.py
@@ -157,15 +157,16 @@ def test_quad_ker(monkeypatch):
 }
 operators_card = {
     "Q2grid": [1, 10],
-    "interpolation_xgrid": [0.1, 1.0],
-    "interpolation_polynomial_degree": 1,
-    "interpolation_is_log": True,
-    "debug_skip_singlet": False,
-    "debug_skip_non_singlet": False,
-    "ev_op_max_order": 1,
-    "ev_op_iterations": 1,
-    "backward_inversion": "exact",
-    "n_integration_cores": 1,
+    "xgrid": [0.1, 1.0],
+    "configs": {
+        "interpolation_polynomial_degree": 1,
+        "interpolation_is_log": True,
+        "ev_op_max_order": 1,
+        "ev_op_iterations": 1,
+        "backward_inversion": "exact",
+        "n_integration_cores": 1,
+    },
+    "debug": {"skip_singlet": False, "skip_non_singlet": False},
 }
 
 

From aea1aa3cdbd00186c6cd44255c40c69f7ba6e212 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 19 Jul 2022 12:00:45 +0200
Subject: [PATCH 073/148] Update error identifiers

---
 doc/source/code/IO.rst                     |  6 +-
 doc/source/overview/tutorials/output.ipynb |  4 +-
 src/eko/evolution_operator/grid.py         | 39 ++++++++-----
 src/eko/output/manipulate.py               | 33 +++++------
 src/ekomark/plots.py                       | 64 +++++++++++-----------
 tests/eko/test_ev_op_grid.py               |  4 +-
 6 files changed, 80 insertions(+), 70 deletions(-)

diff --git a/doc/source/code/IO.rst b/doc/source/code/IO.rst
index c63eb37dd..4879fa75b 100644
--- a/doc/source/code/IO.rst
+++ b/doc/source/code/IO.rst
@@ -67,7 +67,7 @@ The grid elements contains two keys each
 - ``operators`` a :py:obj:`dict` with all evolution kernel operators where the key indicates which distribution is generated by which other one
   and the value represents the eko in matrix representation - this can either be the plain list representation or the binary representation
   (as provided by :py:meth:`numpy.ndarray.tobytes`)
-- ``operator_errors`` a :py:obj:`dict` with the integration errors associated to the respective operators following the same conventions as
+- ``errors`` a :py:obj:`dict` with the integration errors associated to the respective operators following the same conventions as
   the ``operator`` dictionary
 - each element (|EKO|) is a rank-4 tensor with the indices ordered in the following way: ``EKO[pid_out][x_out][pid_in][x_in]`` where ``pid_out`` and ``x_out``
   refer to the outgoing |PDF| and ``pid_in`` and ``x_in`` to the incoming |PDF|. The ordering of ``pid_out/pid_in`` is determined by the ``pids``
@@ -88,7 +88,7 @@ Example Output dump
         - - - - 0
               - 0
               # more values ...
-      operator_errors:
+      errors:
         - - - - 0
               - 0
               # more values ...
@@ -97,7 +97,7 @@ Example Output dump
         - - - - 0
               - 0
               # more values ...
-      operator_errors:
+      errors:
         - - - - 0
               - 0
               # more values ...
diff --git a/doc/source/overview/tutorials/output.ipynb b/doc/source/overview/tutorials/output.ipynb
index b3b9112ce..79bddaec3 100644
--- a/doc/source/overview/tutorials/output.ipynb
+++ b/doc/source/overview/tutorials/output.ipynb
@@ -275,7 +275,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "dict_keys(['operators', 'operator_errors'])\n",
+      "dict_keys(['operators', 'errors'])\n",
       "\n",
       "OPERATOR\n",
       "(14, 5, 14, 5) float64\n",
@@ -288,7 +288,7 @@
    "source": [
     "print(opgrid[100.].keys())\n",
     "op = opgrid[100.][\"operators\"]\n",
-    "operr = opgrid[100.][\"operator_errors\"]\n",
+    "operr = opgrid[100.][\"errors\"]\n",
     "\n",
     "print(f\"\\nOPERATOR\\n{op.shape} {op.dtype}\")\n",
     "print(f\"\\nERROR\\n{operr.shape} {operr.dtype}\")"
diff --git a/src/eko/evolution_operator/grid.py b/src/eko/evolution_operator/grid.py
index e8206073f..4fae2f3ce 100644
--- a/src/eko/evolution_operator/grid.py
+++ b/src/eko/evolution_operator/grid.py
@@ -21,14 +21,33 @@
 
 
 class OperatorGrid(sv.ModeMixin):
-    """
+    """Collection of evolution operators for several scales.
+
     The operator grid is the driver class of the evolution.
 
     It receives as input a threshold holder and a generator of a_s.
     From that point onwards it can compute any operator at any q2.
 
-    Parameters
+    Attributes
     ----------
+    config: dict
+    q2_grid: np.ndarray
+    managers: dict
+
+    """
+
+    def __init__(
+        self,
+        config,
+        q2_grid,
+        thresholds_config,
+        strong_coupling,
+        interpol_dispatcher,
+    ):
+        """Initialize `OperatorGrid`.
+
+        Parameters
+        ----------
         config: dict
             configuration dictionary
         q2_grid: array
@@ -44,16 +63,8 @@ class OperatorGrid(sv.ModeMixin):
         kernel_dispatcher: eko.kernel_generation.KernelDispatcher
             Instance of the :class:`~eko.kernel_generation.KernelDispatcher` with the
             information about the kernels
-    """
 
-    def __init__(
-        self,
-        config,
-        q2_grid,
-        thresholds_config,
-        strong_coupling,
-        interpol_dispatcher,
-    ):
+        """
         # check
         order = config["order"]
         method = config["method"]
@@ -203,7 +214,7 @@ def get_threshold_operators(self, path):
         return thr_ops
 
     def compute(self, q2grid=None):
-        """Computes all ekos for the `q2grid`.
+        """Compute all ekos for the `q2grid`.
 
         Parameters
         ----------
@@ -234,7 +245,7 @@ def compute(self, q2grid=None):
         return grid_return
 
     def generate(self, q2):
-        r"""Computes a single EKO.
+        r"""Compute a single EKO.
 
         Parameters
         ----------
@@ -298,5 +309,5 @@ def generate(self, q2):
         values, errors = final_op.to_flavor_basis_tensor()
         return {
             "operators": values,
-            "operator_errors": errors,
+            "errors": errors,
         }
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index cba8409fb..8a75a6cc4 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""Manipulate output generate by EKO."""
 import logging
 import warnings
 from typing import Optional
@@ -18,17 +19,17 @@ def xgrid_reshape(
     inputgrid: Optional[np.ndarray] = None,
     inplace: bool = True,
 ):
-    """
-    Changes the operators to have in the output targetgrid and/or in the input inputgrid.
+    """Change the operators to have in the output targetgrid and/or in the input inputgrid.
 
     The operation is in-place.
 
     Parameters
     ----------
-        targetgrid : None or list
-            xgrid for the target
-        inputgrid : None or list
-            xgrid for the input
+    targetgrid : None or list
+        xgrid for the target
+    inputgrid : None or list
+        xgrid for the input
+
     """
     # calling with no arguments is an error
     if targetgrid is None and inputgrid is None:
@@ -98,17 +99,17 @@ def flavor_reshape(
     inputbasis: Optional[np.ndarray] = None,
     inplace: bool = True,
 ):
-    """
-    Changes the operators to have in the output targetbasis and/or in the input inputbasis.
+    """Change the operators to have in the output targetbasis and/or in the input inputbasis.
 
     The operation is in-place.
 
     Parameters
     ----------
-        targetbasis : numpy.ndarray
-            target rotation specified in the flavor basis
-        inputbasis : None or list
-            input rotation specified in the flavor basis
+    targetbasis : numpy.ndarray
+        target rotation specified in the flavor basis
+    inputbasis : None or list
+        input rotation specified in the flavor basis
+
     """
     # calling with no arguments is an error
     if targetbasis is None and inputbasis is None:
@@ -148,8 +149,8 @@ def flavor_reshape(
         else:
             ops = np.einsum("ca,ajbk,bd->cjdk", targetbasis, ops, inv_inputbasis)
             errs = np.einsum("ca,ajbk,bd->cjdk", targetbasis, errs, inv_inputbasis)
-        elem.operators = ops
-        elem.operator_errors = errs
+        elem.operator = ops
+        elem.error = errs
     # drop PIDs - keeping them int nevertheless
     #  there is no meaningful way to set them in general, after rotation
     if inputbasis is not None:
@@ -159,8 +160,7 @@ def flavor_reshape(
 
 
 def to_evol(eko: EKO, source: bool = True, target: bool = False, inplace: bool = True):
-    """
-    Rotate the operator into evolution basis.
+    """Rotate the operator into evolution basis.
 
     This also assigns also the pids. The operation is in-place.
 
@@ -170,6 +170,7 @@ def to_evol(eko: EKO, source: bool = True, target: bool = False, inplace: bool =
             rotate on the input tensor
         target : bool
             rotate on the output tensor
+
     """
     # rotate
     inputbasis = br.rotate_flavor_to_evolution if source else None
diff --git a/src/ekomark/plots.py b/src/ekomark/plots.py
index 2fcff96f8..92f821af9 100644
--- a/src/ekomark/plots.py
+++ b/src/ekomark/plots.py
@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""
-Plotting tools to show the evolved PDF and the computed operators
-"""
+"""Plotting tools to show the evolved PDF and the computed operators."""
 import io
 import pprint
 
@@ -15,22 +13,22 @@
 
 
 def input_figure(theory, ops, pdf_name=None):
-    """
-    Pretty-prints the setup to a figure
+    """Pretty-prints the setup to a figure.
 
     Parameters
     ----------
-        theory : dict
-            theory card
-        ops : dict
-            operator card
-        pdf_name : str
-            PDF name
+    theory : dict
+        theory card
+    ops : dict
+        operator card
+    pdf_name : str
+        PDF name
 
     Returns
     -------
-        firstPage : matplotlib.pyplot.Figure
-            figure
+    firstPage : matplotlib.pyplot.Figure
+        figure
+
     """
     firstPage = plt.figure(figsize=(25, 20))
     # theory
@@ -56,8 +54,7 @@ def input_figure(theory, ops, pdf_name=None):
 
 
 def plot_dist(x, y, yerr, yref, title=None, oMx_min=1e-2, oMx_max=0.5):
-    """
-    Compare two distributions.
+    """Compare two distributions.
 
     Generates a plot with 3 areas:
 
@@ -68,28 +65,29 @@ def plot_dist(x, y, yerr, yref, title=None, oMx_min=1e-2, oMx_max=0.5):
 
     Parameters
     ----------
-        x : numpy.ndarray
-            list of abscisses
-        y : numpy.ndarray
-            computed list of ordinates
-        yerr : numpy.ndarray
-            list of ordinate errors
-        yref : numpy.ndarray
-            reference list of ordinates
+    x : numpy.ndarray
+        list of abscisses
+    y : numpy.ndarray
+        computed list of ordinates
+    yerr : numpy.ndarray
+        list of ordinate errors
+    yref : numpy.ndarray
+        reference list of ordinates
 
     Other Parameters
     ----------------
-        title : str, optional
-            additional overall title
-        oMx_min : float
-            maximum value for the large x region, i.e. 1-x > 1 - `oMx_min`
-        oMx_max : float
-            minimum value for the large x region, i.e. 1 - `oMx_max` > 1-x
+    title : str, optional
+        additional overall title
+    oMx_min : float
+        maximum value for the large x region, i.e. 1-x > 1 - `oMx_min`
+    oMx_max : float
+        minimum value for the large x region, i.e. 1 - `oMx_max` > 1-x
 
     Returns
     -------
-        fig : matplotlib.pyplot.figure
-            created figure
+    fig : matplotlib.pyplot.figure
+        created figure
+
     """
     np.seterr(divide="ignore", invalid="ignore")
     fig = plt.figure(figsize=(15, 5))
@@ -164,7 +162,7 @@ def plot_operator(var_name, op, op_err, log_operator=True, abs_operator=True):
     """
     # get
     # op = ret["operators"][var_name]
-    # op_err = ret["operator_errors"][var_name]
+    # op_err = ret["errors"][var_name]
 
     # empty?
     thre = 1e-8
@@ -244,7 +242,7 @@ def save_operators_to_pdf(path, theory, ops, me, skip_pdfs, change_lab=False):
         # it's necessary to reshuffle the eko output
         for q2 in me["Q2grid"]:
             results = me["Q2grid"][q2]["operators"]
-            errors = me["Q2grid"][q2]["operator_errors"]
+            errors = me["Q2grid"][q2]["errors"]
 
             # loop on pids
             for label_out, res, res_err in zip(ops_names, results, errors):
diff --git a/tests/eko/test_ev_op_grid.py b/tests/eko/test_ev_op_grid.py
index 017176d85..b132ee2cb 100644
--- a/tests/eko/test_ev_op_grid.py
+++ b/tests/eko/test_ev_op_grid.py
@@ -112,10 +112,10 @@ def test_compute_q2grid(self):
         # we can also pass a single number
         opg = opgrid.compute()
         assert len(opg) == 2
-        assert all(k in op for k in ["operator", "error"] for op in opg.values())
+        assert all(k in op for k in ["operators", "errors"] for op in opg.values())
         opg = opgrid.compute(3)
         assert len(opg) == 1
-        assert all(k in op for k in ["operator", "error"] for op in opg.values())
+        assert all(k in op for k in ["operators", "errors"] for op in opg.values())
 
     def test_grid_computation_VFNS(self):
         """Checks that the grid can be computed"""

From 588d1e64ed2967ad567b4378da8395d697d5e3a8 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Tue, 19 Jul 2022 12:20:35 +0200
Subject: [PATCH 074/148] Fix operator runcard layout in OME tests

---
 tests/eko/test_ome.py | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/tests/eko/test_ome.py b/tests/eko/test_ome.py
index 178058522..80e0a804b 100644
--- a/tests/eko/test_ome.py
+++ b/tests/eko/test_ome.py
@@ -314,15 +314,16 @@ class TestOperatorMatrixElement:
     }
     operators_card = {
         "Q2grid": [20],
-        "interpolation_xgrid": [0.1, 1.0],
-        "interpolation_polynomial_degree": 1,
-        "interpolation_is_log": True,
-        "debug_skip_singlet": True,
-        "debug_skip_non_singlet": False,
-        "ev_op_max_order": 1,
-        "ev_op_iterations": 1,
-        "backward_inversion": "exact",
-        "n_integration_cores": 1,
+        "xgrid": [0.1, 1.0],
+        "configs": {
+            "interpolation_polynomial_degree": 1,
+            "interpolation_is_log": True,
+            "ev_op_max_order": 1,
+            "ev_op_iterations": 1,
+            "backward_inversion": "exact",
+            "n_integration_cores": 1,
+        },
+        "debug": {"skip_singlet": True, "skip_non_singlet": False},
     }
 
     def test_labels(self):
@@ -421,7 +422,7 @@ def test_compute_n3lo(self):
     def test_compute_lo(self):
         self.theory_card.update({"PTO": (1, 0)})
         self.operators_card.update(
-            dict(debug={"debug_skip_singlet": False, "skip_non_singlet": False})
+            dict(debug={"skip_singlet": False, "skip_non_singlet": False})
         )
         g = OperatorGrid.from_dict(
             self.theory_card,

From 9c40e959c3c9f504a3004f565823596e041dd660 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 20 Jul 2022 11:29:59 +0200
Subject: [PATCH 075/148] Drop alphas, sanify q2 to dump

---
 src/eko/output/legacy.py | 11 ++++-------
 src/eko/output/struct.py |  6 ++----
 src/eko/runner.py        |  2 --
 tests/conftest.py        |  1 -
 tests/eko/test_output.py |  3 +--
 5 files changed, 7 insertions(+), 16 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 536142f94..b95c39aa3 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -42,18 +42,17 @@ def get_raw(eko: struct.EKO, binarize: bool = True, skip_q2_grid: bool = False):
     # make operators raw
     if not skip_q2_grid:
         for q2, op in eko.items():
+            q2 = float(q2)
             out["Q2grid"][q2] = {}
             if op is not None:
                 for k, v in dataclasses.asdict(op).items():
-                    if k == "alphas":
-                        out["Q2grid"][q2][k] = float(v)
-                        continue
                     if binarize:
                         out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
                     else:
                         out["Q2grid"][q2][k] = v.tolist()
     else:
         out["Q2grid"] = obj["Q2grid"]
+
     return out
 
 
@@ -141,7 +140,7 @@ def dump_tar(obj: struct.EKO, tarname: Union[str, os.PathLike]):
         with open(yamlname, "w", encoding="utf-8") as fd:
             yaml.dump(metadata, fd)
 
-        for kind in ["alphas", "operator", "error"]:
+        for kind in ["operator", "error"]:
             elements = []
             for q2, op in obj.items():
                 if op is not None:
@@ -189,9 +188,7 @@ def load_yaml(stream: TextIO, skip_q2_grid=False) -> struct.EKO:
     if not skip_q2_grid:
         for op in obj["Q2grid"].values():
             for k, v in op.items():
-                if k == "alphas":
-                    v = float(v)
-                elif isinstance(v, list):
+                if isinstance(v, list):
                     v = np.array(v)
                 elif isinstance(v, bytes):
                     v = np.frombuffer(lz4.frame.decompress(v))
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 09487ebbe..72c056adc 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -54,7 +54,6 @@ def raw(self):
 
 @dataclass
 class Operator(DictLike):
-    alphas: float
     operator: np.ndarray
     error: Optional[np.ndarray] = None
 
@@ -94,7 +93,7 @@ def load(cls, stream: BinaryIO, compressed: bool = True):
                 "Not possible to load operator, content format not recognized"
             )
 
-        return cls(alphas=0.0, operator=op, error=err)
+        return cls(operator=op, error=err)
 
 
 @dataclass
@@ -362,7 +361,6 @@ def extract(path: PathLike, filename: str) -> str:
                 )
             content = fd.read().decode()
 
-        __import__("pdb").set_trace()
         return content
 
     @property
@@ -411,7 +409,7 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             path=path,
             xgrid=xgrid,
             pids=pids,
-            Q02=operator["Q0"] ** 2,
+            Q02=float(operator["Q0"] ** 2),
             _operators={q2: None for q2 in operator["Q2grid"]},
             configs=Configs.from_dict(operator["configs"]),
             rotations=Rotations.default(xgrid, pids),
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 7ad960b3e..a6777a495 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -40,8 +40,6 @@ class Runner:
 """
 
     def __init__(self, theory_card: dict, operators_card: dict):
-        self.out = EKO()
-
         new_theory, new_operators = compatibility.update(theory_card, operators_card)
 
         # Store inputs
diff --git a/tests/conftest.py b/tests/conftest.py
index 70c08000c..b5fe84e14 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -50,7 +50,6 @@ def mk_g(self, q2s, lpids, lx):
             Q2grid[q2] = {
                 "operator": np.random.rand(lpids, lx, lpids, lx),
                 "error": np.random.rand(lpids, lx, lpids, lx),
-                "alphas": np.random.rand(),
             }
         return Q2grid
 
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 6e0d9853c..737bfb1ff 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -34,6 +34,7 @@ def test_io(self, fake_output, tmp_path):
         o1 = output.EKO.new(theory={}, operator=fake_output)
         for q2, op in fake_output["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
+
         # test streams
         stream = io.StringIO()
         legacy.dump_yaml(o1, stream)
@@ -104,7 +105,6 @@ def test_xgrid_reshape(self, fake_output):
                 dict(
                     operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
                     error=np.zeros((2, len(xg), 2, len(xg))),
-                    alphas=np.random.rand(),
                 )
             )
         }
@@ -169,7 +169,6 @@ def test_flavor_reshape(self, fake_output):
                 dict(
                     operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
                     error=np.zeros((2, len(xg), 2, len(xg))),
-                    alphas=np.random.rand(),
                 )
             )
         }

From 38a37be789a4da8522529bfbeb9b6e46165c3787 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 20 Jul 2022 11:49:03 +0200
Subject: [PATCH 076/148] Convert all dictionaries to operators

---
 src/eko/evolution_operator/grid.py |  4 ++--
 src/eko/output/legacy.py           |  2 +-
 src/eko/output/struct.py           | 18 ++++++++++++++----
 src/eko/runner.py                  |  4 ++--
 src/ekobox/utils.py                |  5 ++---
 tests/eko/test_ev_op_grid.py       |  6 +++---
 6 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/src/eko/evolution_operator/grid.py b/src/eko/evolution_operator/grid.py
index 4fae2f3ce..2ab23c515 100644
--- a/src/eko/evolution_operator/grid.py
+++ b/src/eko/evolution_operator/grid.py
@@ -308,6 +308,6 @@ def generate(self, q2):
 
         values, errors = final_op.to_flavor_basis_tensor()
         return {
-            "operators": values,
-            "errors": errors,
+            "operator": values,
+            "error": errors,
         }
diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index b95c39aa3..81d0d9755 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -265,7 +265,7 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
         q2grid = metadata["Q2grid"]
         operator_grid = {}
         for q2, slices in zip(q2grid, zip(*grids.values())):
-            operator_grid[q2] = dict(zip(grids.keys(), slices))
+            operator_grid[q2] = struct.Operator(**dict(zip(grids.keys(), slices)))
         metadata["Q2grid"] = operator_grid
 
     eko = struct.EKO.new(theory={}, operator=metadata)
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 72c056adc..4ddccbdfe 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -238,6 +238,9 @@ def __getitem__(self, q2: float):
 
     def __setitem__(self, q2: float, op: Optional[Operator], compress: bool = True):
         if op is not None:
+            if not isinstance(op, Operator):
+                raise ValueError("Only an Operator can be added to an EKO")
+
             stream, without_err = op.save(compress)
 
             suffix = "npy" if without_err else "npz"
@@ -448,10 +451,17 @@ def new(cls, theory: dict, operator: dict, path: Optional[PathLike] = None):
             the generated structure
 
         """
-        path = pathlib.Path(
-            path if path is not None else tempfile.mkstemp(suffix=".tar")[1]
-        )
-        path.unlink()
+        givenpath = path is not None
+
+        path = pathlib.Path(path if givenpath else tempfile.mkstemp(suffix=".tar")[1])
+        if path.exists():
+            if givenpath:
+                raise FileExistsError(
+                    f"File exists at given path '{path}', cannot be used for a new operator."
+                )
+            # delete the file created in case of temporary file
+            path.unlink()
+
         with tempfile.TemporaryDirectory() as td:
             td = pathlib.Path(td)
             cls.bootstrap(td, theory=theory, operator=operator)
diff --git a/src/eko/runner.py b/src/eko/runner.py
index a6777a495..7896337ee 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -11,7 +11,7 @@
 from . import compatibility, interpolation, msbar_masses
 from .couplings import Couplings
 from .evolution_operator.grid import OperatorGrid
-from .output import EKO, manipulate
+from .output import EKO, Operator, manipulate
 from .thresholds import ThresholdsAtlas
 
 logger = logging.getLogger(__name__)
@@ -87,7 +87,7 @@ def get_output(self) -> EKO:
         """
         # add all operators
         for final_scale, op in self.op_grid.compute().items():
-            self.out[float(final_scale)] = op
+            self.out[float(final_scale)] = Operator.from_dict(op)
 
         def similar_to_none(name: str) -> Optional[np.ndarray]:
             grid = self.post_process[name]
diff --git a/src/ekobox/utils.py b/src/ekobox/utils.py
index 9fb66d3a9..13622046c 100644
--- a/src/ekobox/utils.py
+++ b/src/ekobox/utils.py
@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from eko.output import EKO
+from eko.output import EKO, Operator
 
 
 # TODO: add a control on the theory (but before we need to implement another
@@ -77,7 +77,6 @@ def ekos_product(
             "ajbk,bkcl -> ajcl", ope1_error, op2.operator
         )
 
-        alphas = eko_fin[q2].alphas
-        final_eko[q2] = dict(operator=op, error=error, alphas=alphas)
+        final_eko[q2] = Operator(operator=op, error=error)
 
     return final_eko
diff --git a/tests/eko/test_ev_op_grid.py b/tests/eko/test_ev_op_grid.py
index b132ee2cb..0fee639e3 100644
--- a/tests/eko/test_ev_op_grid.py
+++ b/tests/eko/test_ev_op_grid.py
@@ -112,10 +112,10 @@ def test_compute_q2grid(self):
         # we can also pass a single number
         opg = opgrid.compute()
         assert len(opg) == 2
-        assert all(k in op for k in ["operators", "errors"] for op in opg.values())
+        assert all(k in op for k in ["operator", "error"] for op in opg.values())
         opg = opgrid.compute(3)
         assert len(opg) == 1
-        assert all(k in op for k in ["operators", "errors"] for op in opg.values())
+        assert all(k in op for k in ["operator", "error"] for op in opg.values())
 
     def test_grid_computation_VFNS(self):
         """Checks that the grid can be computed"""
@@ -140,5 +140,5 @@ def test_mod_expanded(self):
             )
             sv_opg = sv_opgrid.compute(3)
             np.testing.assert_allclose(
-                opg[3]["operators"], sv_opg[3]["operators"], atol=0.7 * epsilon
+                opg[3]["operator"], sv_opg[3]["operator"], atol=0.7 * epsilon
             )

From d40b6c7feb322ff0f11b0e332fdea867969bb364 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 20 Jul 2022 13:25:14 +0200
Subject: [PATCH 077/148] Fix double write to archive

---
 src/eko/output/manipulate.py |  4 +++-
 src/eko/output/struct.py     | 12 ++++++++++++
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 8a75a6cc4..b7237a62d 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -75,7 +75,7 @@ def xgrid_reshape(
         eko.rotations.inputgrid = np.array(inputgrid)
 
     # build new grid
-    for _, elem in eko.items():
+    for q2, elem in eko.items():
         if elem is None:
             continue
         ops = elem.operator
@@ -92,6 +92,8 @@ def xgrid_reshape(
         elem.operator = ops
         elem.error = errs
 
+        eko[q2] = elem
+
 
 def flavor_reshape(
     eko: EKO,
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 4ddccbdfe..d2723680b 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -5,6 +5,7 @@
 import os
 import pathlib
 import shutil
+import subprocess
 import tarfile
 import tempfile
 import time
@@ -254,6 +255,17 @@ def __setitem__(self, q2: float, op: Optional[Operator], compress: bool = True):
             #  info.uname = os.getlogin()
             #  info.gname = os.getlogin()
 
+            # TODO: unfortunately Python has no native support for deleting
+            # files inside tar, so the proper way is to make that function
+            # ourselves, in the inefficient way of constructing a new archive
+            # from the existing one, but for the file to be removed
+            # at the moment, an implicit dependency on `tar` command has been
+            # introduced -> dangerous for portability
+            # since it's not raising any error, it is fine to run in any case:
+            # if the file is not there, nothing happens
+            subprocess.run(
+                f"tar -f {self.path.absolute()} --delete".split() + [info.name]
+            )
             with tarfile.open(self.path, "a") as tar:
                 tar.addfile(info, fileobj=stream)
 

From f227a8ee9d73c2c55764b9e49afa1d177dc34529 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 20 Jul 2022 13:50:26 +0200
Subject: [PATCH 078/148] Fix flavor reshaping, set operator

---
 src/eko/output/manipulate.py | 5 ++++-
 tests/eko/test_output.py     | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index b7237a62d..ca8283819 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -137,7 +137,7 @@ def flavor_reshape(
         inv_inputbasis = np.linalg.inv(inputbasis)
 
     # build new grid
-    for _, elem in eko.items():
+    for q2, elem in eko.items():
         if elem is None:
             continue
         ops = elem.operator
@@ -153,6 +153,9 @@ def flavor_reshape(
             errs = np.einsum("ca,ajbk,bd->cjdk", targetbasis, errs, inv_inputbasis)
         elem.operator = ops
         elem.error = errs
+
+        eko[q2] = elem
+
     # drop PIDs - keeping them int nevertheless
     #  there is no meaningful way to set them in general, after rotation
     if inputbasis is not None:
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 737bfb1ff..bd7695e3c 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -238,7 +238,7 @@ def test_to_evol(self, fake_factory):
             ),
         )
         o00 = output.EKO.new(theory={}, operator=d)
-        o00[q2_out] = Q2grid[q2_out]
+        o00[q2_out] = output.Operator(**Q2grid[q2_out])
         o01 = copy.deepcopy(o00)
         manipulate.to_evol(o01)
         o10 = copy.deepcopy(o00)

From 822d552fef955f4274df7db05fa39c9912c263c0 Mon Sep 17 00:00:00 2001
From: giacomomagni <giac.magni@gmail.com>
Date: Wed, 20 Jul 2022 15:08:33 +0200
Subject: [PATCH 079/148] fix ome test

---
 tests/eko/test_ome.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/eko/test_ome.py b/tests/eko/test_ome.py
index 80e0a804b..c22b4762f 100644
--- a/tests/eko/test_ome.py
+++ b/tests/eko/test_ome.py
@@ -420,7 +420,7 @@ def test_compute_n3lo(self):
             np.testing.assert_allclose(mat, np.triu(mat))
 
     def test_compute_lo(self):
-        self.theory_card.update({"PTO": (1, 0)})
+        self.theory_card.update({"order": (1, 0)})
         self.operators_card.update(
             dict(debug={"skip_singlet": False, "skip_non_singlet": False})
         )

From f5da5c09c31edc343deebfabde07745a2367efec Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Wed, 20 Jul 2022 18:54:38 +0200
Subject: [PATCH 080/148] Check file exists in tar

---
 src/eko/output/manipulate.py |  6 ++++--
 src/eko/output/struct.py     | 13 ++++++++-----
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index ca8283819..161d5d27b 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -137,7 +137,9 @@ def flavor_reshape(
         inv_inputbasis = np.linalg.inv(inputbasis)
 
     # build new grid
-    for q2, elem in eko.items():
+    # for q2, elem in eko.items():
+    for q2 in eko.Q2grid:
+        elem = eko[q2]
         if elem is None:
             continue
         ops = elem.operator
@@ -157,7 +159,7 @@ def flavor_reshape(
         eko[q2] = elem
 
     # drop PIDs - keeping them int nevertheless
-    #  there is no meaningful way to set them in general, after rotation
+    # there is no meaningful way to set them in general, after rotation
     if inputbasis is not None:
         eko.rotations.inputpids = [0] * len(eko.rotations.inputpids)
     if targetbasis is not None:
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index d2723680b..7d9642106 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -262,13 +262,16 @@ def __setitem__(self, q2: float, op: Optional[Operator], compress: bool = True):
             # at the moment, an implicit dependency on `tar` command has been
             # introduced -> dangerous for portability
             # since it's not raising any error, it is fine to run in any case:
-            # if the file is not there, nothing happens
-            subprocess.run(
-                f"tar -f {self.path.absolute()} --delete".split() + [info.name]
-            )
+            has_file = False
+            with tarfile.open(self.path, mode="r") as tar:
+                has_file = f"operators/{q2:8.2f}.{suffix}" in tar.getnames()
+
+            if has_file:
+                subprocess.run(
+                    f"tar -f {self.path.absolute()} --delete".split() + [info.name]
+                )
             with tarfile.open(self.path, "a") as tar:
                 tar.addfile(info, fileobj=stream)
-
         self._operators[q2] = op
 
     def __delitem__(self, q2: float):

From 955126178f9e4380ce0849db2a3eaf6fc6acaa70 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 20 Jul 2022 19:27:40 +0200
Subject: [PATCH 081/148] Unleash workflows

---
 .github/workflows/isobench.yml  | 5 +----
 .github/workflows/unittests.yml | 5 +----
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/isobench.yml b/.github/workflows/isobench.yml
index 74cdaa96d..bd0cbd4e2 100644
--- a/.github/workflows/isobench.yml
+++ b/.github/workflows/isobench.yml
@@ -1,9 +1,6 @@
 name: isolated benchmarks
 
-on:
-  push:
-    branches-ignore:
-      - feature/composite-output
+on: push
 
 jobs:
   isobench:
diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 2e8da37f4..a7dd8eaa7 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -1,9 +1,6 @@
 name: tests
 
-on:
-  push:
-    branches-ignore:
-      - feature/composite-output
+on: push
 
 jobs:
   py38:

From d3e825a6867395dc882e100aed64643c182a8939 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 25 Jul 2022 15:16:19 +0200
Subject: [PATCH 082/148] Add docstrings for DictLike

---
 src/eko/output/struct.py | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 7d9642106..4c44e812e 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""Define output representation structures."""
 import contextlib
 import io
 import logging
@@ -28,15 +29,50 @@
 
 
 class DictLike:
+    """Dictionary compatibility base class, for dataclasses.
+
+    This class add compatibility to import and export from Python :class:`dict`,
+    in such a way to support serialization interfaces working with them.
+
+    Some collections and scalar objects are normalized to native Python
+    structures, in order to simplify the on-disk representation.
+
+    """
+
     def __init__(self, **kwargs):
+        """Empty initializer."""
         pass
 
     @classmethod
     def from_dict(cls, dictionary):
+        """Initialize dataclass object from raw dictionary.
+
+        Parameters
+        ----------
+        dictionary: dict
+            the dictionary to be converted to :class:`DictLike`
+
+        Returns
+        -------
+        DictLike
+            instance with `dictionary` content loaded as attributes
+
+        """
         return cls(**dictionary)
 
     @property
     def raw(self):
+        """Convert dataclass object to raw dictionary.
+
+        Normalize :class:`np.ndarray` to lists (possibly nested), and scalars to
+        the corresponding built-in type.
+
+        Returns
+        -------
+        dict
+            dictionary representation
+
+        """
         dictionary = {}
         for field in fields(self):
             value = getattr(self, field.name)

From dbe7869df2ceda6087757b951836252ff2b3c5b1 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 25 Jul 2022 23:22:07 +0200
Subject: [PATCH 083/148] Init operator docstrings

---
 src/eko/output/struct.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 4c44e812e..4362f5964 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -91,6 +91,21 @@ def raw(self):
 
 @dataclass
 class Operator(DictLike):
+    """Operator representation.
+
+    To be used to hold the result of a computed 4-dim operator (from a given
+    scale to another given one).
+
+    Attributes
+    ----------
+    operator: np.ndarray
+        content of the evolution operator
+    error: np.ndarray or None
+        errors on individual operator elements (mainly used for integration
+        error, but it can host any kind of error)
+
+    """
+
     operator: np.ndarray
     error: Optional[np.ndarray] = None
 
@@ -98,6 +113,7 @@ class Operator(DictLike):
     # disk (keep read from and write to tar file only)
 
     def save(self, compress: bool = True) -> Tuple[io.BytesIO, bool]:
+        """Save content of operator to bytes."""
         stream = io.BytesIO()
         if self.error is None:
             np.save(stream, self.operator)
@@ -115,6 +131,7 @@ def save(self, compress: bool = True) -> Tuple[io.BytesIO, bool]:
 
     @classmethod
     def load(cls, stream: BinaryIO, compressed: bool = True):
+        """Load operator from bytes."""
         if compressed:
             stream = io.BytesIO(lz4.frame.decompress(stream.read()))
         content = np.load(stream)

From 034f7e5dfbb39cc94123ab3d2bf195aa2a93117c Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 26 Jul 2022 17:56:24 +0200
Subject: [PATCH 084/148] Add compatibility test

---
 tests/eko/test_compatibility.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/eko/test_compatibility.py b/tests/eko/test_compatibility.py
index 4fc08c6a9..d5c4e3a41 100644
--- a/tests/eko/test_compatibility.py
+++ b/tests/eko/test_compatibility.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import pytest
 
 from eko import compatibility
 
@@ -23,3 +24,6 @@ def test_compatibility_operators():
     _, new_operator = compatibility.update(theory1, operator_dict)
 
     assert not isinstance(new_operator["configs"]["ev_op_max_order"], int)
+
+    with pytest.raises(ValueError):
+        compatibility.update(theory1, {})

From 76f38aca1619b5c2598ef6f1bb1f57c96b93992a Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 26 Jul 2022 18:11:55 +0200
Subject: [PATCH 085/148] Add CLI test

---
 tests/ekobox/test_cli.py | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 tests/ekobox/test_cli.py

diff --git a/tests/ekobox/test_cli.py b/tests/ekobox/test_cli.py
new file mode 100644
index 000000000..5405e78c3
--- /dev/null
+++ b/tests/ekobox/test_cli.py
@@ -0,0 +1,11 @@
+# -*- coding: utf-8 -*-
+
+from click.testing import CliRunner
+
+from ekobox.cli import command
+
+
+def test_run():
+    runner = CliRunner()
+    result = runner.invoke(command, ["run", "a"])
+    assert "Running EKO for" in result.output

From aec2d6a39bc8b612e3d8d9b999ac55940681094c Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 26 Jul 2022 18:27:23 +0200
Subject: [PATCH 086/148] Fix and test evol_pdf

---
 src/ekobox/evol_pdf.py        | 43 +++++++++++++++++------------------
 tests/ekobox/test_evol_pdf.py |  9 +++++++-
 2 files changed, 29 insertions(+), 23 deletions(-)

diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index 8504c2462..391937031 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""Tools to evolve actual PDFs."""
 import pathlib
 
 import eko
@@ -20,30 +21,28 @@ def evolve_pdfs(
     name="Evolved_PDF",
     info_update=None,
 ):
-    """
-    This function evolves an initial_PDF using a theory card and an operator card
-    and dump the evolved PDF in lhapdf format
+    """Evolves one or several initial_PDFs and dump the evolved PDFs in lhapdf format.
 
     Parameters
     ----------
-        initial_PDF_list : list(lhapdf object)
-            list of PDF members to be evolved
-        theory_card : dict
-            theory card
-        operators_card : dict
-            operators card
-        path : str
-            path to cached eko output (if "None" it will be recomputed)
-        store_path : str
-            path where the eko is stored (if "None" will not be saved)
-        targetgrid : list(float)
-            target x-grid (if different from input x-grid)
-        install : bool
-            set whether to install evolved PDF to lhapdf directory
-        name : str
-            set name of evolved PDF
-        info_update : dict
-            dict of info to add or update to default info file
+    initial_PDF_list : list(lhapdf object)
+        list of PDF members to be evolved
+    theory_card : dict
+        theory card
+    operators_card : dict
+        operators card
+    path : str
+        path to cached eko output (if "None" it will be recomputed)
+    store_path : str
+        path where the eko is stored (if "None" will not be saved)
+    targetgrid : list(float)
+        target x-grid (if different from input x-grid)
+    install : bool
+        set whether to install evolved PDF to lhapdf directory
+    name : str
+        set name of evolved PDF
+    info_update : dict
+        dict of info to add or update to default info file
     """
     eko_output = None
     if path is not None:
@@ -56,7 +55,7 @@ def evolve_pdfs(
     else:
         eko_output = eko.run_dglap(theory_card, operators_card)
         if store_path is not None:
-            eko_output.dump_tar(store_path)
+            eko.output.legacy.dump_tar(eko_output, store_path)
 
     evolved_PDF_list = []
     for initial_PDF in initial_PDF_list:
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index fc833cd90..d2d194802 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -22,10 +22,17 @@ def test_evolve_pdfs_run(fake_lhapdf, cd):
     n = "test_evolve_pdfs_run"
     mytmp = fake_lhapdf / "install"
     mytmp.mkdir()
+    store_path = mytmp / "test.tar"
     with cd(mytmp):
-        ev_p.evolve_pdfs([toy.mkPDF("", 0)], theory, op, install=True, name=n)
+        ev_p.evolve_pdfs(
+            [toy.mkPDF("", 0)], theory, op, install=True, name=n, store_path=store_path
+        )
     p = fake_lhapdf / n
     assert p.exists()
+    # check dumped eko
+    assert store_path.exists()
+    assert store_path.is_file()
+    out.load_tar(store_path)
 
 
 def test_evolve_pdfs_dump_path(fake_lhapdf, cd):

From 0e9537761df53607257a1c605594ce8207d9b9bf Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 26 Jul 2022 18:32:13 +0200
Subject: [PATCH 087/148] Comment runcards

---
 src/eko/runcards.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/eko/runcards.py b/src/eko/runcards.py
index b9be63c4c..eb7f14e3d 100644
--- a/src/eko/runcards.py
+++ b/src/eko/runcards.py
@@ -1,12 +1,13 @@
 # -*- coding: utf-8 -*-
-from dataclasses import dataclass
+"""Runcard definitions."""
+# from dataclasses import dataclass
 
 
-@dataclass
-class TheoryCard:
-    pto: int
+# @dataclass
+# class TheoryCard:
+#     pto: int
 
 
-@dataclass
-class OperatorCard:
-    xgrid: list
+# @dataclass
+# class OperatorCard:
+#     xgrid: list

From 976bc98430534090d031241eaac5b2dd26d60d80 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Tue, 26 Jul 2022 18:49:02 +0200
Subject: [PATCH 088/148] Fix runner test

---
 tests/eko/test_runner.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index c4e54c22f..9c23ecee6 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -69,17 +69,23 @@ def test_targetgrid():
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
     check_shapes(o, eko.interpolation.XGrid(np.array(tgrid)), o.xgrid, tc, oc)
+    # check actual value
+    np.testing.assert_allclose(o.rotations.targetgrid, tgrid)
 
 
-def test_targetbasis():
-    # change targetbasis
+def test_rotate_pids():
+    # change pids
     tc = copy.deepcopy(theory_card)
     oc = copy.deepcopy(operators_card)
-    oc["targetbasis"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
-    oc["inputbasis"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
+    oc["rotations"] = {}
+    oc["rotations"]["targetpids"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
+    oc["rotations"]["inputpids"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
     check_shapes(o, o.xgrid, o.xgrid, tc, oc)
+    # check actual values
+    assert o.rotations.targetpids == [0] * 14
+    assert o.rotations.inputpids == [0] * 14
 
 
 def check_shapes(o, txs, ixs, theory_card, operators_card):

From d5885a8c3c21c19f260e7d8e8697297e2510a7d4 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 15:18:08 +0200
Subject: [PATCH 089/148] Revert "Comment runcards"

This reverts commit 0e9537761df53607257a1c605594ce8207d9b9bf.
---
 src/eko/runcards.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/eko/runcards.py b/src/eko/runcards.py
index eb7f14e3d..b9be63c4c 100644
--- a/src/eko/runcards.py
+++ b/src/eko/runcards.py
@@ -1,13 +1,12 @@
 # -*- coding: utf-8 -*-
-"""Runcard definitions."""
-# from dataclasses import dataclass
+from dataclasses import dataclass
 
 
-# @dataclass
-# class TheoryCard:
-#     pto: int
+@dataclass
+class TheoryCard:
+    pto: int
 
 
-# @dataclass
-# class OperatorCard:
-#     xgrid: list
+@dataclass
+class OperatorCard:
+    xgrid: list

From c426b5f5f9b7b10140e79ab05ce7ffde4b196563 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 15:27:17 +0200
Subject: [PATCH 090/148] Change all {input,target}basis names to {}pids

---
 src/eko/output/manipulate.py | 62 ++++++++++++++++++------------------
 src/eko/runner.py            | 26 +++++++++------
 tests/eko/test_output.py     |  8 ++---
 tests/eko/test_runner.py     |  2 +-
 4 files changed, 53 insertions(+), 45 deletions(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 161d5d27b..9d4af4105 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -97,44 +97,44 @@ def xgrid_reshape(
 
 def flavor_reshape(
     eko: EKO,
-    targetbasis: Optional[np.ndarray] = None,
-    inputbasis: Optional[np.ndarray] = None,
+    targetpids: Optional[np.ndarray] = None,
+    inputpids: Optional[np.ndarray] = None,
     inplace: bool = True,
 ):
-    """Change the operators to have in the output targetbasis and/or in the input inputbasis.
+    """Change the operators to have in the output targetpids and/or in the input inputpids.
 
     The operation is in-place.
 
     Parameters
     ----------
-    targetbasis : numpy.ndarray
+    targetpids : numpy.ndarray
         target rotation specified in the flavor basis
-    inputbasis : None or list
+    inputpids : None or list
         input rotation specified in the flavor basis
 
     """
     # calling with no arguments is an error
-    if targetbasis is None and inputbasis is None:
-        raise ValueError("Nor inputbasis nor targetbasis was given")
+    if targetpids is None and inputpids is None:
+        raise ValueError("Nor inputpids nor targetpids was given")
     # now check to the current status
-    if targetbasis is not None and np.allclose(
-        targetbasis, np.eye(len(eko.rotations.targetpids))
+    if targetpids is not None and np.allclose(
+        targetpids, np.eye(len(eko.rotations.targetpids))
     ):
-        targetbasis = None
-        warnings.warn("The new targetbasis is close to current basis")
-    if inputbasis is not None and np.allclose(
-        inputbasis, np.eye(len(eko.rotations.inputpids))
+        targetpids = None
+        warnings.warn("The new targetpids is close to current basis")
+    if inputpids is not None and np.allclose(
+        inputpids, np.eye(len(eko.rotations.inputpids))
     ):
-        inputbasis = None
-        warnings.warn("The new inputbasis is close to current basis")
+        inputpids = None
+        warnings.warn("The new inputpids is close to current basis")
     # after the checks: if there is still nothing to do, skip
-    if targetbasis is None and inputbasis is None:
+    if targetpids is None and inputpids is None:
         logger.debug("Nothing done.")
         return
 
     # flip input around
-    if inputbasis is not None:
-        inv_inputbasis = np.linalg.inv(inputbasis)
+    if inputpids is not None:
+        inv_inputpids = np.linalg.inv(inputpids)
 
     # build new grid
     # for q2, elem in eko.items():
@@ -144,15 +144,15 @@ def flavor_reshape(
             continue
         ops = elem.operator
         errs = elem.error
-        if targetbasis is not None and inputbasis is None:
-            ops = np.einsum("ca,ajbk->cjbk", targetbasis, ops)
-            errs = np.einsum("ca,ajbk->cjbk", targetbasis, errs)
-        elif inputbasis is not None and targetbasis is None:
-            ops = np.einsum("ajbk,bd->ajdk", ops, inv_inputbasis)
-            errs = np.einsum("ajbk,bd->ajdk", errs, inv_inputbasis)
+        if targetpids is not None and inputpids is None:
+            ops = np.einsum("ca,ajbk->cjbk", targetpids, ops)
+            errs = np.einsum("ca,ajbk->cjbk", targetpids, errs)
+        elif inputpids is not None and targetpids is None:
+            ops = np.einsum("ajbk,bd->ajdk", ops, inv_inputpids)
+            errs = np.einsum("ajbk,bd->ajdk", errs, inv_inputpids)
         else:
-            ops = np.einsum("ca,ajbk,bd->cjdk", targetbasis, ops, inv_inputbasis)
-            errs = np.einsum("ca,ajbk,bd->cjdk", targetbasis, errs, inv_inputbasis)
+            ops = np.einsum("ca,ajbk,bd->cjdk", targetpids, ops, inv_inputpids)
+            errs = np.einsum("ca,ajbk,bd->cjdk", targetpids, errs, inv_inputpids)
         elem.operator = ops
         elem.error = errs
 
@@ -160,9 +160,9 @@ def flavor_reshape(
 
     # drop PIDs - keeping them int nevertheless
     # there is no meaningful way to set them in general, after rotation
-    if inputbasis is not None:
+    if inputpids is not None:
         eko.rotations.inputpids = [0] * len(eko.rotations.inputpids)
-    if targetbasis is not None:
+    if targetpids is not None:
         eko.rotations.targetpids = [0] * len(eko.rotations.targetpids)
 
 
@@ -180,9 +180,9 @@ def to_evol(eko: EKO, source: bool = True, target: bool = False, inplace: bool =
 
     """
     # rotate
-    inputbasis = br.rotate_flavor_to_evolution if source else None
-    targetbasis = br.rotate_flavor_to_evolution if target else None
-    flavor_reshape(eko, inputbasis=inputbasis, targetbasis=targetbasis)
+    inputpids = br.rotate_flavor_to_evolution if source else None
+    targetpids = br.rotate_flavor_to_evolution if target else None
+    flavor_reshape(eko, inputpids=inputpids, targetpids=targetpids)
     # assign pids
     if source:
         eko.rotations.inputpids = br.evol_basis_pids
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 7896337ee..3abcc069d 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""
-    This file contains the main application class of eko
-"""
+"""This file contains the main application class of eko."""
 import copy
 import logging
 from typing import Optional
@@ -18,15 +16,15 @@
 
 
 class Runner:
-    """
-    Represents a single input configuration.
+    """Represents a single input configuration.
 
     For details about the configuration, see :doc:`here </code/IO>`
 
-    Parameters
+    Attributes
     ----------
-        setup : dict
-            input configurations
+    setup : dict
+        input configurations
+
     """
 
     banner = r"""
@@ -40,6 +38,16 @@ class Runner:
 """
 
     def __init__(self, theory_card: dict, operators_card: dict):
+        """Initialize runner.
+
+        Parameters
+        ----------
+        theory_card: dict
+            theory parameters and options
+        operators_card: dict
+            operator specific options
+
+        """
         new_theory, new_operators = compatibility.update(theory_card, operators_card)
 
         # Store inputs
@@ -113,7 +121,7 @@ def similar_to_none(name: str) -> Optional[np.ndarray]:
         targetpids = similar_to_none("targetpids")
         if inputpids is not None or targetpids is not None:
             manipulate.flavor_reshape(
-                self.out, targetbasis=targetpids, inputbasis=inputpids
+                self.out, targetpids=targetpids, inputpids=inputpids
             )
 
         return copy.deepcopy(self.out)
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index bd7695e3c..52aefc18e 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -148,7 +148,7 @@ def test_reshape_io(self, fake_output):
             o1[q2] = output.Operator.from_dict(op)
         o2 = copy.deepcopy(o1)
         manipulate.xgrid_reshape(o2, [0.1, 1.0], [0.1, 1.0])
-        manipulate.flavor_reshape(o2, inputbasis=np.array([[1, -1], [1, 1]]))
+        manipulate.flavor_reshape(o2, inputpids=np.array([[1, -1], [1, 1]]))
         # dump
         stream = io.StringIO()
         legacy.dump_yaml(o2, stream)
@@ -189,14 +189,14 @@ def test_flavor_reshape(self, fake_output):
         # only input
         input_r = np.array([[1, -1], [1, 1]])
         oi = copy.deepcopy(o1)
-        manipulate.flavor_reshape(oi, inputbasis=input_r)
+        manipulate.flavor_reshape(oi, inputpids=input_r)
         chk_keys(o1.raw, oi.raw)
         assert oi[10].operator.shape == (2, len(xg), 2, len(xg))
         oii = copy.deepcopy(oi)
-        manipulate.flavor_reshape(oii, inputbasis=np.linalg.inv(input_r))
+        manipulate.flavor_reshape(oii, inputpids=np.linalg.inv(input_r))
         np.testing.assert_allclose(oii[10].operator, o1[10].operator)
         with pytest.warns(Warning):
-            manipulate.flavor_reshape(oii, inputbasis=np.eye(2))
+            manipulate.flavor_reshape(oii, inputpids=np.eye(2))
             chk_keys(o1.raw, oii.raw)
             np.testing.assert_allclose(oii[10].operator, o1[10].operator)
 
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 9c23ecee6..054d0970e 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -109,7 +109,7 @@ def check_shapes(o, txs, ixs, theory_card, operators_card):
 
 
 def test_vfns():
-    # change targetbasis
+    # change targetpids
     tc = copy.deepcopy(theory_card)
     oc = copy.deepcopy(operators_card)
     tc["kcThr"] = 1.0

From a621d847da996f9498c2a32bf0658d4d8aa28432 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 16:35:19 +0200
Subject: [PATCH 091/148] Remove PathLike in favor of standard library
 os.PathLike

---
 src/eko/output/struct.py | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 4362f5964..1bfa6db4f 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -10,7 +10,6 @@
 import tarfile
 import tempfile
 import time
-import typing
 from dataclasses import dataclass, fields
 from typing import BinaryIO, Dict, Literal, Optional, Tuple
 
@@ -25,8 +24,6 @@
 
 logger = logging.getLogger(__name__)
 
-PathLike = typing.Union[str, os.PathLike]
-
 
 class DictLike:
     """Dictionary compatibility base class, for dataclasses.
@@ -412,7 +409,7 @@ def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
         raise ValueError(f"Multiple values of Q2 have been found close to {q2}")
 
     @staticmethod
-    def bootstrap(tdir: PathLike, theory: dict, operator: dict):
+    def bootstrap(tdir: os.PathLike, theory: dict, operator: dict):
         tdir = pathlib.Path(tdir)
         (tdir / "theory.yaml").write_text(yaml.dump(theory), encoding="utf-8")
         (tdir / "operator.yaml").write_text(yaml.dump(operator), encoding="utf-8")
@@ -421,7 +418,7 @@ def bootstrap(tdir: PathLike, theory: dict, operator: dict):
         (tdir / "operators").mkdir()
 
     @staticmethod
-    def extract(path: PathLike, filename: str) -> str:
+    def extract(path: os.PathLike, filename: str) -> str:
         path = pathlib.Path(path)
 
         with tarfile.open(path, "r") as tar:
@@ -463,7 +460,7 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             the theory card
         operator : dict
             the operator card
-        path : str or os.PathLike
+        path : os.PathLike
             the underlying path (it has to be a valid object, but it is not
             guaranteed, see the note)
 
@@ -488,7 +485,7 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
         )
 
     @classmethod
-    def new(cls, theory: dict, operator: dict, path: Optional[PathLike] = None):
+    def new(cls, theory: dict, operator: dict, path: Optional[os.PathLike] = None):
         """Make structure from runcard-like dictionary.
 
         This constructor is made to be used with loaded runcards, in order to
@@ -509,7 +506,7 @@ def new(cls, theory: dict, operator: dict, path: Optional[PathLike] = None):
             the theory card
         operator : dict
             the operator card
-        path : str or os.PathLike
+        path : os.PathLike
             the underlying path (if not provided, it is created in a temporary
             path)
 
@@ -545,7 +542,7 @@ def new(cls, theory: dict, operator: dict, path: Optional[PathLike] = None):
         return eko
 
     @classmethod
-    def load(cls, path: PathLike):
+    def load(cls, path: os.PathLike):
         path = pathlib.Path(path)
         if not tarfile.is_tarfile(path):
             raise ValueError("EKO: the corresponding file is not a valid tar archive")

From d84e24dd8bb499ca5766059da5f43e0d53869a56 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 17:19:32 +0200
Subject: [PATCH 092/148] Provide native deep copy for EKO

---
 src/eko/output/struct.py | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 1bfa6db4f..32536dec4 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """Define output representation structures."""
 import contextlib
+import copy
 import io
 import logging
 import os
@@ -408,6 +409,45 @@ def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
             return None
         raise ValueError(f"Multiple values of Q2 have been found close to {q2}")
 
+    def unload(self):
+        """Fully unload the operators in memory."""
+
+        for q2 in self:
+            del self[q2]
+
+    def deepcopy(self, path: os.PathLike):
+        """Create a deep copy of current instance.
+
+        The managed on-disk object is copied as well, to the new ``path``
+        location.
+        If you don't want to copy the disk, consider using directly::
+
+            copy.deepcopy(myeko)
+
+        It will perform the exact same operation, without propagating it to the
+        disk counterpart.
+
+        Parameters
+        ----------
+        path: os.PathLike
+            path were to copy the disk counterpart of the operator object
+
+        Returns
+        -------
+        EKO
+            the copy created
+
+        """
+        # return the object fully on disk, in order to avoid expensive copies in
+        # memory (they would be copied on-disk in any case)
+        self.unload()
+
+        new = copy.deepcopy(self)
+        new.path = pathlib.Path(path)
+        shutil.copy2(self.path, new.path)
+
+        return new
+
     @staticmethod
     def bootstrap(tdir: os.PathLike, theory: dict, operator: dict):
         tdir = pathlib.Path(tdir)

From d5c581682ed67989dae8dd6e09db02b6be753273 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 17:44:10 +0200
Subject: [PATCH 093/148] Remove the option to delete item setting it -> use
 delitem

---
 src/eko/output/struct.py | 70 ++++++++++++++++++++--------------------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 32536dec4..ea2964ff8 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -288,41 +288,41 @@ def __getitem__(self, q2: float):
         self._operators[q2] = op
         return op
 
-    def __setitem__(self, q2: float, op: Optional[Operator], compress: bool = True):
-        if op is not None:
-            if not isinstance(op, Operator):
-                raise ValueError("Only an Operator can be added to an EKO")
-
-            stream, without_err = op.save(compress)
-
-            suffix = "npy" if without_err else "npz"
-            if compress:
-                suffix += ".lz4"
-
-            info = tarfile.TarInfo(name=f"operators/{q2:8.2f}.{suffix}")
-            info.size = len(stream.getbuffer())
-            info.mtime = time.time()
-            info.mode = 436
-            #  info.uname = os.getlogin()
-            #  info.gname = os.getlogin()
-
-            # TODO: unfortunately Python has no native support for deleting
-            # files inside tar, so the proper way is to make that function
-            # ourselves, in the inefficient way of constructing a new archive
-            # from the existing one, but for the file to be removed
-            # at the moment, an implicit dependency on `tar` command has been
-            # introduced -> dangerous for portability
-            # since it's not raising any error, it is fine to run in any case:
-            has_file = False
-            with tarfile.open(self.path, mode="r") as tar:
-                has_file = f"operators/{q2:8.2f}.{suffix}" in tar.getnames()
-
-            if has_file:
-                subprocess.run(
-                    f"tar -f {self.path.absolute()} --delete".split() + [info.name]
-                )
-            with tarfile.open(self.path, "a") as tar:
-                tar.addfile(info, fileobj=stream)
+    def __setitem__(self, q2: float, op: Operator, compress: bool = True):
+        if not isinstance(op, Operator):
+            raise ValueError("Only an Operator can be added to an EKO")
+
+        stream, without_err = op.save(compress)
+
+        suffix = "npy" if without_err else "npz"
+        if compress:
+            suffix += ".lz4"
+
+        info = tarfile.TarInfo(name=f"operators/{q2:8.2f}.{suffix}")
+        info.size = len(stream.getbuffer())
+        info.mtime = time.time()
+        info.mode = 436
+        #  info.uname = os.getlogin()
+        #  info.gname = os.getlogin()
+
+        # TODO: unfortunately Python has no native support for deleting
+        # files inside tar, so the proper way is to make that function
+        # ourselves, in the inefficient way of constructing a new archive
+        # from the existing one, but for the file to be removed
+        # at the moment, an implicit dependency on `tar` command has been
+        # introduced -> dangerous for portability
+        # since it's not raising any error, it is fine to run in any case:
+        has_file = False
+        with tarfile.open(self.path, mode="r") as tar:
+            has_file = f"operators/{q2:8.2f}.{suffix}" in tar.getnames()
+
+        if has_file:
+            subprocess.run(
+                f"tar -f {self.path.absolute()} --delete".split() + [info.name]
+            )
+        with tarfile.open(self.path, "a") as tar:
+            tar.addfile(info, fileobj=stream)
+
         self._operators[q2] = op
 
     def __delitem__(self, q2: float):

From 1b8bb42bfa5a9f98670ca007dd78eb67ee9c4dda Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 17:51:22 +0200
Subject: [PATCH 094/148] Replace file and directory names with module level
 constants

---
 src/eko/output/struct.py | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index ea2964ff8..b1997482e 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -25,6 +25,12 @@
 
 logger = logging.getLogger(__name__)
 
+THEORYFILE = "theory.yaml"
+OPERATORFILE = "operator.yaml"
+RECIPESDIR = "recipes"
+PARTSDIR = "parts"
+OPERATORSDIR = "operators"
+
 
 class DictLike:
     """Dictionary compatibility base class, for dataclasses.
@@ -451,11 +457,11 @@ def deepcopy(self, path: os.PathLike):
     @staticmethod
     def bootstrap(tdir: os.PathLike, theory: dict, operator: dict):
         tdir = pathlib.Path(tdir)
-        (tdir / "theory.yaml").write_text(yaml.dump(theory), encoding="utf-8")
-        (tdir / "operator.yaml").write_text(yaml.dump(operator), encoding="utf-8")
-        (tdir / "recipes").mkdir()
-        (tdir / "parts").mkdir()
-        (tdir / "operators").mkdir()
+        (tdir / THEORYFILE).write_text(yaml.dump(theory), encoding="utf-8")
+        (tdir / OPERATORFILE).write_text(yaml.dump(operator), encoding="utf-8")
+        (tdir / RECIPESDIR).mkdir()
+        (tdir / PARTSDIR).mkdir()
+        (tdir / OPERATORSDIR).mkdir()
 
     @staticmethod
     def extract(path: os.PathLike, filename: str) -> str:
@@ -473,7 +479,7 @@ def extract(path: os.PathLike, filename: str) -> str:
 
     @property
     def theory(self) -> dict:
-        return yaml.safe_load(self.extract(self.path, "theory.yaml"))
+        return yaml.safe_load(self.extract(self.path, THEORYFILE))
 
     @property
     def theory_card(self) -> dict:
@@ -481,7 +487,7 @@ def theory_card(self) -> dict:
 
     @property
     def operator_card(self) -> dict:
-        return yaml.safe_load(self.extract(self.path, "operator.yaml"))
+        return yaml.safe_load(self.extract(self.path, OPERATORFILE))
 
     @classmethod
     def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
@@ -587,8 +593,8 @@ def load(cls, path: os.PathLike):
         if not tarfile.is_tarfile(path):
             raise ValueError("EKO: the corresponding file is not a valid tar archive")
 
-        theory = yaml.safe_load(cls.extract(path, "theory.yaml"))
-        operator = yaml.safe_load(cls.extract(path, "operator.yaml"))
+        theory = yaml.safe_load(cls.extract(path, THEORYFILE))
+        operator = yaml.safe_load(cls.extract(path, OPERATORFILE))
 
         eko = cls.detached(theory, operator, path=path)
         logger.info(f"Operator loaded from path '{path}'")

From a8a5818eb007cd1cc3b8815216a7784f001f7e0a Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 17:57:29 +0200
Subject: [PATCH 095/148] Refactor save, to take stream as input

---
 src/eko/output/struct.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index b1997482e..a2f395ac4 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -12,7 +12,7 @@
 import tempfile
 import time
 from dataclasses import dataclass, fields
-from typing import BinaryIO, Dict, Literal, Optional, Tuple
+from typing import BinaryIO, Dict, Literal, Optional
 
 import lz4.frame
 import numpy as np
@@ -100,6 +100,11 @@ class Operator(DictLike):
     To be used to hold the result of a computed 4-dim operator (from a given
     scale to another given one).
 
+    Note
+    ----
+    IO works with streams in memory, in order to avoid intermediate write on
+    disk (keep read from and write to tar file only).
+
     Attributes
     ----------
     operator: np.ndarray
@@ -113,12 +118,8 @@ class Operator(DictLike):
     operator: np.ndarray
     error: Optional[np.ndarray] = None
 
-    # IO works with streams in memory, in order to avoid intermediate write on
-    # disk (keep read from and write to tar file only)
-
-    def save(self, compress: bool = True) -> Tuple[io.BytesIO, bool]:
+    def save(self, stream: io.BytesIO, compress: bool = True) -> bool:
         """Save content of operator to bytes."""
-        stream = io.BytesIO()
         if self.error is None:
             np.save(stream, self.operator)
         else:
@@ -129,9 +130,8 @@ def save(self, compress: bool = True) -> Tuple[io.BytesIO, bool]:
         if compress:
             stream = io.BytesIO(lz4.frame.compress(stream.read()))
 
-        # return the stream ready to be read, and the type of array dumped (i.e.
-        # 'npy' or 'npz')
-        return stream, self.error is None
+        # return the type of array dumped (i.e. 'npy' or 'npz')
+        return self.error is None
 
     @classmethod
     def load(cls, stream: BinaryIO, compressed: bool = True):

From 1be6fa4e8faedfa49065fbacfa5adcb86b3554d0 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Wed, 27 Jul 2022 23:46:35 +0200
Subject: [PATCH 096/148] Replace duplicated string by function call

---
 src/eko/output/struct.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index a2f395ac4..d3ba4fd42 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -264,16 +264,20 @@ def __post_init__(self):
         if not tarfile.is_tarfile(self.path):
             raise ValueError("EKO: the corresponding file is not a valid tar archive")
 
+    @staticmethod
+    def opname(q2: float) -> str:
+        return f"operators/{q2:8.2f}"
+
     def __getitem__(self, q2: float):
         # TODO: autoload
         op = self._operators[q2]
         if op is not None:
             return op
 
-        start = f"operators/{q2:8.2f}"
-
         with tarfile.open(self.path) as tar:
-            names = list(filter(lambda n: n.startswith(start), tar.getnames()))
+            names = list(
+                filter(lambda n: n.startswith(self.opname(q2)), tar.getnames())
+            )
 
             if len(names) == 0:
                 raise ValueError(f"Q2 value '{q2}' not available in '{self.path}'")
@@ -304,7 +308,7 @@ def __setitem__(self, q2: float, op: Operator, compress: bool = True):
         if compress:
             suffix += ".lz4"
 
-        info = tarfile.TarInfo(name=f"operators/{q2:8.2f}.{suffix}")
+        info = tarfile.TarInfo(name=f"{self.opname(q2)}.{suffix}")
         info.size = len(stream.getbuffer())
         info.mtime = time.time()
         info.mode = 436

From 1227f764a344957322c112889b6224acbae0ff29 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 08:36:00 +0200
Subject: [PATCH 097/148] Fix operator save regression

Since now stream is passed as input, we can't overwrite the variable to write compressed content, but instead we have to replace stream content
---
 src/eko/output/struct.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index d3ba4fd42..af53f6189 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -128,7 +128,13 @@ def save(self, stream: io.BytesIO, compress: bool = True) -> bool:
 
         # compress if requested
         if compress:
-            stream = io.BytesIO(lz4.frame.compress(stream.read()))
+            compressed = lz4.frame.compress(stream.read())
+            # remove previous content
+            stream.seek(0)
+            stream.truncate()
+            # write compressed data
+            stream.write(compressed)
+            stream.seek(0)
 
         # return the type of array dumped (i.e. 'npy' or 'npz')
         return self.error is None
@@ -302,7 +308,9 @@ def __setitem__(self, q2: float, op: Operator, compress: bool = True):
         if not isinstance(op, Operator):
             raise ValueError("Only an Operator can be added to an EKO")
 
-        stream, without_err = op.save(compress)
+        stream = io.BytesIO()
+        without_err = op.save(stream, compress)
+        stream.seek(0)
 
         suffix = "npy" if without_err else "npz"
         if compress:
@@ -310,7 +318,7 @@ def __setitem__(self, q2: float, op: Operator, compress: bool = True):
 
         info = tarfile.TarInfo(name=f"{self.opname(q2)}.{suffix}")
         info.size = len(stream.getbuffer())
-        info.mtime = time.time()
+        info.mtime = int(time.time())
         info.mode = 436
         #  info.uname = os.getlogin()
         #  info.gname = os.getlogin()

From 008800066fa1e38fbced8cb6119fae9f44a2f738 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 08:48:37 +0200
Subject: [PATCH 098/148] Remove dead code from legacy

---
 src/eko/output/legacy.py | 118 +++++++++++++++++----------------------
 1 file changed, 50 insertions(+), 68 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 81d0d9755..541f43b6c 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""Support legacy storage formats."""
 import dataclasses
 import io
 import os
@@ -15,7 +16,7 @@
 from . import struct
 
 
-def get_raw(eko: struct.EKO, binarize: bool = True, skip_q2_grid: bool = False):
+def get_raw(eko: struct.EKO, binarize: bool = True):
     """Serialize result as dict/YAML.
 
     This maps the original numpy matrices to lists.
@@ -40,18 +41,15 @@ def get_raw(eko: struct.EKO, binarize: bool = True, skip_q2_grid: bool = False):
         out[f] = obj[f]
 
     # make operators raw
-    if not skip_q2_grid:
-        for q2, op in eko.items():
-            q2 = float(q2)
-            out["Q2grid"][q2] = {}
-            if op is not None:
-                for k, v in dataclasses.asdict(op).items():
-                    if binarize:
-                        out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
-                    else:
-                        out["Q2grid"][q2][k] = v.tolist()
-    else:
-        out["Q2grid"] = obj["Q2grid"]
+    for q2, op in eko.items():
+        q2 = float(q2)
+        out["Q2grid"][q2] = {}
+        if op is not None:
+            for k, v in dataclasses.asdict(op).items():
+                if binarize:
+                    out["Q2grid"][q2][k] = lz4.frame.compress(v.tobytes())
+                else:
+                    out["Q2grid"][q2][k] = v.tolist()
 
     return out
 
@@ -60,7 +58,6 @@ def dump_yaml(
     obj: struct.EKO,
     stream: Optional[TextIO] = None,
     binarize: bool = True,
-    skip_q2_grid: bool = False,
 ):
     """Serialize result as YAML.
 
@@ -70,9 +67,6 @@ def dump_yaml(
         if given, dump is written on it
     binarize : bool
         dump in binary format (instead of list format)
-    skip_q2_grid : bool
-        avoid dumping Q2grid (i.e. the actual operators) into the yaml
-        file (default: ``False``)
 
     Returns
     -------
@@ -81,7 +75,7 @@ def dump_yaml(
         Null, if written successfully to stream
 
     """
-    out = get_raw(obj, binarize, skip_q2_grid=skip_q2_grid)
+    out = get_raw(obj, binarize)
     return yaml.dump(out, stream)
 
 
@@ -89,9 +83,8 @@ def dump_yaml_to_file(
     obj: struct.EKO,
     filename: Union[str, os.PathLike],
     binarize: bool = True,
-    skip_q2_grid: bool = False,
 ):
-    """Writes YAML representation to a file.
+    """Write YAML representation to a file.
 
     Parameters
     ----------
@@ -99,9 +92,6 @@ def dump_yaml_to_file(
         target file name
     binarize : bool
         dump in binary format (instead of list format)
-    skip_q2_grid : bool
-        avoid dumping Q2grid (i.e. the actual operators) into the yaml
-        file (default: ``False``)
 
     Returns
     -------
@@ -110,12 +100,14 @@ def dump_yaml_to_file(
 
     """
     with open(filename, "w", encoding="utf-8") as f:
-        ret = dump_yaml(obj, f, binarize, skip_q2_grid=skip_q2_grid)
+        ret = dump_yaml(obj, f, binarize)
     return ret
 
 
 def dump_tar(obj: struct.EKO, tarname: Union[str, os.PathLike]):
-    """Writes representation into a tar archive containing:
+    """Write representation into a tar archive.
+
+    The written archive will contain:
 
     - metadata (in YAML)
     - operator (in numpy ``.npy`` format)
@@ -143,10 +135,7 @@ def dump_tar(obj: struct.EKO, tarname: Union[str, os.PathLike]):
         for kind in ["operator", "error"]:
             elements = []
             for q2, op in obj.items():
-                if op is not None:
-                    el = getattr(op, kind)
-                else:
-                    el = np.zeros((len(obj.xgrid), 14, len(obj.xgrid), 14))
+                el = getattr(op, kind)
                 elements.append(el)
             operator = np.stack(elements)
             stream = io.BytesIO()
@@ -159,22 +148,19 @@ def dump_tar(obj: struct.EKO, tarname: Union[str, os.PathLike]):
             tar.add(tmpdir, arcname=tarpath.stem)
 
 
-def load_yaml(stream: TextIO, skip_q2_grid=False) -> struct.EKO:
-    """
-    Load YAML representation from stream
+def load_yaml(stream: TextIO) -> struct.EKO:
+    """Load YAML representation from stream.
 
     Parameters
     ----------
-        stream : TextIO
-            source stream
-        skip_q2_grid : bool
-            avoid loading Q2grid (i.e. the actual operators) from the yaml
-            file (default: ``False``)
+    stream : TextIO
+        source stream
 
     Returns
     -------
-        obj : output
-            loaded object
+    obj : output
+        loaded object
+
     """
     obj = yaml.safe_load(stream)
     len_tpids = len(obj["rotations"]["targetpids"])
@@ -185,57 +171,53 @@ def load_yaml(stream: TextIO, skip_q2_grid=False) -> struct.EKO:
     for k, v in obj["rotations"].items():
         obj["rotations"][k] = np.array(v)
     # make operators numpy
-    if not skip_q2_grid:
-        for op in obj["Q2grid"].values():
-            for k, v in op.items():
-                if isinstance(v, list):
-                    v = np.array(v)
-                elif isinstance(v, bytes):
-                    v = np.frombuffer(lz4.frame.decompress(v))
-                    v = v.reshape(len_tpids, len_tgrid, len_ipids, len_igrid)
-                op[k] = v
+    for op in obj["Q2grid"].values():
+        for k, v in op.items():
+            if isinstance(v, list):
+                v = np.array(v)
+            elif isinstance(v, bytes):
+                v = np.frombuffer(lz4.frame.decompress(v))
+                v = v.reshape(len_tpids, len_tgrid, len_ipids, len_igrid)
+            op[k] = v
+
     return struct.EKO.new(theory={}, operator=obj)
 
 
-def load_yaml_from_file(
-    filename: Union[str, os.PathLike], skip_q2_grid: bool = False
-) -> struct.EKO:
-    """
-    Load YAML representation from file
+def load_yaml_from_file(filename: Union[str, os.PathLike]) -> struct.EKO:
+    """Load YAML representation from file.
 
     Parameters
     ----------
-        filename : str
-            source file name
-        skip_q2_grid : bool
-            avoid loading Q2grid (i.e. the actual operators) from the yaml
-            file (default: ``False``)
+    filename : str
+        source file name
 
     Returns
     -------
-        obj : output
-            loaded object
+    obj : output
+        loaded object
+
     """
     obj = None
     with open(filename, encoding="utf-8") as o:
-        obj = load_yaml(o, skip_q2_grid)
+        obj = load_yaml(o)
     return obj
 
 
 def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
-    """
-    Load tar representation from file (compliant with :meth:`dump_tar`
-    output).
+    """Load tar representation from file.
+
+    Compliant with :meth:`dump_tar` output.
 
     Parameters
     ----------
-        tarname : str
-            source tar name
+    tarname : str
+        source tar name
 
     Returns
     -------
-        obj : output
-            loaded object
+    obj : output
+        loaded object
+
     """
     tarpath = pathlib.Path(tarname)
 

From 21f7b430662a2a029193b3f6e74d995eaca31afe Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 09:02:01 +0200
Subject: [PATCH 099/148] Remove dead code from manipulate

---
 src/eko/output/manipulate.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 9d4af4105..899f21d51 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -19,16 +19,16 @@ def xgrid_reshape(
     inputgrid: Optional[np.ndarray] = None,
     inplace: bool = True,
 ):
-    """Change the operators to have in the output targetgrid and/or in the input inputgrid.
+    """Reinterpolate operators on output and/or input grids.
 
     The operation is in-place.
 
     Parameters
     ----------
     targetgrid : None or list
-        xgrid for the target
+        xgrid for the target (output PDF)
     inputgrid : None or list
-        xgrid for the input
+        xgrid for the input (input PDF)
 
     """
     # calling with no arguments is an error
@@ -76,8 +76,6 @@ def xgrid_reshape(
 
     # build new grid
     for q2, elem in eko.items():
-        if elem is None:
-            continue
         ops = elem.operator
         errs = elem.error
         if targetgrid is not None and inputgrid is None:
@@ -137,11 +135,10 @@ def flavor_reshape(
         inv_inputpids = np.linalg.inv(inputpids)
 
     # build new grid
+    # TODO: restore items
     # for q2, elem in eko.items():
     for q2 in eko.Q2grid:
         elem = eko[q2]
-        if elem is None:
-            continue
         ops = elem.operator
         errs = elem.error
         if targetpids is not None and inputpids is None:

From e4078f77c2c57a0dc084489efd900a8d19d89da0 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 09:15:08 +0200
Subject: [PATCH 100/148] Remove dead code from struct

---
 src/eko/output/struct.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index af53f6189..cfefe8f00 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -45,7 +45,6 @@ class DictLike:
 
     def __init__(self, **kwargs):
         """Empty initializer."""
-        pass
 
     @classmethod
     def from_dict(cls, dictionary):
@@ -491,14 +490,18 @@ def extract(path: os.PathLike, filename: str) -> str:
 
     @property
     def theory(self) -> dict:
+        # TODO: make an actual attribute, move load to `theory_card`, and the
+        # type of the attribute will be `eko.runcards.TheoryCard`
         return yaml.safe_load(self.extract(self.path, THEORYFILE))
 
     @property
     def theory_card(self) -> dict:
+        # TODO: return `eko.runcards.TheoryCard`
         return self.theory
 
     @property
     def operator_card(self) -> dict:
+        # TODO: return `eko.runcards.OperatorCard`
         return yaml.safe_load(self.extract(self.path, OPERATORFILE))
 
     @classmethod

From e6d5a36102ad549dca3c2a76788f5311ae946a6b Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 11:41:36 +0200
Subject: [PATCH 101/148] Document dataclass attributes in place

---
 doc/source/conf.py       |   3 ++
 src/eko/output/struct.py | 102 +++++++++++++++++++++++----------------
 2 files changed, 64 insertions(+), 41 deletions(-)

diff --git a/doc/source/conf.py b/doc/source/conf.py
index eee87debb..2f1becb11 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -103,6 +103,9 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
 
+# Criterion to sort class members
+autodoc_member_order = "bysource"
+
 # A string to be included at the beginning of all files
 shared = here / "shared"
 rst_prolog = "\n".join(
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index cfefe8f00..f9ecfe4ea 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -104,21 +104,33 @@ class Operator(DictLike):
     IO works with streams in memory, in order to avoid intermediate write on
     disk (keep read from and write to tar file only).
 
-    Attributes
-    ----------
-    operator: np.ndarray
-        content of the evolution operator
-    error: np.ndarray or None
-        errors on individual operator elements (mainly used for integration
-        error, but it can host any kind of error)
-
     """
 
     operator: np.ndarray
+    """Content of the evolution operator."""
     error: Optional[np.ndarray] = None
+    """Errors on individual operator elements (mainly used for integration
+    error, but it can host any kind of error).
+    """
+
+    def save(self, stream: BinaryIO, compress: bool = True) -> bool:
+        """Save content of operator to bytes.
+
+        Parameters
+        ----------
+        stream: BinaryIO
+            a stream where to save the operator content (in order to be able to
+            perform the operation both on disk and in memory)
+        compress: bool
+            flag to control optional compression (default: `True`)
+
+        Returns
+        -------
+        bool
+            whether the operator saved contained or not the error (this control
+            even the format, ``npz`` with errors, ``npy`` otherwise)
 
-    def save(self, stream: io.BytesIO, compress: bool = True) -> bool:
-        """Save content of operator to bytes."""
+        """
         if self.error is None:
             np.save(stream, self.operator)
         else:
@@ -140,7 +152,22 @@ def save(self, stream: io.BytesIO, compress: bool = True) -> bool:
 
     @classmethod
     def load(cls, stream: BinaryIO, compressed: bool = True):
-        """Load operator from bytes."""
+        """Load operator from bytes.
+
+        Parameters
+        ----------
+        stream: BinaryIO
+            a stream to load the operator from (to support the operation both on
+            disk and in memory)
+        compressed: bool
+            declare whether the stream is or is not compressed (default: `True`)
+
+        Returns
+        -------
+        Operator
+            the loaded instance
+
+        """
         if compressed:
             stream = io.BytesIO(lz4.frame.decompress(stream.read()))
         content = np.load(stream)
@@ -161,6 +188,8 @@ def load(cls, stream: BinaryIO, compressed: bool = True):
 
 @dataclass
 class Debug(DictLike):
+    """Debug configurations."""
+
     skip_singlet: bool = False
     skip_non_singlet: bool = False
 
@@ -208,42 +237,18 @@ class EKO:
     loading is done by this class (for the Python library, other
     implementations are possible and encouraged).
 
-    For this reason, a core component of an :cls:`EKO` object is a path,
+    For this reason, a core component of an :class:`EKO` object is a path,
     referring to the location on disk of the corresponding operator.
-    Any :cls:`EKO` has an associated path:
+    Any :class:`EKO` has an associated path:
 
-    - for the computed object, it corresponds to the path where the actual
-    result of the computation is already saved
-    - for a new object, it is the path at which any result of final or
-    intermediate computation is stored, as soon as it is produced
+        - for the computed object, it corresponds to the path where the actual
+          result of the computation is already saved
+        - for a new object, it is the path at which any result of final or
+          intermediate computation is stored, as soon as it is produced
 
     The computation can be stopped at any time, without the loss of any of the
     intermediate results.
 
-    Attributes
-    ----------
-    path : pathlib.Path
-        path on disk, to which this object is linked (and for which it is
-        essentially an interface)
-    Q02 : float
-        inital scale
-    xgrid : interpolation.XGrid
-        momentum fraction internal grid
-    pids : np.ndarray
-        array of integers, corresponding to internal PIDs
-    configs : Configs
-        specific configuration to be used during the calculation of these
-        operators
-    rotations : Rotations
-        manipulation information, describing the current status of the EKO (e.g.
-        `inputgrid` and `targetgrid`)
-    debug : Debug
-        debug configurations
-    version : str
-        library version used to create the corresponding file
-    data_version : str
-        specs version, to which the file adheres
-
     """
 
     # operators cache, contains the Q2 grid information
@@ -252,16 +257,31 @@ class EKO:
     # -----------------
     # mandatory, identifying features
     path: pathlib.Path
+    """Path on disk, to which this object is linked (and for which it is
+    essentially an interface).
+    """
     Q02: float
+    """Inital scale."""
     xgrid: interpolation.XGrid
+    """Momentum fraction internal grid."""
     pids: np.ndarray
+    """Array of integers, corresponding to internal PIDs."""
     # collections
     configs: Configs
+    """Specific configuration to be used during the calculation of these
+    operators.
+    """
     rotations: Rotations
+    """Manipulation information, describing the current status of the EKO (e.g.
+    `inputgrid` and `targetgrid`).
+    """
     debug: Debug
+    """Debug configurations."""
     # tagging information
     version: str = vmod.__version__
+    """Library version used to create the corresponding file."""
     data_version: str = vmod.__data_version__
+    """Specs version, to which the file adheres."""
 
     def __post_init__(self):
         if self.path.suffix != ".tar":

From a57be9d459b02cbcc03f5aceee3abd8209d1070e Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 11:42:39 +0200
Subject: [PATCH 102/148] Fix tests

---
 benchmarks/lha_paper_bench.py   |  4 +-
 src/eko/output/legacy.py        | 15 ++++----
 src/eko/output/manipulate.py    |  5 +--
 tests/conftest.py               |  7 +++-
 tests/eko/test_output.py        | 66 ++++++++++++++++-----------------
 tests/eko/test_output_struct.py | 16 ++++----
 tests/ekomark/test_apply.py     | 39 ++++++++-----------
 7 files changed, 72 insertions(+), 80 deletions(-)

diff --git a/benchmarks/lha_paper_bench.py b/benchmarks/lha_paper_bench.py
index 9d3bc36d1..451c638d1 100644
--- a/benchmarks/lha_paper_bench.py
+++ b/benchmarks/lha_paper_bench.py
@@ -224,8 +224,8 @@ def benchmark_sv(self, pto):
     obj = BenchmarkVFNS()
     # obj = BenchmarkFFNS()
 
-    # obj.benchmark_plain(0)
-    obj.benchmark_sv(2)
+    obj.benchmark_plain(0)
+    # obj.benchmark_sv(2)
 
     # # VFNS benchmarks with LHA settings
     # programs = ["LHA", "pegasus", "apfel"]
diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 541f43b6c..97e8962ca 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -221,20 +221,20 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
     """
     tarpath = pathlib.Path(tarname)
 
+    operator_grid = {}
     with tempfile.TemporaryDirectory() as tmpdir:
         tmpdir = pathlib.Path(tmpdir)
 
         with tarfile.open(tarpath, "r") as tar:
             tar.extractall(tmpdir)
 
-        # metadata = cls(**{str(k): v for k, v in obj.items() if k != "Q2grid"})
-        # metadata["Q2grid"] = list(obj["Q2grid"].keys())
-
+        # load metadata
         innerdir = list(tmpdir.glob("*"))[0]
         yamlname = innerdir / "metadata.yaml"
         with open(yamlname, encoding="utf-8") as fd:
             metadata = yaml.safe_load(fd)
 
+        # get actual grids
         grids = {}
         for fp in innerdir.glob("*.npy.lz4"):
             with lz4.frame.open(fp, "rb") as fd:
@@ -245,13 +245,12 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
             fp.unlink()
 
         q2grid = metadata["Q2grid"]
-        operator_grid = {}
         for q2, slices in zip(q2grid, zip(*grids.values())):
-            operator_grid[q2] = struct.Operator(**dict(zip(grids.keys(), slices)))
-        metadata["Q2grid"] = operator_grid
+            operator_grid[q2] = dict(zip(grids.keys(), slices))
 
+    # now eveything is in place
     eko = struct.EKO.new(theory={}, operator=metadata)
-    for q2, op in metadata["Q2grid"].items():
-        eko[q2] = op
+    for q2, op in operator_grid.items():
+        eko[q2] = struct.Operator.from_dict(op)
 
     return eko
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 899f21d51..b437ba1c6 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -135,10 +135,7 @@ def flavor_reshape(
         inv_inputpids = np.linalg.inv(inputpids)
 
     # build new grid
-    # TODO: restore items
-    # for q2, elem in eko.items():
-    for q2 in eko.Q2grid:
-        elem = eko[q2]
+    for q2, elem in eko.items():
         ops = elem.operator
         errs = elem.error
         if targetpids is not None and inputpids is None:
diff --git a/tests/conftest.py b/tests/conftest.py
index b5fe84e14..d7b0734ba 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8,6 +8,8 @@
 import numpy as np
 import pytest
 
+from eko import output
+
 
 @pytest.fixture
 def cd():
@@ -82,7 +84,10 @@ def fake_output(self):
             ),
             Q2grid=Q2grid,
         )
-        return d
+        obj = output.EKO.new(theory={}, operator=d)
+        for q2, op in Q2grid.items():
+            obj[q2] = output.struct.Operator.from_dict(op)
+        return obj, d
 
 
 @pytest.fixture
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 52aefc18e..1959dfa99 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -31,8 +31,8 @@ def chk_keys(a, b):
 class TestLegacy:
     def test_io(self, fake_output, tmp_path):
         # create object
-        o1 = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        o1, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
 
         # test streams
@@ -41,19 +41,19 @@ def test_io(self, fake_output, tmp_path):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid.raw, fake_output["xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid.raw, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid.raw, fake_card["xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid.raw, fake_card["xgrid"])
         # fake output files
         fpyaml = tmp_path / "test.yaml"
         legacy.dump_yaml_to_file(o1, fpyaml)
         # fake input file
         o3 = legacy.load_yaml_from_file(fpyaml)
-        np.testing.assert_almost_equal(o3.xgrid.raw, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o3.xgrid.raw, fake_card["xgrid"])
         # repeat for tar
         fptar = tmp_path / "test.tar"
         legacy.dump_tar(o1, fptar)
         o4 = legacy.load_tar(fptar)
-        np.testing.assert_almost_equal(o4.xgrid.raw, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o4.xgrid.raw, fake_card["xgrid"])
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
             legacy.dump_tar(o1, fn)
@@ -61,8 +61,8 @@ def test_io(self, fake_output, tmp_path):
     def test_rename_issue81(self, fake_output):
         # https://github.com/N3PDF/eko/issues/81
         # create object
-        o1 = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        o1, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
 
         with tempfile.TemporaryDirectory() as folder:
@@ -75,12 +75,12 @@ def test_rename_issue81(self, fake_output):
             shutil.move(fp1, fp2)
             # reload
             o4 = legacy.load_tar(fp2)
-            np.testing.assert_almost_equal(o4.xgrid.raw, fake_output["xgrid"])
+            np.testing.assert_almost_equal(o4.xgrid.raw, fake_card["xgrid"])
 
     def test_io_bin(self, fake_output):
         # create object
-        o1 = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        o1, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         # test streams
         stream = io.StringIO()
@@ -88,15 +88,15 @@ def test_io_bin(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid.raw, fake_output["xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid.raw, fake_output["xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid.raw, fake_card["xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid.raw, fake_card["xgrid"])
 
 
 class TestManipulate:
     def test_xgrid_reshape(self, fake_output):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
-        o1 = output.EKO.new(theory={}, operator=fake_output)
+        o1, _fake_card = fake_output
         o1.xgrid = xg
         o1.rotations.targetgrid = xg
         o1.rotations.inputgrid = xg
@@ -143,8 +143,8 @@ def test_xgrid_reshape(self, fake_output):
 
     def test_reshape_io(self, fake_output):
         # create object
-        o1 = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        o1, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         o2 = copy.deepcopy(o1)
         manipulate.xgrid_reshape(o2, [0.1, 1.0], [0.1, 1.0])
@@ -157,28 +157,26 @@ def test_reshape_io(self, fake_output):
         o3 = legacy.load_yaml(stream)
         chk_keys(o1.raw, o3.raw)
 
-    def test_flavor_reshape(self, fake_output):
+    def test_flavor_reshape(self, fake_output, tmp_path):
         # create object
         xg = np.geomspace(1e-5, 1.0, 21)
-        o1 = output.EKO.new(theory={}, operator=fake_output)
+        o1, _fake_card = fake_output
         o1.xgrid = xg
         o1.rotations.targetgrid = xg
         o1.rotations.inputgrid = xg
-        o1._operators = {
-            10: output.Operator.from_dict(
-                dict(
-                    operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
-                    error=np.zeros((2, len(xg), 2, len(xg))),
-                )
+        o1[10.0] = output.Operator.from_dict(
+            dict(
+                operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],
+                error=np.zeros((2, len(xg), 2, len(xg))),
             )
-        }
+        )
         # only target
         target_r = np.array([[1, -1], [1, 1]])
-        ot = copy.deepcopy(o1)
+        ot = o1.deepcopy(tmp_path / "ot.tar")
         manipulate.flavor_reshape(ot, target_r)
         chk_keys(o1.raw, ot.raw)
         assert ot[10].operator.shape == (2, len(xg), 2, len(xg))
-        ott = copy.deepcopy(ot)
+        ott = ot.deepcopy(tmp_path / "ott.tar")
         manipulate.flavor_reshape(ott, np.linalg.inv(target_r))
         np.testing.assert_allclose(ott[10].operator, o1[10].operator)
         with pytest.warns(Warning):
@@ -188,7 +186,7 @@ def test_flavor_reshape(self, fake_output):
 
         # only input
         input_r = np.array([[1, -1], [1, 1]])
-        oi = copy.deepcopy(o1)
+        oi = o1.deepcopy(tmp_path / "oi.tar")
         manipulate.flavor_reshape(oi, inputpids=input_r)
         chk_keys(o1.raw, oi.raw)
         assert oi[10].operator.shape == (2, len(xg), 2, len(xg))
@@ -201,7 +199,7 @@ def test_flavor_reshape(self, fake_output):
             np.testing.assert_allclose(oii[10].operator, o1[10].operator)
 
         # both
-        oit = copy.deepcopy(o1)
+        oit = o1.deepcopy(tmp_path / "oit.tar")
         manipulate.flavor_reshape(
             oit, np.array([[1, -1], [1, 1]]), np.array([[1, -1], [1, 1]])
         )
@@ -210,9 +208,9 @@ def test_flavor_reshape(self, fake_output):
         np.testing.assert_allclose(oit[10].operator, op[0], atol=1e-10)
         # error
         with pytest.raises(ValueError):
-            manipulate.flavor_reshape(copy.deepcopy(o1))
+            manipulate.flavor_reshape(o1.deepcopy(tmp_path / "fail.tar"))
 
-    def test_to_evol(self, fake_factory):
+    def test_to_evol(self, fake_factory, tmp_path):
         xgrid = np.array([0.5, 1.0])
         interpolation_polynomial_degree = 1
         interpolation_is_log = False
@@ -239,11 +237,11 @@ def test_to_evol(self, fake_factory):
         )
         o00 = output.EKO.new(theory={}, operator=d)
         o00[q2_out] = output.Operator(**Q2grid[q2_out])
-        o01 = copy.deepcopy(o00)
+        o01 = o00.deepcopy(tmp_path / "o01.tar")
         manipulate.to_evol(o01)
-        o10 = copy.deepcopy(o00)
+        o10 = o00.deepcopy(tmp_path / "o10.tar")
         manipulate.to_evol(o10, False, True)
-        o11 = copy.deepcopy(o00)
+        o11 = o00.deepcopy(tmp_path / "o11.tar")
         manipulate.to_evol(o11, True, True)
         chk_keys(o00.raw, o11.raw)
 
diff --git a/tests/eko/test_output_struct.py b/tests/eko/test_output_struct.py
index 01bbe4456..c850766a0 100644
--- a/tests/eko/test_output_struct.py
+++ b/tests/eko/test_output_struct.py
@@ -6,11 +6,11 @@
 class TestLegacy:
     def test_items(self, fake_output):
         """Test autodump, autoload, and manual unload."""
-        eko = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        eko, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             eko[q2] = output.Operator.from_dict(op)
 
-        q2 = next(iter(fake_output["Q2grid"]))
+        q2 = next(iter(fake_card["Q2grid"]))
 
         eko._operators[q2] = None
         assert isinstance(eko[q2], struct.Operator)
@@ -22,8 +22,8 @@ def test_items(self, fake_output):
 
     def test_iter(self, fake_output):
         """Test managed iteration."""
-        eko = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        eko, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             eko[q2] = output.Operator.from_dict(op)
 
         q2prev = None
@@ -35,11 +35,11 @@ def test_iter(self, fake_output):
 
     def test_context_operator(self, fake_output):
         """Test automated handling through context."""
-        eko = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
+        eko, fake_card = fake_output
+        for q2, op in fake_card["Q2grid"].items():
             eko[q2] = output.Operator.from_dict(op)
 
-        q2 = next(iter(fake_output["Q2grid"]))
+        q2 = next(iter(fake_card["Q2grid"]))
 
         with eko.operator(q2) as op:
             assert isinstance(op, struct.Operator)
diff --git a/tests/ekomark/test_apply.py b/tests/ekomark/test_apply.py
index 1f048322a..48b044636 100644
--- a/tests/ekomark/test_apply.py
+++ b/tests/ekomark/test_apply.py
@@ -1,28 +1,24 @@
 # -*- coding: utf-8 -*-
 import numpy as np
 
-from eko import output
 from ekomark import apply
 
 
 class TestApply:
     def test_apply(self, fake_output, fake_pdf):
-        q2_out = list(fake_output["Q2grid"].keys())[0]
-        # create object
-        o = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
-            o[q2] = output.Operator.from_dict(op)
+        o, fake_card = fake_output
+        q2_out = list(fake_card["Q2grid"].keys())[0]
         # fake pdfs
         pdf_grid = apply.apply_pdf(o, fake_pdf)
-        assert len(pdf_grid) == len(fake_output["Q2grid"])
+        assert len(pdf_grid) == len(fake_card["Q2grid"])
         pdfs = pdf_grid[q2_out]["pdfs"]
-        assert list(pdfs.keys()) == fake_output["rotations"]["targetpids"]
-        ref_pid1 = fake_output["Q2grid"][q2_out]["operator"][0, :, 1, :] @ np.ones(
-            len(fake_output["xgrid"])
+        assert list(pdfs.keys()) == fake_card["rotations"]["targetpids"]
+        ref_pid1 = fake_card["Q2grid"][q2_out]["operator"][0, :, 1, :] @ np.ones(
+            len(fake_card["xgrid"])
         )
         np.testing.assert_allclose(pdfs[0], ref_pid1)
-        ref_pid2 = fake_output["Q2grid"][q2_out]["operator"][1, :, 1, :] @ np.ones(
-            len(fake_output["xgrid"])
+        ref_pid2 = fake_card["Q2grid"][q2_out]["operator"][1, :, 1, :] @ np.ones(
+            len(fake_card["xgrid"])
         )
         np.testing.assert_allclose(pdfs[1], ref_pid2)
         # rotate to target_grid
@@ -30,30 +26,27 @@ def test_apply(self, fake_output, fake_pdf):
         pdf_grid = apply.apply_pdf(o, fake_pdf, target_grid)
         assert len(pdf_grid) == 1
         pdfs = pdf_grid[q2_out]["pdfs"]
-        assert list(pdfs.keys()) == fake_output["rotations"]["targetpids"]
+        assert list(pdfs.keys()) == fake_card["rotations"]["targetpids"]
 
     def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
-        q2_out = list(fake_output["Q2grid"].keys())[0]
-        # create object
-        o = output.EKO.new(theory={}, operator=fake_output)
-        for q2, op in fake_output["Q2grid"].items():
-            o[q2] = output.Operator.from_dict(op)
+        o, fake_card = fake_output
+        q2_out = list(fake_card["Q2grid"].keys())[0]
         # fake pdfs
         monkeypatch.setattr(
             "eko.basis_rotation.rotate_flavor_to_evolution", np.ones((2, 2))
         )
         monkeypatch.setattr(
             "eko.basis_rotation.flavor_basis_pids",
-            fake_output["rotations"]["targetpids"],
+            fake_card["rotations"]["targetpids"],
         )
         fake_evol_basis = ("a", "b")
         monkeypatch.setattr("eko.basis_rotation.evol_basis", fake_evol_basis)
         pdf_grid = apply.apply_pdf(o, fake_pdf, rotate_to_evolution_basis=True)
-        assert len(pdf_grid) == len(fake_output["Q2grid"])
+        assert len(pdf_grid) == len(fake_card["Q2grid"])
         pdfs = pdf_grid[q2_out]["pdfs"]
         assert list(pdfs.keys()) == list(fake_evol_basis)
         ref_a = (
-            fake_output["Q2grid"][q2_out]["operator"][0, :, 1, :]
-            + fake_output["Q2grid"][q2_out]["operator"][1, :, 1, :]
-        ) @ np.ones(len(fake_output["xgrid"]))
+            fake_card["Q2grid"][q2_out]["operator"][0, :, 1, :]
+            + fake_card["Q2grid"][q2_out]["operator"][1, :, 1, :]
+        ) @ np.ones(len(fake_card["xgrid"]))
         np.testing.assert_allclose(pdfs["a"], ref_a)

From 16c6fdda3c968805b42843fa96e1f54102bc61a5 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 11:52:37 +0200
Subject: [PATCH 103/148] Document configs and rotations, remove useless
 default constructor

The default is useless because the class already have defaults: everything to None
---
 src/eko/output/struct.py | 32 +++++++++++++++++++++++++-------
 1 file changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index f9ecfe4ea..bd36612e7 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -191,32 +191,50 @@ class Debug(DictLike):
     """Debug configurations."""
 
     skip_singlet: bool = False
+    """Whether to skip QCD singlet computation."""
     skip_non_singlet: bool = False
+    """Whether to skip QCD non-singlet computation."""
 
 
 @dataclass
 class Configs(DictLike):
+    """Solution specific configurations."""
+
     ev_op_max_order: int
+    """Maximum order to use in U matrices expansion.
+    Used only in ``perturbative`` solutions.
+    """
     ev_op_iterations: int
+    """Number of intervals in which to break the global path."""
     interpolation_polynomial_degree: int
+    """Degree of elements of the intepolation polynomial basis."""
     interpolation_is_log: bool
+    r"""Whether to use polynomials in :math:`\log(x)`.
+    If `false`, polynomials are in :math:`x`.
+    """
     backward_inversion: Literal["exact", "expanded"]
+    """Which method to use for backward matching conditions."""
     n_integration_cores: int = 1
+    """Number of cores used to parallelize integration."""
 
 
 @dataclass
 class Rotations(DictLike):
+    """Rotations related configurations.
+
+    Here "Rotation" is intended in a broad sense: it includes both rotations in
+    flavor space (labeled with suffix `pids`) and in :math:`x`-space (labeled
+    with suffix `grid`).
+    Rotations in :math:`x`-space correspond to reinterpolate the result on a
+    different basis of polynomials.
+
+    """
+
     targetgrid: Optional[np.ndarray] = None
     inputgrid: Optional[np.ndarray] = None
     targetpids: Optional[np.ndarray] = None
     inputpids: Optional[np.ndarray] = None
 
-    @classmethod
-    def default(cls, xgrid: interpolation.XGrid, pids: np.ndarray):
-        return cls(
-            targetgrid=xgrid.raw, inputgrid=xgrid.raw, targetpids=pids, inputpids=pids
-        )
-
 
 @dataclass
 class EKO:
@@ -561,7 +579,7 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             Q02=float(operator["Q0"] ** 2),
             _operators={q2: None for q2 in operator["Q2grid"]},
             configs=Configs.from_dict(operator["configs"]),
-            rotations=Rotations.default(xgrid, pids),
+            rotations=Rotations(),
             debug=Debug.from_dict(operator.get("debug", {})),
         )
 

From eba344cfe698c69a5d310a786c2f2e7d77e79c06 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 11:59:47 +0200
Subject: [PATCH 104/148] Restore defaults, since None unsupported in
 manipulate

---
 src/eko/output/struct.py | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index bd36612e7..59983c977 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -235,6 +235,37 @@ class Rotations(DictLike):
     targetpids: Optional[np.ndarray] = None
     inputpids: Optional[np.ndarray] = None
 
+    @classmethod
+    def default(cls, xgrid: interpolation.XGrid, pids: np.ndarray):
+        """Create instance with default rotations.
+
+        Default is no rotation at all, that you can also specify leaving the
+        rotations empty.
+        This method instead set them to the internal values, such that the
+        rotation results in an identity, and no operation is performed.
+
+        Note
+        ----
+        Setting them to `None` is not currently an option, since methods to
+        perform manipulations do not recognize this value.
+
+        Parameters
+        ----------
+        xgrid: interpolation.XGrid
+            the :math:`x`-grid used internally for computation
+        pids: np.ndarray
+            the PIDs used internally for computation
+
+        Returns
+        -------
+        Rotations
+            the instance with default values
+
+        """
+        return cls(
+            targetgrid=xgrid.raw, inputgrid=xgrid.raw, targetpids=pids, inputpids=pids
+        )
+
 
 @dataclass
 class EKO:
@@ -579,7 +610,7 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             Q02=float(operator["Q0"] ** 2),
             _operators={q2: None for q2 in operator["Q2grid"]},
             configs=Configs.from_dict(operator["configs"]),
-            rotations=Rotations(),
+            rotations=Rotations.default(xgrid, pids),
             debug=Debug.from_dict(operator.get("debug", {})),
         )
 

From ff02f256e75510fc88ee7135618f1d1dfc3296dd Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 16:29:06 +0200
Subject: [PATCH 105/148] Serialize properly grids

---
 src/eko/interpolation.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index afe56a458..86554463e 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -452,6 +452,13 @@ def size(self) -> int:
     def tolist(self) -> list:
         return self.raw.tolist()
 
+    def dump(self) -> dict:
+        return dict(grid=self.tolist(), log=self.log)
+
+    @classmethod
+    def load(cls, doc: dict):
+        return cls(doc["grid"], log=doc["log"])
+
 
 class InterpolatorDispatcher:
     """

From d529c4b351034cde2eae048a4a9ba205be54ae95 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 16:31:02 +0200
Subject: [PATCH 106/148] Extend compatibility layer

---
 src/eko/compatibility.py | 46 ++++++++++++++++++++++++----------------
 1 file changed, 28 insertions(+), 18 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index 34d44b4f1..aa3dd61a0 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -5,33 +5,38 @@
 
 """
 import copy
+from typing import Optional
 
 
-def update(theory, operators):
-    """
-    Upgrade the legacy theory and observable runcards with the new settings.
+def update(theory: dict, operators: Optional[dict]):
+    """Upgrade the legacy theory and observable runcards with the new settings.
 
     Parameters
     ----------
-        theory : dict
-            theory runcard
-        observables : dict
-            observable runcard
+    theory : dict
+        theory runcard
+    observables : dict or None
+        observable runcard (default: `None`)
 
     Returns
     -------
-        new_theory : dict
-            upgraded theory runcard
-        new_obs : dict
-            upgraded observable runcard
+    new_theory : dict
+        upgraded theory runcard
+    new_obs : dict
+        upgraded observable runcard
+
     """
     new_theory = copy.deepcopy(theory)
     new_operators = copy.deepcopy(operators)
+
     if "alphaqed" in new_theory:
         new_theory["alphaem"] = new_theory.pop("alphaqed")
     if "QED" in new_theory:
         new_theory["order"] = (new_theory.pop("PTO") + 1, new_theory.pop("QED"))
+
     if operators is not None:
+        if new_operators is None:
+            raise ValueError("Unreachable.")
         if "configs" not in operators:
             raise ValueError("No subsections, old format.")
 
@@ -41,21 +46,26 @@ def update(theory, operators):
                 max_order,
                 new_theory["order"][1],
             )
+
+        new_operators["rotations"]["xgrid"] = operators["xgrid"]
+        for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
+            new_operators["rotations"][f"_{basis}"] = operators["rotations"][basis]
+
     return new_theory, new_operators
 
 
-def update_theory(theory):
-    """
-    Upgrade the legacy theory runcards with the new settings.
+def update_theory(theory: dict):
+    """Upgrade the legacy theory runcards with the new settings.
 
     Parameters
     ----------
-        theory : dict
-            theory runcard
+    theory : dict
+        theory runcard
 
     Returns
     -------
-        new_theory : dict
-            upgraded theory runcard
+    new_theory : dict
+        upgraded theory runcard
+
     """
     return update(theory, None)[0]

From d74207ef90272f21c3d9d84a1da91434b52c0d7f Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 16:47:46 +0200
Subject: [PATCH 107/148] Fix compatibility tests

---
 src/eko/compatibility.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index aa3dd61a0..2cc4f5c32 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -35,21 +35,22 @@ def update(theory: dict, operators: Optional[dict]):
         new_theory["order"] = (new_theory.pop("PTO") + 1, new_theory.pop("QED"))
 
     if operators is not None:
-        if new_operators is None:
-            raise ValueError("Unreachable.")
-        if "configs" not in operators:
-            raise ValueError("No subsections, old format.")
+        assert new_operators is not None
 
-        max_order = new_operators["configs"]["ev_op_max_order"]
+        new_operators["configs"] = {}
+        new_operators["rotations"] = {}
+        new_operators["debug"] = {}
+
+        max_order = operators["ev_op_max_order"]
         if isinstance(max_order, int):
             new_operators["configs"]["ev_op_max_order"] = (
                 max_order,
                 new_theory["order"][1],
             )
 
-        new_operators["rotations"]["xgrid"] = operators["xgrid"]
+        new_operators["rotations"]["xgrid"] = operators["interpolation_xgrid"]
         for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
-            new_operators["rotations"][f"_{basis}"] = operators["rotations"][basis]
+            new_operators["rotations"][f"_{basis}"] = operators[basis]
 
     return new_theory, new_operators
 

From cdaed45d9d543c0846c045186000167fba64ab1b Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 17:00:41 +0200
Subject: [PATCH 108/148] Skip compatibility for new cards

---
 src/eko/compatibility.py        | 2 +-
 tests/eko/test_compatibility.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index 2cc4f5c32..a1c10aa36 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -34,7 +34,7 @@ def update(theory: dict, operators: Optional[dict]):
     if "QED" in new_theory:
         new_theory["order"] = (new_theory.pop("PTO") + 1, new_theory.pop("QED"))
 
-    if operators is not None:
+    if operators is not None and "configs" not in operators:
         assert new_operators is not None
 
         new_operators["configs"] = {}
diff --git a/tests/eko/test_compatibility.py b/tests/eko/test_compatibility.py
index d5c4e3a41..2d4c0b25b 100644
--- a/tests/eko/test_compatibility.py
+++ b/tests/eko/test_compatibility.py
@@ -23,7 +23,7 @@ def test_compatibility():
 def test_compatibility_operators():
     _, new_operator = compatibility.update(theory1, operator_dict)
 
-    assert not isinstance(new_operator["configs"]["ev_op_max_order"], int)
+    assert isinstance(new_operator["configs"]["ev_op_max_order"], int)
 
-    with pytest.raises(ValueError):
+    with pytest.raises(KeyError):
         compatibility.update(theory1, {})

From 5f457a4d34715340113685eb2123280506434296 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 17:02:20 +0200
Subject: [PATCH 109/148] Load legacy YAML output

---
 src/eko/output/legacy.py        | 44 ++++++++++++----
 src/eko/output/manipulate.py    | 16 +++---
 src/eko/output/struct.py        | 91 +++++++++++++++++----------------
 src/eko/runner.py               |  2 +-
 tests/conftest.py               | 49 ++++++++++++++----
 tests/eko/test_compatibility.py | 22 +++++---
 tests/eko/test_output.py        | 38 +++++++-------
 7 files changed, 164 insertions(+), 98 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 97e8962ca..72b31698a 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Support legacy storage formats."""
+import copy
 import dataclasses
 import io
 import os
@@ -37,7 +38,7 @@ def get_raw(eko: struct.EKO, binarize: bool = True):
     # prepare output dict
     out = {"Q2grid": {}, "eko_version": version.__version__}
     # dump raw elements
-    for f in ["Q0", "xgrid", "configs", "rotations"]:
+    for f in ["Q0", "configs", "rotations"]:
         out[f] = obj[f]
 
     # make operators raw
@@ -54,6 +55,32 @@ def get_raw(eko: struct.EKO, binarize: bool = True):
     return out
 
 
+def upgrade(raw: dict) -> dict:
+    """Upgrade raw representation to new layout.
+
+    Parameters
+    ----------
+    raw: dict
+        legacy raw representation of Output
+
+    Returns
+    -------
+    dict
+        upgraded dict representation
+
+    """
+    upgraded = copy.deepcopy(raw)
+
+    if "rotations" not in raw:
+        upgraded["rotations"] = {}
+        upgraded["rotations"]["xgrid"] = raw["interpolation_xgrid"]
+        upgraded["rotations"]["pids"] = raw["pids"]
+        for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
+            upgraded["rotations"][f"_{basis}"] = raw[basis]
+
+    return upgraded
+
+
 def dump_yaml(
     obj: struct.EKO,
     stream: Optional[TextIO] = None,
@@ -162,14 +189,11 @@ def load_yaml(stream: TextIO) -> struct.EKO:
         loaded object
 
     """
-    obj = yaml.safe_load(stream)
-    len_tpids = len(obj["rotations"]["targetpids"])
-    len_ipids = len(obj["rotations"]["inputpids"])
-    len_tgrid = len(obj["rotations"]["targetgrid"])
-    len_igrid = len(obj["rotations"]["inputgrid"])
-    # cast lists to numpy
-    for k, v in obj["rotations"].items():
-        obj["rotations"][k] = np.array(v)
+    obj = upgrade(yaml.safe_load(stream))
+    len_tpids = len(obj["rotations"]["_targetpids"])
+    len_ipids = len(obj["rotations"]["_inputpids"])
+    len_tgrid = len(obj["rotations"]["_targetgrid"])
+    len_igrid = len(obj["rotations"]["_inputgrid"])
     # make operators numpy
     for op in obj["Q2grid"].values():
         for k, v in op.items():
@@ -232,7 +256,7 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
         innerdir = list(tmpdir.glob("*"))[0]
         yamlname = innerdir / "metadata.yaml"
         with open(yamlname, encoding="utf-8") as fd:
-            metadata = yaml.safe_load(fd)
+            metadata = upgrade(yaml.safe_load(fd))
 
         # get actual grids
         grids = {}
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index b437ba1c6..6dbe90254 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -17,7 +17,6 @@ def xgrid_reshape(
     eko: EKO,
     targetgrid: Optional[np.ndarray] = None,
     inputgrid: Optional[np.ndarray] = None,
-    inplace: bool = True,
 ):
     """Reinterpolate operators on output and/or input grids.
 
@@ -63,7 +62,7 @@ def xgrid_reshape(
             False,
         )
         target_rot = b.get_interpolation(targetgrid)
-        eko.rotations.targetgrid = np.array(targetgrid)
+        eko.rotations._targetgrid = interpolation.XGrid(targetgrid)
     if inputgrid is not None:
         b = interpolation.InterpolatorDispatcher(
             inputgrid,
@@ -72,7 +71,7 @@ def xgrid_reshape(
             False,
         )
         input_rot = b.get_interpolation(eko.rotations.inputgrid)
-        eko.rotations.inputgrid = np.array(inputgrid)
+        eko.rotations._inputgrid = interpolation.XGrid(inputgrid)
 
     # build new grid
     for q2, elem in eko.items():
@@ -97,7 +96,6 @@ def flavor_reshape(
     eko: EKO,
     targetpids: Optional[np.ndarray] = None,
     inputpids: Optional[np.ndarray] = None,
-    inplace: bool = True,
 ):
     """Change the operators to have in the output targetpids and/or in the input inputpids.
 
@@ -155,12 +153,12 @@ def flavor_reshape(
     # drop PIDs - keeping them int nevertheless
     # there is no meaningful way to set them in general, after rotation
     if inputpids is not None:
-        eko.rotations.inputpids = [0] * len(eko.rotations.inputpids)
+        eko.rotations._inputpids = np.array([0] * len(eko.rotations.inputpids))
     if targetpids is not None:
-        eko.rotations.targetpids = [0] * len(eko.rotations.targetpids)
+        eko.rotations._targetpids = np.array([0] * len(eko.rotations.targetpids))
 
 
-def to_evol(eko: EKO, source: bool = True, target: bool = False, inplace: bool = True):
+def to_evol(eko: EKO, source: bool = True, target: bool = False):
     """Rotate the operator into evolution basis.
 
     This also assigns also the pids. The operation is in-place.
@@ -179,6 +177,6 @@ def to_evol(eko: EKO, source: bool = True, target: bool = False, inplace: bool =
     flavor_reshape(eko, inputpids=inputpids, targetpids=targetpids)
     # assign pids
     if source:
-        eko.rotations.inputpids = br.evol_basis_pids
+        eko.rotations._inputpids = br.evol_basis_pids
     if target:
-        eko.rotations.targetpids = br.evol_basis_pids
+        eko.rotations._targetpids = br.evol_basis_pids
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 59983c977..8564b897b 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -19,7 +19,6 @@
 import numpy.lib.npyio as npyio
 import yaml
 
-from .. import basis_rotation as br
 from .. import interpolation
 from .. import version as vmod
 
@@ -86,6 +85,8 @@ def raw(self):
             # replace numpy scalars with python ones
             elif isinstance(value, float):
                 value = float(value)
+            elif isinstance(value, interpolation.XGrid):
+                value = value.dump()
 
             dictionary[field.name] = value
 
@@ -230,41 +231,46 @@ class Rotations(DictLike):
 
     """
 
-    targetgrid: Optional[np.ndarray] = None
-    inputgrid: Optional[np.ndarray] = None
-    targetpids: Optional[np.ndarray] = None
-    inputpids: Optional[np.ndarray] = None
-
-    @classmethod
-    def default(cls, xgrid: interpolation.XGrid, pids: np.ndarray):
-        """Create instance with default rotations.
+    xgrid: interpolation.XGrid
+    """Momentum fraction internal grid."""
+    pids: np.ndarray
+    """Array of integers, corresponding to internal PIDs."""
+    _targetgrid: Optional[interpolation.XGrid] = None
+    _inputgrid: Optional[interpolation.XGrid] = None
+    _targetpids: Optional[np.ndarray] = None
+    _inputpids: Optional[np.ndarray] = None
 
-        Default is no rotation at all, that you can also specify leaving the
-        rotations empty.
-        This method instead set them to the internal values, such that the
-        rotation results in an identity, and no operation is performed.
+    def __post_init__(self):
+        for attr in ("xgrid", "_inputgrid", "_targetgrid"):
+            value = getattr(self, attr)
+            if isinstance(value, np.ndarray):
+                setattr(self, attr, interpolation.XGrid(value))
+            elif not isinstance(value, interpolation.XGrid):
+                setattr(self, attr, interpolation.XGrid.load(value))
 
-        Note
-        ----
-        Setting them to `None` is not currently an option, since methods to
-        perform manipulations do not recognize this value.
+    @property
+    def inputpids(self) -> np.ndarray:
+        if self._inputpids is None:
+            return self.pids
+        return self._inputpids
 
-        Parameters
-        ----------
-        xgrid: interpolation.XGrid
-            the :math:`x`-grid used internally for computation
-        pids: np.ndarray
-            the PIDs used internally for computation
+    @property
+    def targetpids(self) -> np.ndarray:
+        if self._targetpids is None:
+            return self.pids
+        return self._targetpids
 
-        Returns
-        -------
-        Rotations
-            the instance with default values
+    @property
+    def inputgrid(self) -> interpolation.XGrid:
+        if self._inputgrid is None:
+            return self.xgrid
+        return self._inputgrid
 
-        """
-        return cls(
-            targetgrid=xgrid.raw, inputgrid=xgrid.raw, targetpids=pids, inputpids=pids
-        )
+    @property
+    def targetgrid(self) -> interpolation.XGrid:
+        if self._targetgrid is None:
+            return self.xgrid
+        return self._targetgrid
 
 
 @dataclass
@@ -311,10 +317,6 @@ class EKO:
     """
     Q02: float
     """Inital scale."""
-    xgrid: interpolation.XGrid
-    """Momentum fraction internal grid."""
-    pids: np.ndarray
-    """Array of integers, corresponding to internal PIDs."""
     # collections
     configs: Configs
     """Specific configuration to be used during the calculation of these
@@ -332,6 +334,16 @@ class EKO:
     data_version: str = vmod.__data_version__
     """Specs version, to which the file adheres."""
 
+    @property
+    def xgrid(self) -> interpolation.XGrid:
+        """Momentum fraction internal grid."""
+        return self.rotations.xgrid
+
+    @xgrid.setter
+    def xgrid(self, value: interpolation.XGrid):
+        """Set `xgrid` value."""
+        self.rotations.xgrid = value
+
     def __post_init__(self):
         if self.path.suffix != ".tar":
             raise ValueError("Not a valid path for an EKO")
@@ -600,17 +612,12 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             the generated structure
 
         """
-        xgrid = interpolation.XGrid(operator["xgrid"])
-        pids = np.array(operator.get("pids", np.array(br.flavor_basis_pids)))
-
         return cls(
             path=path,
-            xgrid=xgrid,
-            pids=pids,
             Q02=float(operator["Q0"] ** 2),
             _operators={q2: None for q2 in operator["Q2grid"]},
             configs=Configs.from_dict(operator["configs"]),
-            rotations=Rotations.default(xgrid, pids),
+            rotations=Rotations.from_dict(operator["rotations"]),
             debug=Debug.from_dict(operator.get("debug", {})),
         )
 
@@ -688,8 +695,6 @@ def load(cls, path: os.PathLike):
     def raw(self):
         return dict(
             path=str(self.path),
-            xgrid=self.xgrid.tolist(),
-            pids=self.pids.tolist(),
             Q0=float(np.sqrt(self.Q02)),
             Q2grid=self.Q2grid,
             configs=self.configs.raw,
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 3abcc069d..6ce6ccfd8 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -100,7 +100,7 @@ def get_output(self) -> EKO:
         def similar_to_none(name: str) -> Optional[np.ndarray]:
             grid = self.post_process[name]
 
-            default = self.out.xgrid.grid if "grid" in name else self.out.pids
+            default = self.out.xgrid.grid if "grid" in name else self.out.rotations.pids
             if grid is None or (
                 len(grid) == default.size and np.allclose(grid, default, atol=1e-12)
             ):
diff --git a/tests/conftest.py b/tests/conftest.py
index d7b0734ba..6b2e12a3e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -9,6 +9,7 @@
 import pytest
 
 from eko import output
+from eko.output import legacy
 
 
 @pytest.fixture
@@ -55,8 +56,7 @@ def mk_g(self, q2s, lpids, lx):
             }
         return Q2grid
 
-    def fake_output(self):
-        # build data
+    def mk_dump(self) -> dict:
         xgrid = np.array([0.5, 1.0])
         interpolation_polynomial_degree = 1
         interpolation_is_log = False
@@ -64,14 +64,14 @@ def fake_output(self):
         q2_ref = 1
         q2_out = 2
         Q2grid = self.mk_g([q2_out], len(pids), len(xgrid))
-        d = dict(
-            xgrid=xgrid,
-            pids=pids,
+        return dict(
             rotations=dict(
-                targetgrid=xgrid,
-                inputgrid=xgrid,
-                inputpids=pids,
-                targetpids=pids,
+                xgrid=xgrid,
+                pids=pids,
+                _targetgrid=xgrid,
+                _inputgrid=xgrid,
+                _inputpids=pids,
+                _targetpids=pids,
             ),
             Q0=np.sqrt(q2_ref),
             couplings=dict(),
@@ -84,8 +84,32 @@ def fake_output(self):
             ),
             Q2grid=Q2grid,
         )
+
+    def fake_output(self):
+        d = self.mk_dump()
+        # build data
         obj = output.EKO.new(theory={}, operator=d)
-        for q2, op in Q2grid.items():
+        for q2, op in d["Q2grid"].items():
+            obj[q2] = output.struct.Operator.from_dict(op)
+        return obj, d
+
+    def fake_legacy(self):
+        d = self.mk_dump()
+        bases = d["rotations"].copy()
+
+        d["inputgrid"] = bases["_inputgrid"]
+        d["targetgrid"] = bases["_targetgrid"]
+        d["inputpids"] = bases["_inputpids"]
+        d["targetpids"] = bases["_targetpids"]
+
+        d["interpolation_xgrid"] = bases["xgrid"]
+        d["pids"] = bases["pids"]
+
+        del d["rotations"]
+
+        # build data
+        obj = output.EKO.new(theory={}, operator=legacy.upgrade(d))
+        for q2, op in d["Q2grid"].items():
             obj[q2] = output.struct.Operator.from_dict(op)
         return obj, d
 
@@ -100,6 +124,11 @@ def fake_output():
     return FakeOutput().fake_output()
 
 
+@pytest.fixture
+def fake_legacy():
+    return FakeOutput().fake_legacy()
+
+
 @pytest.fixture
 def fake_lhapdf(tmp_path):
     def lhapdf_paths():
diff --git a/tests/eko/test_compatibility.py b/tests/eko/test_compatibility.py
index 2d4c0b25b..6925751a1 100644
--- a/tests/eko/test_compatibility.py
+++ b/tests/eko/test_compatibility.py
@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
-import pytest
-
 from eko import compatibility
 
 theory1 = {
@@ -17,13 +15,23 @@ def test_compatibility():
     assert new_theory["order"][0] == theory1["PTO"] + 1
 
 
-operator_dict = {"configs": {"ev_op_max_order": 2}}
+def operator_dict(xgrid, pids):
+    return dict(
+        ev_op_max_order=2,
+        interpolation_xgrid=xgrid,
+        inputgrid=xgrid,
+        targetgrid=xgrid,
+        pids=pids,
+        inputpids=pids,
+        targetpids=pids,
+    )
 
 
 def test_compatibility_operators():
-    _, new_operator = compatibility.update(theory1, operator_dict)
+    xgrid = [1e-3, 1e-2, 1e-1, 1.0]
+    pids = [21, -1, 1]
 
-    assert isinstance(new_operator["configs"]["ev_op_max_order"], int)
+    _, new_operator = compatibility.update(theory1, operator_dict(xgrid, pids))
 
-    with pytest.raises(KeyError):
-        compatibility.update(theory1, {})
+    assert new_operator is not None
+    assert not isinstance(new_operator["configs"]["ev_op_max_order"], int)
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 1959dfa99..0e8b99740 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -29,9 +29,9 @@ def chk_keys(a, b):
 
 
 class TestLegacy:
-    def test_io(self, fake_output, tmp_path):
+    def test_io(self, fake_legacy, tmp_path):
         # create object
-        o1, fake_card = fake_output
+        o1, fake_card = fake_legacy
         for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
 
@@ -41,27 +41,27 @@ def test_io(self, fake_output, tmp_path):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid.raw, fake_card["xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid.raw, fake_card["xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid.raw, fake_card["interpolation_xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid.raw, fake_card["interpolation_xgrid"])
         # fake output files
         fpyaml = tmp_path / "test.yaml"
         legacy.dump_yaml_to_file(o1, fpyaml)
         # fake input file
         o3 = legacy.load_yaml_from_file(fpyaml)
-        np.testing.assert_almost_equal(o3.xgrid.raw, fake_card["xgrid"])
+        np.testing.assert_almost_equal(o3.xgrid.raw, fake_card["interpolation_xgrid"])
         # repeat for tar
         fptar = tmp_path / "test.tar"
         legacy.dump_tar(o1, fptar)
         o4 = legacy.load_tar(fptar)
-        np.testing.assert_almost_equal(o4.xgrid.raw, fake_card["xgrid"])
+        np.testing.assert_almost_equal(o4.xgrid.raw, fake_card["interpolation_xgrid"])
         fn = "test"
         with pytest.raises(ValueError, match="wrong suffix"):
             legacy.dump_tar(o1, fn)
 
-    def test_rename_issue81(self, fake_output):
+    def test_rename_issue81(self, fake_legacy):
         # https://github.com/N3PDF/eko/issues/81
         # create object
-        o1, fake_card = fake_output
+        o1, fake_card = fake_legacy
         for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
 
@@ -75,11 +75,13 @@ def test_rename_issue81(self, fake_output):
             shutil.move(fp1, fp2)
             # reload
             o4 = legacy.load_tar(fp2)
-            np.testing.assert_almost_equal(o4.xgrid.raw, fake_card["xgrid"])
+            np.testing.assert_almost_equal(
+                o4.xgrid.raw, fake_card["interpolation_xgrid"]
+            )
 
-    def test_io_bin(self, fake_output):
+    def test_io_bin(self, fake_legacy):
         # create object
-        o1, fake_card = fake_output
+        o1, fake_card = fake_legacy
         for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         # test streams
@@ -88,8 +90,8 @@ def test_io_bin(self, fake_output):
         # rewind and read again
         stream.seek(0)
         o2 = legacy.load_yaml(stream)
-        np.testing.assert_almost_equal(o1.xgrid.raw, fake_card["xgrid"])
-        np.testing.assert_almost_equal(o2.xgrid.raw, fake_card["xgrid"])
+        np.testing.assert_almost_equal(o1.xgrid.raw, fake_card["interpolation_xgrid"])
+        np.testing.assert_almost_equal(o2.xgrid.raw, fake_card["interpolation_xgrid"])
 
 
 class TestManipulate:
@@ -98,8 +100,8 @@ def test_xgrid_reshape(self, fake_output):
         xg = np.geomspace(1e-5, 1.0, 21)
         o1, _fake_card = fake_output
         o1.xgrid = xg
-        o1.rotations.targetgrid = xg
-        o1.rotations.inputgrid = xg
+        o1.rotations._targetgrid = xg
+        o1.rotations._inputgrid = xg
         o1._operators = {
             10: output.Operator.from_dict(
                 dict(
@@ -111,7 +113,7 @@ def test_xgrid_reshape(self, fake_output):
         xgp = np.geomspace(1e-5, 1.0, 11)
         # only target
         ot = copy.deepcopy(o1)
-        manipulate.xgrid_reshape(ot, xgp, inplace=True)
+        manipulate.xgrid_reshape(ot, xgp)
         chk_keys(o1.raw, ot.raw)
         assert ot[10].operator.shape == (2, len(xgp), 2, len(xg))
         ott = copy.deepcopy(o1)
@@ -162,8 +164,8 @@ def test_flavor_reshape(self, fake_output, tmp_path):
         xg = np.geomspace(1e-5, 1.0, 21)
         o1, _fake_card = fake_output
         o1.xgrid = xg
-        o1.rotations.targetgrid = xg
-        o1.rotations.inputgrid = xg
+        o1.rotations._targetgrid = xg
+        o1.rotations._inputgrid = xg
         o1[10.0] = output.Operator.from_dict(
             dict(
                 operator=eko_identity([1, 2, len(xg), 2, len(xg)])[0],

From 0cd40bed210624ab2761851a6f8bae4fbd1cd992 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 17:32:15 +0200
Subject: [PATCH 110/148] Fix ekomark/apply

---
 src/eko/output/struct.py    | 22 ++++++++++++++++++++++
 src/ekomark/apply.py        |  7 +++++--
 tests/ekomark/test_apply.py | 20 ++++++++++----------
 3 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 8564b897b..5a40d4ab8 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -585,6 +585,28 @@ def operator_card(self) -> dict:
         # TODO: return `eko.runcards.OperatorCard`
         return yaml.safe_load(self.extract(self.path, OPERATORFILE))
 
+    def interpolator(
+        self, mode_N: bool, use_target: bool
+    ) -> interpolation.InterpolatorDispatcher:
+        """Return associated interpolation.
+
+        Paramters
+        ---------
+        mode_N : bool
+            interpolate in N-space?
+        use_target : bool
+            use target grid? If False, use input grid
+
+        Returns
+        -------
+        interpolation.InterpolatorDispatcher
+            interpolator
+        """
+        grid = self.rotations.targetgrid if use_target else self.rotations.inputgrid
+        return interpolation.InterpolatorDispatcher(
+            grid.raw, self.configs.interpolation_polynomial_degree, grid.log, mode_N
+        )
+
     @classmethod
     def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
         """Build the in-memory object alone.
diff --git a/src/ekomark/apply.py b/src/ekomark/apply.py
index d8dfa3f45..e738acdaf 100644
--- a/src/ekomark/apply.py
+++ b/src/ekomark/apply.py
@@ -60,7 +60,10 @@ def apply_pdf_flavor(eko, lhapdf_like, targetgrid=None, flavor_rotation=None):
         if not lhapdf_like.hasFlavor(pid):
             continue
         pdfs[j] = np.array(
-            [lhapdf_like.xfxQ2(pid, x, eko.Q02) / x for x in eko.rotations.inputgrid]
+            [
+                lhapdf_like.xfxQ2(pid, x, eko.Q02) / x
+                for x in eko.rotations.inputgrid.raw
+            ]
         )
 
     # build output
@@ -87,7 +90,7 @@ def apply_pdf_flavor(eko, lhapdf_like, targetgrid=None, flavor_rotation=None):
 
     # rotate/interpolate to target grid
     if targetgrid is not None:
-        b = interpolation.InterpolatorDispatcher.from_dict(eko.raw, False)
+        b = eko.interpolator(False, True)
         rot = b.get_interpolation(targetgrid)
         for evpdf in out_grid.values():
             for pdf_label in evpdf["pdfs"]:
diff --git a/tests/ekomark/test_apply.py b/tests/ekomark/test_apply.py
index 48b044636..46c6997c8 100644
--- a/tests/ekomark/test_apply.py
+++ b/tests/ekomark/test_apply.py
@@ -5,20 +5,20 @@
 
 
 class TestApply:
-    def test_apply(self, fake_output, fake_pdf):
-        o, fake_card = fake_output
+    def test_apply(self, fake_legacy, fake_pdf):
+        o, fake_card = fake_legacy
         q2_out = list(fake_card["Q2grid"].keys())[0]
         # fake pdfs
         pdf_grid = apply.apply_pdf(o, fake_pdf)
         assert len(pdf_grid) == len(fake_card["Q2grid"])
         pdfs = pdf_grid[q2_out]["pdfs"]
-        assert list(pdfs.keys()) == fake_card["rotations"]["targetpids"]
+        assert list(pdfs.keys()) == o.rotations.targetpids
         ref_pid1 = fake_card["Q2grid"][q2_out]["operator"][0, :, 1, :] @ np.ones(
-            len(fake_card["xgrid"])
+            len(o.rotations.xgrid)
         )
         np.testing.assert_allclose(pdfs[0], ref_pid1)
         ref_pid2 = fake_card["Q2grid"][q2_out]["operator"][1, :, 1, :] @ np.ones(
-            len(fake_card["xgrid"])
+            len(o.rotations.xgrid)
         )
         np.testing.assert_allclose(pdfs[1], ref_pid2)
         # rotate to target_grid
@@ -26,10 +26,10 @@ def test_apply(self, fake_output, fake_pdf):
         pdf_grid = apply.apply_pdf(o, fake_pdf, target_grid)
         assert len(pdf_grid) == 1
         pdfs = pdf_grid[q2_out]["pdfs"]
-        assert list(pdfs.keys()) == fake_card["rotations"]["targetpids"]
+        assert list(pdfs.keys()) == o.rotations.targetpids
 
-    def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
-        o, fake_card = fake_output
+    def test_apply_flavor(self, fake_legacy, fake_pdf, monkeypatch):
+        o, fake_card = fake_legacy
         q2_out = list(fake_card["Q2grid"].keys())[0]
         # fake pdfs
         monkeypatch.setattr(
@@ -37,7 +37,7 @@ def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
         )
         monkeypatch.setattr(
             "eko.basis_rotation.flavor_basis_pids",
-            fake_card["rotations"]["targetpids"],
+            o.rotations.targetpids,
         )
         fake_evol_basis = ("a", "b")
         monkeypatch.setattr("eko.basis_rotation.evol_basis", fake_evol_basis)
@@ -48,5 +48,5 @@ def test_apply_flavor(self, fake_output, fake_pdf, monkeypatch):
         ref_a = (
             fake_card["Q2grid"][q2_out]["operator"][0, :, 1, :]
             + fake_card["Q2grid"][q2_out]["operator"][1, :, 1, :]
-        ) @ np.ones(len(fake_card["xgrid"]))
+        ) @ np.ones(len(o.rotations.xgrid))
         np.testing.assert_allclose(pdfs["a"], ref_a)

From fae26225d351893bff0d6d1f1265aa77e8d35927 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 17:47:09 +0200
Subject: [PATCH 111/148] Drop InterpolatorDispatcher constructor from dict

---
 src/eko/interpolation.py        | 83 ++++++++++++---------------------
 src/eko/runner.py               | 10 +++-
 tests/eko/test_interpolation.py | 63 ++++++-------------------
 tests/eko/test_runner.py        | 11 ++++-
 4 files changed, 62 insertions(+), 105 deletions(-)

diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index 86554463e..a530b41c3 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -8,9 +8,11 @@
 """
 import logging
 import math
+from typing import Sequence, Union
 
 import numba as nb
 import numpy as np
+import numpy.typing as npt
 import scipy.special as sp
 
 logger = logging.getLogger(__name__)
@@ -415,7 +417,7 @@ def __call__(self, *args, **kwargs):
 
 
 class XGrid:
-    def __init__(self, xgrid: np.ndarray, log: bool = True):
+    def __init__(self, xgrid: Union[Sequence, npt.NDArray], log: bool = True):
         ugrid = np.array(np.unique(xgrid), np.float_)
         if len(xgrid) != len(ugrid):
             raise ValueError(f"xgrid is not unique: {xgrid}")
@@ -459,6 +461,20 @@ def dump(self) -> dict:
     def load(cls, doc: dict):
         return cls(doc["grid"], log=doc["log"])
 
+    @classmethod
+    def fromcard(cls, value: list, log: bool):
+        if len(value) == 0:
+            raise ValueError("Empty xgrid!")
+
+        if value[0] == "make_grid":
+            xgrid = make_grid(*value[1:])
+        elif value[0] == "make_lambert_grid":
+            xgrid = make_lambert_grid(*value[1:])
+        else:
+            xgrid = np.array(value)
+
+        return cls(xgrid, log=log)
+
 
 class InterpolatorDispatcher:
     """
@@ -482,8 +498,12 @@ class InterpolatorDispatcher:
             if true compiles the function on N, otherwise compiles x
     """
 
-    def __init__(self, xgrid, polynomial_degree, log=True, mode_N=True):
-        xgrid = XGrid(xgrid, log=log)
+    def __init__(
+        self, xgrid: Union[XGrid, Sequence, npt.NDArray], polynomial_degree, mode_N=True
+    ):
+        if not isinstance(xgrid, XGrid):
+            xgrid = XGrid(xgrid)
+
         # sanity checks
         if polynomial_degree < 1:
             raise ValueError(
@@ -498,12 +518,12 @@ def __init__(self, xgrid, polynomial_degree, log=True, mode_N=True):
         # Save the different variables
         self.xgrid = xgrid
         self.polynomial_degree = polynomial_degree
-        self.log = log
+        self.log = xgrid.log
         logger.info(
             "Interpolation: number of points = %d, polynomial degree = %d, logarithmic = %s",
             len(xgrid),
             polynomial_degree,
-            log,
+            xgrid.log,
         )
 
         # Create blocks
@@ -528,54 +548,11 @@ def __init__(self, xgrid, polynomial_degree, log=True, mode_N=True):
         basis_functions = []
         for i in range(len(xgrid)):
             new_basis = BasisFunction(
-                xgrid.grid, i, list_of_blocks, mode_log=log, mode_N=mode_N
+                xgrid.grid, i, list_of_blocks, mode_log=xgrid.log, mode_N=mode_N
             )
             basis_functions.append(new_basis)
         self.basis = basis_functions
 
-    @classmethod
-    def from_dict(cls, operators_card, mode_N=True):
-        """
-        Create object from dictionary.
-
-        .. list-table:: operators runcard parameters
-            :header-rows: 1
-
-            *   - Name
-                - Type
-                - description
-            *   - ``xgrid``
-                - :py:obj:`list(float)`
-                - the interpolation grid
-            *   - ``interpolation_polynomial_degree``
-                - :py:obj:`int`
-                - polynomial degree of the interpolating function
-            *   - ``interpolation_is_log``
-                - :py:obj:`bool`
-                - use logarithmic interpolation?
-
-        Parameters
-        ----------
-            operators_card : dict
-                input configurations
-        """
-        # load xgrid
-        xgrid = operators_card["xgrid"]
-        if len(xgrid) == 0:
-            raise ValueError("Empty xgrid!")
-        if xgrid[0] == "make_grid":
-            xgrid = make_grid(*xgrid[1:])
-        elif xgrid[0] == "make_lambert_grid":
-            xgrid = make_lambert_grid(*xgrid[1:])
-        is_log_interpolation = bool(operators_card["configs"]["interpolation_is_log"])
-        polynom_rank = operators_card["configs"]["interpolation_polynomial_degree"]
-        return cls(
-            xgrid,
-            polynom_rank,
-            log=is_log_interpolation,
-            mode_N=mode_N,
-        )
-
     def __eq__(self, other):
         """Checks equality"""
         checks = [
@@ -639,11 +616,9 @@ def to_dict(self):
                 full grid configuration
         """
         ret = {
-            "xgrid": self.xgrid.tolist(),
-            "configs": {
-                "interpolation_polynomial_degree": self.polynomial_degree,
-                "interpolation_is_log": self.log,
-            },
+            "xgrid": self.xgrid.dump(),
+            "polynomial_degree": self.polynomial_degree,
+            "is_log": self.log,
         }
         return ret
 
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 6ce6ccfd8..0ff0301ca 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -54,7 +54,15 @@ def __init__(self, theory_card: dict, operators_card: dict):
         self._theory = new_theory
 
         # setup basis grid
-        bfd = interpolation.InterpolatorDispatcher.from_dict(new_operators)
+        bfd = interpolation.InterpolatorDispatcher(
+            xgrid=interpolation.XGrid(
+                new_operators["rotations"]["xgrid"],
+                log=new_operators["configs"]["interpolation_is_log"],
+            ),
+            polynomial_degree=new_operators["configs"][
+                "interpolation_polynomial_degree"
+            ],
+        )
 
         # setup the Threshold path, compute masses if necessary
         masses = None
diff --git a/tests/eko/test_interpolation.py b/tests/eko/test_interpolation.py
index 3c377300f..046b36f1c 100644
--- a/tests/eko/test_interpolation.py
+++ b/tests/eko/test_interpolation.py
@@ -100,62 +100,29 @@ def test_init(self):
         with pytest.raises(ValueError):
             interpolation.InterpolatorDispatcher([], 1)
 
-    def test_from_dict(self):
-        d = {
-            "xgrid": ["make_grid", 3, 3],
-            "configs": {
-                "interpolation_is_log": False,
-                "interpolation_polynomial_degree": 1,
-            },
-        }
-        a = interpolation.InterpolatorDispatcher.from_dict(d)
-        np.testing.assert_array_almost_equal(
-            a.xgrid.grid, np.array([1e-7, 1e-4, 1e-1, 0.55, 1.0])
-        )
-        assert a.polynomial_degree == 1
-        dd = {
-            "xgrid": ["make_lambert_grid", 20],
-            "configs": {
-                "interpolation_is_log": False,
-                "interpolation_polynomial_degree": 1,
-            },
-        }
-        aa = interpolation.InterpolatorDispatcher.from_dict(dd)
-        assert len(aa.xgrid) == 20
-        with pytest.raises(ValueError):
-            d = {
-                "xgrid": [],
-                "configs": {
-                    "interpolation_is_log": False,
-                    "interpolation_polynomial_degree": 1,
-                },
-            }
-            interpolation.InterpolatorDispatcher.from_dict(d)
-
     def test_eq(self):
-        a = interpolation.InterpolatorDispatcher(
-            np.linspace(0.1, 1, 10), 4, log=False, mode_N=False
-        )
-        b = interpolation.InterpolatorDispatcher(
-            np.linspace(0.1, 1, 9), 4, log=False, mode_N=False
-        )
+        # define grids
+        x9 = interpolation.XGrid(np.linspace(0.1, 1, 9), log=False)
+        x10 = interpolation.XGrid(np.linspace(0.1, 1, 10), log=False)
+        # test various options
+        a = interpolation.InterpolatorDispatcher(x10, 4, mode_N=False)
+        b = interpolation.InterpolatorDispatcher(x9, 4, mode_N=False)
         assert a != b
-        c = interpolation.InterpolatorDispatcher(
-            np.linspace(0.1, 1, 10), 3, log=False, mode_N=False
-        )
+        c = interpolation.InterpolatorDispatcher(x10, 3, mode_N=False)
         assert a != c
         d = interpolation.InterpolatorDispatcher(
-            np.linspace(0.1, 1, 10), 4, log=True, mode_N=False
+            np.linspace(0.1, 1, 10), 4, mode_N=False
         )
         assert a != d
-        e = interpolation.InterpolatorDispatcher(
-            np.linspace(0.1, 1, 10), 4, log=False, mode_N=False
-        )
+        e = interpolation.InterpolatorDispatcher(x10, 4, mode_N=False)
         assert a == e
         # via dict
         dd = a.to_dict()
         assert isinstance(dd, dict)
-        assert a == interpolation.InterpolatorDispatcher.from_dict(dd)
+        assert a == interpolation.InterpolatorDispatcher(
+            interpolation.XGrid.load(dd["xgrid"]),
+            polynomial_degree=dd["polynomial_degree"],
+        )
 
     def test_iter(self):
         xgrid = np.linspace(0.1, 1, 10)
@@ -165,8 +132,8 @@ def test_iter(self):
             assert bf == inter_x[k]
 
     def test_get_interpolation(self):
-        xg = [0.5, 1.0]
-        inter_x = interpolation.InterpolatorDispatcher(xg, 1, False, False)
+        xg = interpolation.XGrid([0.5, 1.0], log=False)
+        inter_x = interpolation.InterpolatorDispatcher(xg, 1, False)
         i = inter_x.get_interpolation(xg)
         np.testing.assert_array_almost_equal(i, np.eye(len(xg)))
         # .75 is exactly inbetween
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 054d0970e..fc46dac4b 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -5,7 +5,7 @@
 
 import eko
 import eko.interpolation
-from eko import compatibility
+from eko import basis_rotation as br
 
 theory_card = {
     "alphas": 0.35,
@@ -38,7 +38,6 @@
 }
 operators_card = {
     "Q2grid": [10, 100],
-    "xgrid": [0.01, 0.1, 1.0],
     "configs": {
         "interpolation_polynomial_degree": 1,
         "interpolation_is_log": True,
@@ -47,6 +46,14 @@
         "backward_inversion": "exact",
         "n_integration_cores": 1,
     },
+    "rotations": {
+        "xgrid": [0.01, 0.1, 1.0],
+        "pids": np.array(br.flavor_basis_pids),
+        "inputgrid": None,
+        "targetgrid": None,
+        "inputpids": None,
+        "targetpids": None,
+    },
     "debug": {"skip_singlet": True, "skip_non_singlet": True},
 }
 

From 3a799f82b7729242728685ce5333d48b0740ee00 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 17:55:29 +0200
Subject: [PATCH 112/148] Fix most interpolation tests

---
 tests/eko/test_interpolation.py | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/tests/eko/test_interpolation.py b/tests/eko/test_interpolation.py
index 046b36f1c..df57bc341 100644
--- a/tests/eko/test_interpolation.py
+++ b/tests/eko/test_interpolation.py
@@ -141,14 +141,14 @@ def test_get_interpolation(self):
         np.testing.assert_array_almost_equal(i, [[0.5, 0.5]])
 
     def test_evaluate_x(self):
-        xgrid = np.linspace(0.1, 1, 10)
         poly_degree = 4
         for log in [True, False]:
+            xgrid = interpolation.XGrid(np.linspace(0.1, 1, 10), log=log)
             inter_x = interpolation.InterpolatorDispatcher(
-                xgrid, poly_degree, log=log, mode_N=False
+                xgrid, poly_degree, mode_N=False
             )
             inter_N = interpolation.InterpolatorDispatcher(
-                xgrid, poly_degree, log=log, mode_N=True
+                xgrid, poly_degree, mode_N=True
             )
             for x in [0.2, 0.5]:
                 for bx, bN in zip(inter_x, inter_N):
@@ -156,16 +156,14 @@ def test_evaluate_x(self):
 
     def test_math(self):
         """Test math properties of interpolator"""
-        xgrid = np.linspace(0.09, 1, 10)
         poly_deg = 4
         for log in [True, False]:
+            xgrid = interpolation.XGrid(np.linspace(0.09, 1, 10), log=log)
             inter_x = interpolation.InterpolatorDispatcher(
-                xgrid, poly_deg, log=log, mode_N=False
+                xgrid, poly_deg, mode_N=False
             )
             check_is_interpolator(inter_x)
-            inter_N = interpolation.InterpolatorDispatcher(
-                xgrid, poly_deg, log=log, mode_N=True
-            )
+            inter_N = interpolation.InterpolatorDispatcher(xgrid, poly_deg, mode_N=True)
             check_correspondence_interpolators(inter_x, inter_N)
 
 
@@ -176,8 +174,8 @@ def test_init(self):
             interpolation.BasisFunction([0.1, 1.0], 0, [])
 
     def test_eval_N(self):
-        xg = [0.0, 1.0]
-        inter_N = interpolation.InterpolatorDispatcher(xg, 1, log=False)
+        xg = interpolation.XGrid([0.0, 1.0], log=False)
+        inter_N = interpolation.InterpolatorDispatcher(xg, 1)
         # p_0(x) = 1-x -> \tilde p_0(N) = 1/N - 1/(N+1)
         p0N = inter_N[0]
         assert len(p0N.areas) == 1
@@ -210,7 +208,7 @@ def p1Nref(N, lnx):
 
     def test_log_eval_N(self):
         xg = [np.exp(-1), 1.0]
-        inter_N = interpolation.InterpolatorDispatcher(xg, 1, log=True)
+        inter_N = interpolation.InterpolatorDispatcher(xg, 1)
         # p_0(x) = -ln(x)
         p0N = inter_N[0]
         assert len(p0N.areas) == 1
@@ -282,9 +280,8 @@ def test_is_below_x(self):
                     "res": [True, True, False, False, False],
                 },
             ]:
-                inter_x = interpolation.InterpolatorDispatcher(
-                    cfg["xg"], cfg["pd"], log=log
-                )
+                xg = interpolation.XGrid(cfg["xg"], log=log)
+                inter_x = interpolation.InterpolatorDispatcher(xg, cfg["pd"])
                 actual = [bf.is_below_x(cfg["x"]) for bf in inter_x]
                 assert actual == cfg["res"]
 

From aafa27fa38300476b71dc5e8f2e8e431d0d41caa Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 17:57:54 +0200
Subject: [PATCH 113/148] Fix get_interpolation test

---
 tests/eko/test_interpolation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/eko/test_interpolation.py b/tests/eko/test_interpolation.py
index df57bc341..6096d4ffc 100644
--- a/tests/eko/test_interpolation.py
+++ b/tests/eko/test_interpolation.py
@@ -134,7 +134,7 @@ def test_iter(self):
     def test_get_interpolation(self):
         xg = interpolation.XGrid([0.5, 1.0], log=False)
         inter_x = interpolation.InterpolatorDispatcher(xg, 1, False)
-        i = inter_x.get_interpolation(xg)
+        i = inter_x.get_interpolation(xg.raw)
         np.testing.assert_array_almost_equal(i, np.eye(len(xg)))
         # .75 is exactly inbetween
         i = inter_x.get_interpolation([0.75])

From ac117bfa7e6ce125f02da9452a8f3a482a0fac88 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 17:58:06 +0200
Subject: [PATCH 114/148] On the way to fix test_utils

---
 src/eko/compatibility.py      | 10 ++++++++++
 src/eko/runner.py             |  2 +-
 src/ekomark/data/operators.py | 29 +++++++++++++++--------------
 tests/ekobox/test_evol_pdf.py |  4 ++--
 tests/ekobox/test_utils.py    |  8 ++++----
 5 files changed, 32 insertions(+), 21 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index a1c10aa36..530d838f3 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -38,8 +38,18 @@ def update(theory: dict, operators: Optional[dict]):
         assert new_operators is not None
 
         new_operators["configs"] = {}
+        for k in (
+            "interpolation_polynomial_degree",
+            "interpolation_is_log",
+            "ev_op_iterations",
+            "backward_inversion",
+            "n_integration_cores",
+        ):
+            new_operators["configs"][k] = operators[k]
         new_operators["rotations"] = {}
         new_operators["debug"] = {}
+        for k in ("debug_skip_non_singlet", "debug_skip_singlet"):
+            new_operators["debug"][k[len("debug_") :]] = operators[k]
 
         max_order = operators["ev_op_max_order"]
         if isinstance(max_order, int):
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 0ff0301ca..5c354eaea 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -83,7 +83,7 @@ def __init__(self, theory_card: dict, operators_card: dict):
         }
 
         self.out = EKO.new(
-            theory=theory_card, operator=dict(Q0=np.sqrt(tc.q2_ref), **operators_card)
+            theory=theory_card, operator=dict(Q0=np.sqrt(tc.q2_ref), **new_operators)
         )
 
     def get_output(self) -> EKO:
diff --git a/src/ekomark/data/operators.py b/src/ekomark/data/operators.py
index 146ed70c8..faab3960c 100644
--- a/src/ekomark/data/operators.py
+++ b/src/ekomark/data/operators.py
@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""
-Operator card configurations.
-"""
+"""Operator card configurations."""
 from banana.data import cartesian_product, sql
 
 from eko import interpolation
@@ -11,17 +9,20 @@
 default_card = dict(
     sorted(
         dict(
-            xgrid=interpolation.make_grid(30, 20).tolist(),
-            configs=dict(
-                interpolation_polynomial_degree=4,
-                interpolation_is_log=True,
-                ev_op_max_order=10,
-                ev_op_iterations=10,
-                backward_inversion="expanded",
-                n_integration_cores=0,
-            ),
-            debug=dict(skip_non_singlet=False, skip_singlet=False),
+            interpolation_xgrid=interpolation.make_grid(30, 20).tolist(),
+            interpolation_polynomial_degree=4,
+            interpolation_is_log=True,
+            ev_op_max_order=10,
+            ev_op_iterations=10,
+            backward_inversion="expanded",
+            n_integration_cores=0,
+            debug_skip_non_singlet=False,
+            debug_skip_singlet=False,
             Q2grid=[100],
+            inputgrid=None,
+            targetgrid=None,
+            inputpids=None,
+            targetpids=None,
         ).items()
     )
 )
@@ -54,7 +55,7 @@
 
 def build(update=None):
     """
-    Generate all operator card updates
+    Generate all operator card updates.
 
     Parameters
     ----------
diff --git a/tests/ekobox/test_evol_pdf.py b/tests/ekobox/test_evol_pdf.py
index d2d194802..cb8ffd703 100644
--- a/tests/ekobox/test_evol_pdf.py
+++ b/tests/ekobox/test_evol_pdf.py
@@ -11,8 +11,8 @@
 op = oc.generate(
     [100.0],
     update={
-        "xgrid": [0.1, 0.5, 1.0],
-        "configs": {"interpolation_polynomial_degree": 1},
+        "interpolation_xgrid": [0.1, 0.5, 1.0],
+        "interpolation_polynomial_degree": 1,
     },
 )
 theory = tc.generate(0, 1.65)
diff --git a/tests/ekobox/test_utils.py b/tests/ekobox/test_utils.py
index ccf6198be..e773696bb 100644
--- a/tests/ekobox/test_utils.py
+++ b/tests/ekobox/test_utils.py
@@ -13,8 +13,8 @@ def test_ekos_product():
     op1 = oc.generate(
         [60.0, 80.0, 100.0],
         update={
-            "xgrid": [0.1, 0.5, 1.0],
-            "configs": {"interpolation_polynomial_degree": 1},
+            "interpolation_xgrid": [0.1, 0.5, 1.0],
+            "interpolation_polynomial_degree": 1,
         },
     )
     theory1 = tc.generate(0, 5.0)
@@ -22,8 +22,8 @@ def test_ekos_product():
     op2 = oc.generate(
         [80.0, 100.0, 120.0],
         update={
-            "xgrid": [0.1, 0.5, 1.0],
-            "configs": {"interpolation_polynomial_degree": 1},
+            "interpolation_xgrid": [0.1, 0.5, 1.0],
+            "interpolation_polynomial_degree": 1,
         },
     )
     theory2 = tc.generate(0, 10.0)

From 3767943fc117a53fa3636f0bd09acf674a829c1c Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 18:02:52 +0200
Subject: [PATCH 115/148] Propagate new InterpolatorDispatcher construction

---
 tests/eko/test_ev_op_grid.py  | 16 ++++++++++++----
 tests/eko/test_ev_operator.py | 26 ++++++++++++++++++++++----
 2 files changed, 34 insertions(+), 8 deletions(-)

diff --git a/tests/eko/test_ev_op_grid.py b/tests/eko/test_ev_op_grid.py
index 0fee639e3..d2ae1519f 100644
--- a/tests/eko/test_ev_op_grid.py
+++ b/tests/eko/test_ev_op_grid.py
@@ -73,8 +73,12 @@ def _get_operator_grid(self, use_FFNS=True, theory_update=None):
         if theory_update is not None:
             theory_card.update(theory_update)
         # create objects
-        basis_function_dispatcher = interpolation.InterpolatorDispatcher.from_dict(
-            operators_card
+        basis_function_dispatcher = interpolation.InterpolatorDispatcher(
+            interpolation.XGrid(
+                operators_card["xgrid"],
+                log=operators_card["configs"]["interpolation_is_log"],
+            ),
+            operators_card["configs"]["interpolation_polynomial_degree"],
         )
         threshold_holder = ThresholdsAtlas.from_dict(theory_card)
         a_s = Couplings.from_dict(theory_card)
@@ -91,8 +95,12 @@ def test_sanity(self):
         # errors
         with pytest.raises(ValueError):
             theory_card, operators_card = self._get_setup(True)
-            basis_function_dispatcher = interpolation.InterpolatorDispatcher.from_dict(
-                operators_card
+            basis_function_dispatcher = interpolation.InterpolatorDispatcher(
+                interpolation.XGrid(
+                    operators_card["xgrid"],
+                    log=operators_card["configs"]["interpolation_is_log"],
+                ),
+                operators_card["configs"]["interpolation_polynomial_degree"],
             )
             threshold_holder = ThresholdsAtlas.from_dict(theory_card)
             a_s = Couplings.from_dict(theory_card)
diff --git a/tests/eko/test_ev_operator.py b/tests/eko/test_ev_operator.py
index 60ddd6355..f3e1b6935 100644
--- a/tests/eko/test_ev_operator.py
+++ b/tests/eko/test_ev_operator.py
@@ -11,7 +11,7 @@
 from eko.couplings import Couplings
 from eko.evolution_operator import Operator, quad_ker
 from eko.evolution_operator.grid import OperatorGrid
-from eko.interpolation import InterpolatorDispatcher
+from eko.interpolation import InterpolatorDispatcher, XGrid
 from eko.kernels import non_singlet as ns
 from eko.kernels import singlet as s
 from eko.thresholds import ThresholdsAtlas
@@ -228,7 +228,13 @@ def test_exponentiated(self):
             ocard,
             ThresholdsAtlas.from_dict(tcard),
             Couplings.from_dict(tcard),
-            InterpolatorDispatcher.from_dict(ocard),
+            InterpolatorDispatcher(
+                XGrid(
+                    operators_card["xgrid"],
+                    log=operators_card["configs"]["interpolation_is_log"],
+                ),
+                operators_card["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         # setup objs
         o = Operator(g.config, g.managers, 3, 2.0, 10.0)
@@ -245,7 +251,13 @@ def test_compute_parallel(self, monkeypatch):
             ocard,
             ThresholdsAtlas.from_dict(tcard),
             Couplings.from_dict(tcard),
-            InterpolatorDispatcher.from_dict(ocard),
+            InterpolatorDispatcher(
+                XGrid(
+                    operators_card["xgrid"],
+                    log=operators_card["configs"]["interpolation_is_log"],
+                ),
+                operators_card["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         # setup objs
         o = Operator(g.config, g.managers, 3, 2.0, 10.0)
@@ -276,7 +288,13 @@ def test_compute(self, monkeypatch):
             ocard,
             ThresholdsAtlas.from_dict(tcard),
             Couplings.from_dict(tcard),
-            InterpolatorDispatcher.from_dict(ocard),
+            InterpolatorDispatcher(
+                XGrid(
+                    operators_card["xgrid"],
+                    log=operators_card["configs"]["interpolation_is_log"],
+                ),
+                operators_card["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         # setup objs
         o = Operator(g.config, g.managers, 3, 2.0, 10.0)

From 4e9b67bed62e068e26abfc0accde687d6fad37a8 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 18:06:51 +0200
Subject: [PATCH 116/148] Propagate also into OME tests

---
 tests/eko/test_ome.py | 34 +++++++++++++++++++++++++++++-----
 1 file changed, 29 insertions(+), 5 deletions(-)

diff --git a/tests/eko/test_ome.py b/tests/eko/test_ome.py
index c22b4762f..f288b5c57 100644
--- a/tests/eko/test_ome.py
+++ b/tests/eko/test_ome.py
@@ -9,7 +9,7 @@
 from eko.couplings import Couplings
 from eko.evolution_operator.grid import OperatorGrid
 from eko.harmonics import compute_cache
-from eko.interpolation import InterpolatorDispatcher
+from eko.interpolation import InterpolatorDispatcher, XGrid
 from eko.matching_conditions.operator_matrix_element import (
     A_non_singlet,
     A_singlet,
@@ -350,7 +350,13 @@ def test_labels(self):
                     operators_card,
                     ThresholdsAtlas.from_dict(self.theory_card),
                     Couplings.from_dict(self.theory_card),
-                    InterpolatorDispatcher.from_dict(operators_card),
+                    InterpolatorDispatcher(
+                        XGrid(
+                            operators_card["xgrid"],
+                            log=operators_card["configs"]["interpolation_is_log"],
+                        ),
+                        operators_card["configs"]["interpolation_polynomial_degree"],
+                    ),
                 )
                 o = OperatorMatrixElement(
                     g.config,
@@ -394,7 +400,13 @@ def test_compute_n3lo(self):
             self.operators_card,
             ThresholdsAtlas.from_dict(self.theory_card),
             Couplings.from_dict(self.theory_card),
-            InterpolatorDispatcher.from_dict(self.operators_card),
+            InterpolatorDispatcher(
+                XGrid(
+                    self.operators_card["xgrid"],
+                    log=self.operators_card["configs"]["interpolation_is_log"],
+                ),
+                self.operators_card["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         o = OperatorMatrixElement(
             g.config,
@@ -429,7 +441,13 @@ def test_compute_lo(self):
             self.operators_card,
             ThresholdsAtlas.from_dict(self.theory_card),
             Couplings.from_dict(self.theory_card),
-            InterpolatorDispatcher.from_dict(self.operators_card),
+            InterpolatorDispatcher(
+                XGrid(
+                    self.operators_card["xgrid"],
+                    log=self.operators_card["configs"]["interpolation_is_log"],
+                ),
+                self.operators_card["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         o = OperatorMatrixElement(
             g.config,
@@ -491,7 +509,13 @@ def test_compute_nlo(self):
             operators_card,
             ThresholdsAtlas.from_dict(t),
             Couplings.from_dict(t),
-            InterpolatorDispatcher.from_dict(operators_card),
+            InterpolatorDispatcher(
+                XGrid(
+                    operators_card["xgrid"],
+                    log=operators_card["configs"]["interpolation_is_log"],
+                ),
+                operators_card["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         o = OperatorMatrixElement(
             g.config,

From 3e668ab71decc09e4f0a493710e0025ce3b61660 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 18:23:28 +0200
Subject: [PATCH 117/148] Fix test_utils

---
 src/eko/output/struct.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 5a40d4ab8..f34876029 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -19,6 +19,7 @@
 import numpy.lib.npyio as npyio
 import yaml
 
+from .. import basis_rotation as br
 from .. import interpolation
 from .. import version as vmod
 
@@ -243,6 +244,8 @@ class Rotations(DictLike):
     def __post_init__(self):
         for attr in ("xgrid", "_inputgrid", "_targetgrid"):
             value = getattr(self, attr)
+            if value is None:
+                continue
             if isinstance(value, np.ndarray):
                 setattr(self, attr, interpolation.XGrid(value))
             elif not isinstance(value, interpolation.XGrid):
@@ -634,12 +637,22 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             the generated structure
 
         """
+        g = operator["rotations"]
+        g["pids"] = br.flavor_basis_pids
+        for k in ("xgrid", "_inputgrid", "_targetgrid"):
+            if operator["rotations"][k] is None:
+                continue
+            g[k] = {
+                "grid": operator["rotations"][k],
+                "log": operator["configs"]["interpolation_is_log"],
+            }
+
         return cls(
             path=path,
             Q02=float(operator["Q0"] ** 2),
             _operators={q2: None for q2 in operator["Q2grid"]},
             configs=Configs.from_dict(operator["configs"]),
-            rotations=Rotations.from_dict(operator["rotations"]),
+            rotations=Rotations.from_dict(g),
             debug=Debug.from_dict(operator.get("debug", {})),
         )
 

From fd632fc3884d84db021212ce79787f9391939682 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 18:24:53 +0200
Subject: [PATCH 118/148] Fix manipulate compatibility with
 InterpolatorDispatcher

---
 src/eko/interpolation.py     |  2 +-
 src/eko/output/manipulate.py | 18 ++++++++----------
 tests/eko/test_output.py     | 10 ++++++----
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/eko/interpolation.py b/src/eko/interpolation.py
index a530b41c3..72c3f78b5 100644
--- a/src/eko/interpolation.py
+++ b/src/eko/interpolation.py
@@ -570,7 +570,7 @@ def __iter__(self):
     def __getitem__(self, item):
         return self.basis[item]
 
-    def get_interpolation(self, targetgrid):
+    def get_interpolation(self, targetgrid: Union[npt.NDArray, Sequence]):
         """Computes interpolation matrix between `targetgrid` and `xgrid`.
 
         .. math::
diff --git a/src/eko/output/manipulate.py b/src/eko/output/manipulate.py
index 6dbe90254..5a91f114d 100644
--- a/src/eko/output/manipulate.py
+++ b/src/eko/output/manipulate.py
@@ -15,8 +15,8 @@
 
 def xgrid_reshape(
     eko: EKO,
-    targetgrid: Optional[np.ndarray] = None,
-    inputgrid: Optional[np.ndarray] = None,
+    targetgrid: Optional[interpolation.XGrid] = None,
+    inputgrid: Optional[interpolation.XGrid] = None,
 ):
     """Reinterpolate operators on output and/or input grids.
 
@@ -37,14 +37,14 @@ def xgrid_reshape(
     if (
         targetgrid is not None
         and len(targetgrid) == len(eko.rotations.targetgrid)
-        and np.allclose(targetgrid, eko.rotations.targetgrid)
+        and np.allclose(targetgrid.raw, eko.rotations.targetgrid.raw)
     ):
         targetgrid = None
         warnings.warn("The new targetgrid is close to the current targetgrid")
     if (
         inputgrid is not None
         and len(inputgrid) == len(eko.rotations.inputgrid)
-        and np.allclose(inputgrid, eko.rotations.inputgrid)
+        and np.allclose(inputgrid.raw, eko.rotations.inputgrid.raw)
     ):
         inputgrid = None
         warnings.warn("The new inputgrid is close to the current inputgrid")
@@ -58,20 +58,18 @@ def xgrid_reshape(
         b = interpolation.InterpolatorDispatcher(
             eko.rotations.targetgrid,
             eko.configs.interpolation_polynomial_degree,
-            eko.configs.interpolation_is_log,
             False,
         )
-        target_rot = b.get_interpolation(targetgrid)
-        eko.rotations._targetgrid = interpolation.XGrid(targetgrid)
+        target_rot = b.get_interpolation(targetgrid.raw)
+        eko.rotations._targetgrid = targetgrid
     if inputgrid is not None:
         b = interpolation.InterpolatorDispatcher(
             inputgrid,
             eko.configs.interpolation_polynomial_degree,
-            eko.configs.interpolation_is_log,
             False,
         )
-        input_rot = b.get_interpolation(eko.rotations.inputgrid)
-        eko.rotations._inputgrid = interpolation.XGrid(inputgrid)
+        input_rot = b.get_interpolation(eko.rotations.inputgrid.raw)
+        eko.rotations._inputgrid = inputgrid
 
     # build new grid
     for q2, elem in eko.items():
diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index 0e8b99740..c176eca37 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -9,7 +9,7 @@
 import pytest
 
 from eko import basis_rotation as br
-from eko import output
+from eko import interpolation, output
 from eko.output import legacy, manipulate
 
 
@@ -97,7 +97,7 @@ def test_io_bin(self, fake_legacy):
 class TestManipulate:
     def test_xgrid_reshape(self, fake_output):
         # create object
-        xg = np.geomspace(1e-5, 1.0, 21)
+        xg = interpolation.XGrid(np.geomspace(1e-5, 1.0, 21))
         o1, _fake_card = fake_output
         o1.xgrid = xg
         o1.rotations._targetgrid = xg
@@ -110,7 +110,7 @@ def test_xgrid_reshape(self, fake_output):
                 )
             )
         }
-        xgp = np.geomspace(1e-5, 1.0, 11)
+        xgp = interpolation.XGrid(np.geomspace(1e-5, 1.0, 11))
         # only target
         ot = copy.deepcopy(o1)
         manipulate.xgrid_reshape(ot, xgp)
@@ -149,7 +149,9 @@ def test_reshape_io(self, fake_output):
         for q2, op in fake_card["Q2grid"].items():
             o1[q2] = output.Operator.from_dict(op)
         o2 = copy.deepcopy(o1)
-        manipulate.xgrid_reshape(o2, [0.1, 1.0], [0.1, 1.0])
+        manipulate.xgrid_reshape(
+            o2, interpolation.XGrid([0.1, 1.0]), interpolation.XGrid([0.1, 1.0])
+        )
         manipulate.flavor_reshape(o2, inputpids=np.array([[1, -1], [1, 1]]))
         # dump
         stream = io.StringIO()

From 984b6050fcca0a3359cce342f8ba10c17ddd34f9 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 18:33:17 +0200
Subject: [PATCH 119/148] Fix eko.interpolator

---
 src/eko/output/struct.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index f34876029..96be975e5 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -607,7 +607,7 @@ def interpolator(
         """
         grid = self.rotations.targetgrid if use_target else self.rotations.inputgrid
         return interpolation.InterpolatorDispatcher(
-            grid.raw, self.configs.interpolation_polynomial_degree, grid.log, mode_N
+            grid, self.configs.interpolation_polynomial_degree, mode_N
         )
 
     @classmethod

From 18c8c314166d5e81787cea1dd63de2b98425de36 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 18:38:19 +0200
Subject: [PATCH 120/148] Fix test_op_cards

---
 tests/ekobox/test_operators_card.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/tests/ekobox/test_operators_card.py b/tests/ekobox/test_operators_card.py
index de196191c..55fc51ffa 100644
--- a/tests/ekobox/test_operators_card.py
+++ b/tests/ekobox/test_operators_card.py
@@ -7,17 +7,15 @@
 def test_generate_ocard():
     op = oc.generate([10, 100])
     assert op["Q2grid"] == [10, 100]
-    assert op["configs"]["interpolation_polynomial_degree"] == 4
+    assert op["interpolation_polynomial_degree"] == 4
     up_err = {"Prova": "Prova"}
     with pytest.raises(ValueError):
         op = oc.generate([10], update=up_err)
-    up = {
-        "configs": {"interpolation_polynomial_degree": 2, "interpolation_is_log": False}
-    }
+    up = {"interpolation_polynomial_degree": 2, "interpolation_is_log": False}
     op = oc.generate([100], update=up)
     assert op["Q2grid"] == [100]
-    assert op["configs"]["interpolation_polynomial_degree"] == 2
-    assert op["configs"]["interpolation_is_log"] is False
+    assert op["interpolation_polynomial_degree"] == 2
+    assert op["interpolation_is_log"] is False
 
 
 def test_dump_load_op_card(tmp_path, cd):

From a9b4532972bc963c035df632f00dc69e8d108d4a Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 18:38:29 +0200
Subject: [PATCH 121/148] Fix compatibility tests

---
 src/eko/output/struct.py        | 14 +++++++-------
 tests/eko/test_compatibility.py |  7 +++++++
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 96be975e5..521b795d0 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -637,22 +637,22 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
             the generated structure
 
         """
-        g = operator["rotations"]
-        g["pids"] = br.flavor_basis_pids
+        bases = operator["rotations"]
+        bases["pids"] = np.array(br.flavor_basis_pids)
         for k in ("xgrid", "_inputgrid", "_targetgrid"):
             if operator["rotations"][k] is None:
                 continue
-            g[k] = {
-                "grid": operator["rotations"][k],
-                "log": operator["configs"]["interpolation_is_log"],
-            }
+            bases[k] = interpolation.XGrid(
+                operator["rotations"][k],
+                log=operator["configs"]["interpolation_is_log"],
+            )
 
         return cls(
             path=path,
             Q02=float(operator["Q0"] ** 2),
             _operators={q2: None for q2 in operator["Q2grid"]},
             configs=Configs.from_dict(operator["configs"]),
-            rotations=Rotations.from_dict(g),
+            rotations=Rotations.from_dict(bases),
             debug=Debug.from_dict(operator.get("debug", {})),
         )
 
diff --git a/tests/eko/test_compatibility.py b/tests/eko/test_compatibility.py
index 6925751a1..8bc46d3f0 100644
--- a/tests/eko/test_compatibility.py
+++ b/tests/eko/test_compatibility.py
@@ -18,7 +18,14 @@ def test_compatibility():
 def operator_dict(xgrid, pids):
     return dict(
         ev_op_max_order=2,
+        ev_op_iterations=1,
         interpolation_xgrid=xgrid,
+        interpolation_polynomial_degree=4,
+        interpolation_is_log=True,
+        backward_inversion=None,
+        n_integration_cores=1,
+        debug_skip_singlet=False,
+        debug_skip_non_singlet=False,
         inputgrid=xgrid,
         targetgrid=xgrid,
         pids=pids,

From 6cb49a2bc26e6a0605c5a11c4644cbf51d5832c0 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 28 Jul 2022 18:52:00 +0200
Subject: [PATCH 122/148] Fix info_file and its test

---
 src/ekobox/info_file.py        | 29 +++++++++++++++--------------
 tests/ekobox/test_info_file.py |  4 ++--
 2 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/src/ekobox/info_file.py b/src/ekobox/info_file.py
index 668ffdd5c..8476d0bd5 100644
--- a/src/ekobox/info_file.py
+++ b/src/ekobox/info_file.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""LHAPDF info file utilities."""
 import copy
 import math
 
@@ -6,24 +7,23 @@
 
 
 def build(theory_card, operators_card, num_members, info_update):
-    """
-    Generate a lhapdf info file from theory and operators card
+    """Generate a lhapdf info file from theory and operators card.
 
     Parameters
     ----------
-        theory_card : dict
-            theory card
-        operators_card : dict
-            operators_card
-        num_members : int
-            number of pdf set members
-        info_update : dict
-            info to update
+    theory_card : dict
+        theory card
+    operators_card : dict
+        operators_card
+    num_members : int
+        number of pdf set members
+    info_update : dict
+        info to update
 
     Returns
     -------
-        dict
-            info file in lhapdf format
+    dict
+        info file in lhapdf format
     """
     template_info = copy.deepcopy(load.template_info)
     template_info["SetDesc"] = "Evolved PDF from " + str(theory_card["Q0"]) + " GeV"
@@ -32,8 +32,9 @@ def build(theory_card, operators_card, num_members, info_update):
     template_info.update(info_update)
     template_info["NumFlavors"] = 14
     template_info["Flavors"] = [-6, -5, -4, -3, -2, -1, 1, 2, 3, 4, 5, 6, 21, 22]
-    template_info["XMin"] = operators_card["xgrid"][0]
-    template_info["XMax"] = operators_card["xgrid"][-1]
+    # TODO actually point to input grid
+    template_info["XMin"] = operators_card["interpolation_xgrid"][0]
+    template_info["XMax"] = operators_card["interpolation_xgrid"][-1]
     template_info["NumMembers"] = num_members
     template_info["OrderQCD"] = theory_card["PTO"]
     template_info["QMin"] = round(math.sqrt(operators_card["Q2grid"][0]), 4)
diff --git a/tests/ekobox/test_info_file.py b/tests/ekobox/test_info_file.py
index 643d02745..8cdadabc4 100644
--- a/tests/ekobox/test_info_file.py
+++ b/tests/ekobox/test_info_file.py
@@ -20,5 +20,5 @@ def test_build():
     assert info["NumMembers"] == 4
     assert info["MTop"] == theory["mt"]
     np.testing.assert_allclose(info["QMin"], math.sqrt(op["Q2grid"][0]), rtol=1e-5)
-    assert info["XMin"] == op["xgrid"][0]
-    assert info["XMax"] == op["xgrid"][-1] == 1.0
+    assert info["XMin"] == op["interpolation_xgrid"][0]
+    assert info["XMax"] == op["interpolation_xgrid"][-1] == 1.0

From 996fbf47d7e25e67ecc29e5aa70f5a91bac3ab31 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 19:31:42 +0200
Subject: [PATCH 123/148] Fix legacy tests

---
 src/eko/compatibility.py |  2 +-
 src/eko/output/legacy.py | 53 +++++++++++++++++++++++++---------------
 src/eko/output/struct.py |  4 +++
 tests/conftest.py        | 25 ++++++++++---------
 tests/eko/test_runner.py |  9 +++----
 5 files changed, 55 insertions(+), 38 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index 530d838f3..bc7fd0816 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -60,7 +60,7 @@ def update(theory: dict, operators: Optional[dict]):
 
         new_operators["rotations"]["xgrid"] = operators["interpolation_xgrid"]
         for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
-            new_operators["rotations"][f"_{basis}"] = operators[basis]
+            new_operators["rotations"][f"{basis}"] = operators[basis]
 
     return new_theory, new_operators
 
diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 72b31698a..e81eff76d 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -37,9 +37,18 @@ def get_raw(eko: struct.EKO, binarize: bool = True):
 
     # prepare output dict
     out = {"Q2grid": {}, "eko_version": version.__version__}
+    out["Q0"] = obj["Q0"]
     # dump raw elements
-    for f in ["Q0", "configs", "rotations"]:
-        out[f] = obj[f]
+    for sec in ["configs", "rotations"]:
+        for key, value in obj[sec].items():
+            if key.startswith("_"):
+                key = key[1:]
+            if "grid" in key:
+                value = value["grid"]
+            out[key] = value
+
+    out["interpolation_xgrid"] = out["xgrid"]
+    del out["xgrid"]
 
     # make operators raw
     for q2, op in eko.items():
@@ -55,8 +64,8 @@ def get_raw(eko: struct.EKO, binarize: bool = True):
     return out
 
 
-def upgrade(raw: dict) -> dict:
-    """Upgrade raw representation to new layout.
+def tocard(raw: dict) -> dict:
+    """Upgrade raw representation to new card.
 
     Parameters
     ----------
@@ -66,19 +75,23 @@ def upgrade(raw: dict) -> dict:
     Returns
     -------
     dict
-        upgraded dict representation
+        new format operator card
 
     """
-    upgraded = copy.deepcopy(raw)
+    card = copy.deepcopy(raw)
+
+    card["rotations"] = {}
+    card["rotations"]["xgrid"] = raw["interpolation_xgrid"]
+    card["rotations"]["pids"] = raw["pids"]
+    for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
+        card["rotations"][basis] = raw[basis]
 
-    if "rotations" not in raw:
-        upgraded["rotations"] = {}
-        upgraded["rotations"]["xgrid"] = raw["interpolation_xgrid"]
-        upgraded["rotations"]["pids"] = raw["pids"]
-        for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
-            upgraded["rotations"][f"_{basis}"] = raw[basis]
+    card["configs"] = {}
+    for field in dataclasses.fields(struct.Configs):
+        card["configs"][field.name] = raw[field.name]
+        del card[field.name]
 
-    return upgraded
+    return card
 
 
 def dump_yaml(
@@ -152,7 +165,7 @@ def dump_tar(obj: struct.EKO, tarname: Union[str, os.PathLike]):
     with tempfile.TemporaryDirectory() as tmpdir:
         tmpdir = pathlib.Path(tmpdir)
 
-        metadata = {str(k): v for k, v in obj.raw.items() if k != "Q2grid"}
+        metadata = {str(k): v for k, v in get_raw(obj).items() if k != "Q2grid"}
         metadata["Q2grid"] = obj.Q2grid.tolist()
 
         yamlname = tmpdir / "metadata.yaml"
@@ -189,11 +202,11 @@ def load_yaml(stream: TextIO) -> struct.EKO:
         loaded object
 
     """
-    obj = upgrade(yaml.safe_load(stream))
-    len_tpids = len(obj["rotations"]["_targetpids"])
-    len_ipids = len(obj["rotations"]["_inputpids"])
-    len_tgrid = len(obj["rotations"]["_targetgrid"])
-    len_igrid = len(obj["rotations"]["_inputgrid"])
+    obj = tocard(yaml.safe_load(stream))
+    len_tpids = len(obj["rotations"]["targetpids"])
+    len_ipids = len(obj["rotations"]["inputpids"])
+    len_tgrid = len(obj["rotations"]["targetgrid"])
+    len_igrid = len(obj["rotations"]["inputgrid"])
     # make operators numpy
     for op in obj["Q2grid"].values():
         for k, v in op.items():
@@ -256,7 +269,7 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
         innerdir = list(tmpdir.glob("*"))[0]
         yamlname = innerdir / "metadata.yaml"
         with open(yamlname, encoding="utf-8") as fd:
-            metadata = upgrade(yaml.safe_load(fd))
+            metadata = tocard(yaml.safe_load(fd))
 
         # get actual grids
         grids = {}
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 521b795d0..ba75f693e 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -709,6 +709,10 @@ def new(cls, theory: dict, operator: dict, path: Optional[os.PathLike] = None):
 
             shutil.rmtree(td)
 
+        for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
+            operator["rotations"][f"_{basis}"] = operator["rotations"][basis]
+            del operator["rotations"][basis]
+
         eko = cls.detached(theory, operator, path=path)
         logger.info(f"New operator created at path '{path}'")
         return eko
diff --git a/tests/conftest.py b/tests/conftest.py
index 6b2e12a3e..2e72bad70 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -68,10 +68,10 @@ def mk_dump(self) -> dict:
             rotations=dict(
                 xgrid=xgrid,
                 pids=pids,
-                _targetgrid=xgrid,
-                _inputgrid=xgrid,
-                _inputpids=pids,
-                _targetpids=pids,
+                targetgrid=xgrid,
+                inputgrid=xgrid,
+                inputpids=pids,
+                targetpids=pids,
             ),
             Q0=np.sqrt(q2_ref),
             couplings=dict(),
@@ -97,20 +97,21 @@ def fake_legacy(self):
         d = self.mk_dump()
         bases = d["rotations"].copy()
 
-        d["inputgrid"] = bases["_inputgrid"]
-        d["targetgrid"] = bases["_targetgrid"]
-        d["inputpids"] = bases["_inputpids"]
-        d["targetpids"] = bases["_targetpids"]
+        # build data
+        obj = output.EKO.new(theory={}, operator=d)
+        for q2, op in d["Q2grid"].items():
+            obj[q2] = output.struct.Operator.from_dict(op)
+
+        d["inputgrid"] = bases["inputgrid"]
+        d["targetgrid"] = bases["targetgrid"]
+        d["inputpids"] = bases["inputpids"]
+        d["targetpids"] = bases["targetpids"]
 
         d["interpolation_xgrid"] = bases["xgrid"]
         d["pids"] = bases["pids"]
 
         del d["rotations"]
 
-        # build data
-        obj = output.EKO.new(theory={}, operator=legacy.upgrade(d))
-        for q2, op in d["Q2grid"].items():
-            obj[q2] = output.struct.Operator.from_dict(op)
         return obj, d
 
 
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index fc46dac4b..725765d93 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -72,7 +72,7 @@ def test_targetgrid():
     tc = copy.deepcopy(theory_card)
     oc = copy.deepcopy(operators_card)
     tgrid = [0.1, 1.0]
-    oc["rotations"] = dict(targetgrid=tgrid)
+    oc["rotations"]["targetgrid"] = tgrid
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
     check_shapes(o, eko.interpolation.XGrid(np.array(tgrid)), o.xgrid, tc, oc)
@@ -84,7 +84,6 @@ def test_rotate_pids():
     # change pids
     tc = copy.deepcopy(theory_card)
     oc = copy.deepcopy(operators_card)
-    oc["rotations"] = {}
     oc["rotations"]["targetpids"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
     oc["rotations"]["inputpids"] = np.eye(14) + 0.1 * np.random.rand(14, 14)
     r = eko.runner.Runner(tc, oc)
@@ -101,9 +100,9 @@ def check_shapes(o, txs, ixs, theory_card, operators_card):
     op_shape = (tpids, len(txs), ipids, len(ixs))
 
     # check output = input
-    np.testing.assert_allclose(o.xgrid.raw, operators_card["xgrid"])
-    np.testing.assert_allclose(o.rotations.targetgrid, txs.raw)
-    np.testing.assert_allclose(o.rotations.inputgrid, ixs.raw)
+    np.testing.assert_allclose(o.xgrid.raw, operators_card["rotations"]["xgrid"])
+    np.testing.assert_allclose(o.rotations.targetgrid.raw, txs.raw)
+    np.testing.assert_allclose(o.rotations.inputgrid.raw, ixs.raw)
     for k in ["interpolation_polynomial_degree", "interpolation_is_log"]:
         assert getattr(o.configs, k) == operators_card["configs"][k]
     np.testing.assert_allclose(o.Q02, theory_card["Q0"] ** 2)

From 225c1be8c7620146b4975713a8081399708ea11b Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 19:35:04 +0200
Subject: [PATCH 124/148] Fix last output test

---
 tests/eko/test_output.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/eko/test_output.py b/tests/eko/test_output.py
index c176eca37..12ce82fa8 100644
--- a/tests/eko/test_output.py
+++ b/tests/eko/test_output.py
@@ -222,10 +222,10 @@ def test_to_evol(self, fake_factory, tmp_path):
         q2_out = 2
         Q2grid = fake_factory.mk_g([q2_out], len(br.flavor_basis_pids), len(xgrid))
         d = dict(
-            xgrid=xgrid,
             Q0=np.sqrt(q2_ref),
             Q2grid=Q2grid,
             rotations=dict(
+                xgrid=xgrid,
                 targetgrid=xgrid,
                 inputgrid=xgrid,
                 inputpids=br.flavor_basis_pids,

From e4d059a1adac4b80b27f5efae941ae02dec7aac2 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 19:45:03 +0200
Subject: [PATCH 125/148] Restore one further test in runner

---
 src/eko/runner.py        | 4 ++++
 tests/eko/test_runner.py | 9 +++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/eko/runner.py b/src/eko/runner.py
index 5c354eaea..8f10f3bcc 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -120,6 +120,10 @@ def similar_to_none(name: str) -> Optional[np.ndarray]:
         inputgrid = similar_to_none("inputgrid")
         targetgrid = similar_to_none("targetgrid")
         if inputgrid is not None or targetgrid is not None:
+            if inputgrid is not None:
+                inputgrid = interpolation.XGrid(inputgrid)
+            if targetgrid is not None:
+                targetgrid = interpolation.XGrid(targetgrid)
             manipulate.xgrid_reshape(
                 self.out, targetgrid=targetgrid, inputgrid=inputgrid
             )
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 725765d93..205a154c0 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -74,10 +74,11 @@ def test_targetgrid():
     tgrid = [0.1, 1.0]
     oc["rotations"]["targetgrid"] = tgrid
     r = eko.runner.Runner(tc, oc)
+    __import__("pdb").set_trace()
     o = r.get_output()
-    check_shapes(o, eko.interpolation.XGrid(np.array(tgrid)), o.xgrid, tc, oc)
+    check_shapes(o, eko.interpolation.XGrid(tgrid), o.xgrid, tc, oc)
     # check actual value
-    np.testing.assert_allclose(o.rotations.targetgrid, tgrid)
+    np.testing.assert_allclose(o.rotations.targetgrid.raw, tgrid)
 
 
 def test_rotate_pids():
@@ -90,8 +91,8 @@ def test_rotate_pids():
     o = r.get_output()
     check_shapes(o, o.xgrid, o.xgrid, tc, oc)
     # check actual values
-    assert o.rotations.targetpids == [0] * 14
-    assert o.rotations.inputpids == [0] * 14
+    assert all(o.rotations.targetpids == [0] * 14)
+    assert all(o.rotations.inputpids == [0] * 14)
 
 
 def check_shapes(o, txs, ixs, theory_card, operators_card):

From df64b9935650ffbd43f02fcc9ff3b37d35fff872 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 20:43:57 +0200
Subject: [PATCH 126/148] Fix evolve pdf tests

---
 src/eko/output/legacy.py | 2 +-
 src/eko/output/struct.py | 6 ++++--
 src/ekobox/evol_pdf.py   | 6 ++++--
 tests/eko/test_runner.py | 1 -
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index e81eff76d..089280dc6 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -43,7 +43,7 @@ def get_raw(eko: struct.EKO, binarize: bool = True):
         for key, value in obj[sec].items():
             if key.startswith("_"):
                 key = key[1:]
-            if "grid" in key:
+            if "grid" in key and value is not None:
                 value = value["grid"]
             out[key] = value
 
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index ba75f693e..76136d309 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -12,7 +12,7 @@
 import tempfile
 import time
 from dataclasses import dataclass, fields
-from typing import BinaryIO, Dict, Literal, Optional
+from typing import BinaryIO, Dict, Literal, Optional, Tuple
 
 import lz4.frame
 import numpy as np
@@ -88,6 +88,8 @@ def raw(self):
                 value = float(value)
             elif isinstance(value, interpolation.XGrid):
                 value = value.dump()
+            elif isinstance(value, tuple):
+                value = list(value)
 
             dictionary[field.name] = value
 
@@ -202,7 +204,7 @@ class Debug(DictLike):
 class Configs(DictLike):
     """Solution specific configurations."""
 
-    ev_op_max_order: int
+    ev_op_max_order: Tuple[int]
     """Maximum order to use in U matrices expansion.
     Used only in ``perturbative`` solutions.
     """
diff --git a/src/ekobox/evol_pdf.py b/src/ekobox/evol_pdf.py
index 391937031..66eec9025 100644
--- a/src/ekobox/evol_pdf.py
+++ b/src/ekobox/evol_pdf.py
@@ -2,6 +2,8 @@
 """Tools to evolve actual PDFs."""
 import pathlib
 
+import numpy as np
+
 import eko
 import eko.output.legacy
 from eko import basis_rotation as br
@@ -62,7 +64,7 @@ def evolve_pdfs(
         evolved_PDF_list.append(apply.apply_pdf(eko_output, initial_PDF, targetgrid))
 
     if targetgrid is None:
-        targetgrid = operators_card["xgrid"]
+        targetgrid = operators_card["interpolation_xgrid"]
     if info_update is None:
         info_update = {}
     info_update["XMin"] = targetgrid[0]
@@ -81,7 +83,7 @@ def evolve_pdfs(
             * evolved_PDF[Q2]["pdfs"][pid][targetgrid.index(x)],
             xgrid=targetgrid,
             Q2grid=operators_card["Q2grid"],
-            pids=br.flavor_basis_pids,
+            pids=np.array(br.flavor_basis_pids),
         )
         # all_blocks will be useful in case there will be necessity to dump many blocks
         # for a single member
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 205a154c0..03d267c12 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -74,7 +74,6 @@ def test_targetgrid():
     tgrid = [0.1, 1.0]
     oc["rotations"]["targetgrid"] = tgrid
     r = eko.runner.Runner(tc, oc)
-    __import__("pdb").set_trace()
     o = r.get_output()
     check_shapes(o, eko.interpolation.XGrid(tgrid), o.xgrid, tc, oc)
     # check actual value

From c00fc3becfac7bb86d53c282c702c30e67622488 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 20:59:31 +0200
Subject: [PATCH 127/148] Fix last runner tests

---
 src/eko/compatibility.py | 4 +---
 src/eko/runner.py        | 8 ++++----
 tests/eko/test_runner.py | 4 ++--
 3 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index bc7fd0816..baa76fbff 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -27,7 +27,7 @@ def update(theory: dict, operators: Optional[dict]):
 
     """
     new_theory = copy.deepcopy(theory)
-    new_operators = copy.deepcopy(operators)
+    new_operators = copy.deepcopy(operators) if operators is not None else {}
 
     if "alphaqed" in new_theory:
         new_theory["alphaem"] = new_theory.pop("alphaqed")
@@ -35,8 +35,6 @@ def update(theory: dict, operators: Optional[dict]):
         new_theory["order"] = (new_theory.pop("PTO") + 1, new_theory.pop("QED"))
 
     if operators is not None and "configs" not in operators:
-        assert new_operators is not None
-
         new_operators["configs"] = {}
         for k in (
             "interpolation_polynomial_degree",
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 8f10f3bcc..8c3a364d5 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -77,10 +77,10 @@ def __init__(self, theory_card: dict, operators_card: dict):
 
         # save bases manipulations for a post processing step
         rot = operators_card.get("rotations", {})
-        self.post_process = {
-            key: rot.get(key, None)
-            for key in ("inputgrid", "targetgrid", "inputpids", "targetpids")
-        }
+        self.post_process = {}
+        for key in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
+            self.post_process[key] = rot.get(key, None)
+            new_operators["rotations"][key] = None
 
         self.out = EKO.new(
             theory=theory_card, operator=dict(Q0=np.sqrt(tc.q2_ref), **new_operators)
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 03d267c12..0b9002846 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -90,8 +90,8 @@ def test_rotate_pids():
     o = r.get_output()
     check_shapes(o, o.xgrid, o.xgrid, tc, oc)
     # check actual values
-    assert all(o.rotations.targetpids == [0] * 14)
-    assert all(o.rotations.inputpids == [0] * 14)
+    assert (o.rotations.targetpids == [0] * 14).all()
+    assert (o.rotations.inputpids == [0] * 14).all()
 
 
 def check_shapes(o, txs, ixs, theory_card, operators_card):

From 73be7ef15b5ea5be6976ad314a618f905178f144 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 21:10:01 +0200
Subject: [PATCH 128/148] Propagate InterpolatorDispatcher update to isolated
 benchmarks

---
 benchmarks/eko/benchmark_evol_to_unity.py | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/benchmarks/eko/benchmark_evol_to_unity.py b/benchmarks/eko/benchmark_evol_to_unity.py
index eb2e9d07d..f18d4584d 100644
--- a/benchmarks/eko/benchmark_evol_to_unity.py
+++ b/benchmarks/eko/benchmark_evol_to_unity.py
@@ -7,7 +7,7 @@
 from eko.couplings import Couplings
 from eko.evolution_operator import Operator
 from eko.evolution_operator.grid import OperatorGrid
-from eko.interpolation import InterpolatorDispatcher
+from eko.interpolation import InterpolatorDispatcher, XGrid
 from eko.thresholds import ThresholdsAtlas
 
 # from eko.matching_conditions.operator_matrix_element import OperatorMatrixElement
@@ -64,7 +64,13 @@ class BenchmarkBackwardForward:
         new_operators,
         ThresholdsAtlas.from_dict(new_theory),
         Couplings.from_dict(new_theory),
-        InterpolatorDispatcher.from_dict(new_operators),
+        InterpolatorDispatcher(
+            XGrid(
+                new_operators["xgrid"],
+                log=new_operators["configs"]["interpolation_is_log"],
+            ),
+            new_operators["configs"]["interpolation_polynomial_degree"],
+        ),
     )
 
     def test_operator_grid(
@@ -76,7 +82,13 @@ def test_operator_grid(
             self.new_operators,
             ThresholdsAtlas.from_dict(self.new_theory),
             Couplings.from_dict(self.new_theory),
-            InterpolatorDispatcher.from_dict(self.new_operators),
+            InterpolatorDispatcher(
+                XGrid(
+                    self.new_operators["xgrid"],
+                    log=self.new_operators["configs"]["interpolation_is_log"],
+                ),
+                self.new_operators["configs"]["interpolation_polynomial_degree"],
+            ),
         )
         q20 = 30
         q21 = 50

From 0d92a57e036c64b9cc1da0cb431bf557f19afacb Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Thu, 28 Jul 2022 21:21:17 +0200
Subject: [PATCH 129/148] Keep using legacy runcards in ekobox, including
 benchmarks

---
 benchmarks/ekobox/benchmark_evol_pdf.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/benchmarks/ekobox/benchmark_evol_pdf.py b/benchmarks/ekobox/benchmark_evol_pdf.py
index 1b0c13d26..035b3a38d 100644
--- a/benchmarks/ekobox/benchmark_evol_pdf.py
+++ b/benchmarks/ekobox/benchmark_evol_pdf.py
@@ -55,11 +55,11 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
         all_blocks = (load.load_blocks_from_file("EvPDF", 0))[1]
         info = load.load_info_from_file("EvPDF")
         ev_pdf = lhapdf.mkPDF("EvPDF", 0)
-    assert info["XMin"] == op["xgrid"][0]
+    assert info["XMin"] == op["interpolation_xgrid"][0]
     assert info["SetDesc"] == "MyEvolvedPDF"
     assert info["MZ"] == theory["MZ"]
     assert info["Debug"] == "Debug"
-    xgrid = op["xgrid"]
+    xgrid = op["interpolation_xgrid"]
     for Q2 in [20.0, 100.0, 10000.0]:
         for x in xgrid[10:40]:
             for pid in [21, 1, -1, 2, -2, 3, -3]:
@@ -79,7 +79,9 @@ def benchmark_evolve_single_member(tmp_path, cd, lhapdf_path):
 
 @pytest.mark.isolated
 def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
-    op = oc.generate([10, 100], update={"xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]})
+    op = oc.generate(
+        [10, 100], update={"interpolation_xgrid": [1e-7, 0.01, 0.1, 0.2, 0.3]}
+    )
     theory = tc.generate(0, 1.0)
     with lhapdf_path(test_pdf):
         pdfs = lhapdf.mkPDFs("myMSTW2008nlo90cl")
@@ -93,7 +95,7 @@ def benchmark_evolve_more_members(tmp_path, cd, lhapdf_path):
         new_pdf_1 = lhapdf.mkPDF("Debug", 0)
         new_pdf_2 = lhapdf.mkPDF("Debug", 1)
         info = load.load_info_from_file("Debug")
-    assert info["XMin"] == op["xgrid"][0]
+    assert info["XMin"] == op["interpolation_xgrid"][0]
     assert len(pdfs) == len(new_pdfs)
     for Q2 in [10, 100]:
         for x in [1e-7, 0.01, 0.1, 0.2, 0.3]:

From 3ba82e472e0bce9103096509663a26726c689357 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 11:32:24 +0200
Subject: [PATCH 130/148] Only support old layout of opcard in ekobox

---
 src/ekobox/operators_card.py | 40 +++++++++++++++---------------------
 1 file changed, 17 insertions(+), 23 deletions(-)

diff --git a/src/ekobox/operators_card.py b/src/ekobox/operators_card.py
index 49de99240..afcfe3332 100644
--- a/src/ekobox/operators_card.py
+++ b/src/ekobox/operators_card.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""Tools to generate operator cards."""
 import copy
 
 import yaml
@@ -8,8 +9,7 @@
 
 
 def generate(Q2grid, update=None, name=None):
-    """
-    Generate operators card.
+    """Generate operators card.
 
     Generates an operators card with some mandatory user choice
     (in this case only the Q2 grid) and some default values which
@@ -17,17 +17,17 @@ def generate(Q2grid, update=None, name=None):
 
     Parameters
     ----------
-        Q2grid : list(float)
-            grid for Q2
-        update : dict
-            dictionary of info to update in op. card
-        name : str
-            name of exported op.card (if name not None)
+    Q2grid : list(float)
+        grid for Q2
+    update : dict
+        dictionary of info to update in op. card
+    name : str
+        name of exported op.card (if name not None)
 
     Returns
     -------
-        dict
-            operators card
+    dict
+        operators card
     """
     # Constructing the dictionary with some default value
     def_op = copy.deepcopy(operators.default_card)
@@ -38,11 +38,7 @@ def generate(Q2grid, update=None, name=None):
             if k not in def_op.keys():
                 raise ValueError("Provided key not in operators card")
         for key, value in update.items():
-            # properly update sections
-            if isinstance(value, dict):
-                def_op[key].update(value)
-            else:
-                def_op[key] = value
+            def_op[key] = value
     serialized = sql.serialize(def_op)
     def_op["hash"] = (sql.add_hash(serialized))[-1]
     if name is not None:
@@ -51,8 +47,7 @@ def generate(Q2grid, update=None, name=None):
 
 
 def dump(name, op):
-    """
-    Export the operators card in the current directory
+    """Export the operators card.
 
     Parameters
     ----------
@@ -67,18 +62,17 @@ def dump(name, op):
 
 
 def load(path):
-    """
-    Import the operators card specified by path
+    """Import the operators card.
 
     Parameters
     ----------
-        path : str
-            path to operators card in yaml format
+    path : str
+        path to operators card in yaml format
 
     Returns
     -------
-        dict
-            operators card
+    dict
+        operators card
     """
     with open(path, "r", encoding="utf-8") as o:
         op = yaml.safe_load(o)

From 03db302a6560f5cd4a5a7a5be7fb07c1c809ead3 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 29 Jul 2022 11:34:12 +0200
Subject: [PATCH 131/148] Provide some more docstrings for output structs

---
 src/eko/output/struct.py | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 76136d309..274e80403 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -67,8 +67,12 @@ def from_dict(cls, dictionary):
     def raw(self):
         """Convert dataclass object to raw dictionary.
 
-        Normalize :class:`np.ndarray` to lists (possibly nested), and scalars to
-        the corresponding built-in type.
+        Normalize:
+
+            - :class:`np.ndarray` to lists (possibly nested)
+            - scalars to the corresponding built-in type (e.g. :class:`float`)
+            - :class:`tuple` to lists
+            - :class:`interpolation.XGrid` to the intrinsic serialization format
 
         Returns
         -------
@@ -244,6 +248,7 @@ class Rotations(DictLike):
     _inputpids: Optional[np.ndarray] = None
 
     def __post_init__(self):
+        """Adjust types when loaded from serialized object."""
         for attr in ("xgrid", "_inputgrid", "_targetgrid"):
             value = getattr(self, attr)
             if value is None:
@@ -255,24 +260,28 @@ def __post_init__(self):
 
     @property
     def inputpids(self) -> np.ndarray:
+        """The pids expected on the input PDF."""
         if self._inputpids is None:
             return self.pids
         return self._inputpids
 
     @property
     def targetpids(self) -> np.ndarray:
+        """The pids corresponding to the output PDF."""
         if self._targetpids is None:
             return self.pids
         return self._targetpids
 
     @property
     def inputgrid(self) -> interpolation.XGrid:
+        """The :math:`x`-grid expected on the input PDF."""
         if self._inputgrid is None:
             return self.xgrid
         return self._inputgrid
 
     @property
     def targetgrid(self) -> interpolation.XGrid:
+        """The :math:`x`-grid corresponding to the output PDF."""
         if self._targetgrid is None:
             return self.xgrid
         return self._targetgrid
@@ -350,6 +359,7 @@ def xgrid(self, value: interpolation.XGrid):
         self.rotations.xgrid = value
 
     def __post_init__(self):
+        """Validate class members."""
         if self.path.suffix != ".tar":
             raise ValueError("Not a valid path for an EKO")
         if not tarfile.is_tarfile(self.path):
@@ -357,6 +367,7 @@ def __post_init__(self):
 
     @staticmethod
     def opname(q2: float) -> str:
+        """Operator file name from :math:`Q^2` value."""
         return f"operators/{q2:8.2f}"
 
     def __getitem__(self, q2: float):

From e37e40d490b063d040c8d51b9b7c56f4e2911e00 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 11:44:16 +0200
Subject: [PATCH 132/148] Complete test_interpolation

---
 tests/eko/test_interpolation.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/tests/eko/test_interpolation.py b/tests/eko/test_interpolation.py
index 6096d4ffc..014ab2329 100644
--- a/tests/eko/test_interpolation.py
+++ b/tests/eko/test_interpolation.py
@@ -323,6 +323,27 @@ def test_reference_indices(self):
             a = interpolation.Area(0, 3, (0, 2), xgrid)
 
 
+class TestXGrid:
+    def test_fromcard(self):
+        aa = [0.1, 1.0]
+        a = interpolation.XGrid.fromcard(aa, False)
+        np.testing.assert_array_almost_equal(a.raw, aa)
+        assert a.size == len(aa)
+
+        bargs = (3, 3)
+        bb = interpolation.make_grid(*bargs)
+        b = interpolation.XGrid.fromcard(["make_grid", *bargs], False)
+        np.testing.assert_array_almost_equal(b.raw, bb)
+
+        cargs = (10,)
+        cc = interpolation.make_lambert_grid(*cargs)
+        c = interpolation.XGrid.fromcard(["make_lambert_grid", *cargs], False)
+        np.testing.assert_array_almost_equal(c.raw, cc)
+
+        with pytest.raises(ValueError):
+            interpolation.XGrid.fromcard([], False)
+
+
 def test_make_grid():
     xg = interpolation.make_grid(3, 3)
     np.testing.assert_array_almost_equal(xg, np.array([1e-7, 1e-4, 1e-1, 0.55, 1.0]))

From 67d53395e9a6788f0b392db12b7c542e5c83242c Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 11:48:06 +0200
Subject: [PATCH 133/148] Complete runner

---
 tests/eko/test_runner.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 0b9002846..796556b95 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -71,11 +71,15 @@ def test_targetgrid():
     # change targetgrid
     tc = copy.deepcopy(theory_card)
     oc = copy.deepcopy(operators_card)
+    igrid = [0.1, 1.0]
+    oc["rotations"]["inputgrid"] = igrid
     tgrid = [0.1, 1.0]
     oc["rotations"]["targetgrid"] = tgrid
     r = eko.runner.Runner(tc, oc)
     o = r.get_output()
-    check_shapes(o, eko.interpolation.XGrid(tgrid), o.xgrid, tc, oc)
+    check_shapes(
+        o, eko.interpolation.XGrid(tgrid), eko.interpolation.XGrid(igrid), tc, oc
+    )
     # check actual value
     np.testing.assert_allclose(o.rotations.targetgrid.raw, tgrid)
 

From aeddb040bc1b17fac4e44bb7cc1d4170835fb3fe Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 29 Jul 2022 12:11:58 +0200
Subject: [PATCH 134/148] Provide even more docstrings

---
 src/eko/output/struct.py | 191 +++++++++++++++++++++++++++++++++------
 1 file changed, 161 insertions(+), 30 deletions(-)

diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index 274e80403..eb9d20fa8 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -17,6 +17,7 @@
 import lz4.frame
 import numpy as np
 import numpy.lib.npyio as npyio
+import numpy.typing as npt
 import yaml
 
 from .. import basis_rotation as br
@@ -114,9 +115,9 @@ class Operator(DictLike):
 
     """
 
-    operator: np.ndarray
+    operator: npt.NDArray
     """Content of the evolution operator."""
-    error: Optional[np.ndarray] = None
+    error: Optional[npt.NDArray] = None
     """Errors on individual operator elements (mainly used for integration
     error, but it can host any kind of error).
     """
@@ -240,12 +241,12 @@ class Rotations(DictLike):
 
     xgrid: interpolation.XGrid
     """Momentum fraction internal grid."""
-    pids: np.ndarray
+    pids: npt.NDArray
     """Array of integers, corresponding to internal PIDs."""
     _targetgrid: Optional[interpolation.XGrid] = None
     _inputgrid: Optional[interpolation.XGrid] = None
-    _targetpids: Optional[np.ndarray] = None
-    _inputpids: Optional[np.ndarray] = None
+    _targetpids: Optional[npt.NDArray] = None
+    _inputpids: Optional[npt.NDArray] = None
 
     def __post_init__(self):
         """Adjust types when loaded from serialized object."""
@@ -259,29 +260,29 @@ def __post_init__(self):
                 setattr(self, attr, interpolation.XGrid.load(value))
 
     @property
-    def inputpids(self) -> np.ndarray:
-        """The pids expected on the input PDF."""
+    def inputpids(self) -> npt.NDArray:
+        """Provide pids expected on the input PDF."""
         if self._inputpids is None:
             return self.pids
         return self._inputpids
 
     @property
-    def targetpids(self) -> np.ndarray:
-        """The pids corresponding to the output PDF."""
+    def targetpids(self) -> npt.NDArray:
+        """Provide pids corresponding to the output PDF."""
         if self._targetpids is None:
             return self.pids
         return self._targetpids
 
     @property
     def inputgrid(self) -> interpolation.XGrid:
-        """The :math:`x`-grid expected on the input PDF."""
+        """Provide :math:`x`-grid expected on the input PDF."""
         if self._inputgrid is None:
             return self.xgrid
         return self._inputgrid
 
     @property
     def targetgrid(self) -> interpolation.XGrid:
-        """The :math:`x`-grid corresponding to the output PDF."""
+        """Provide :math:`x`-grid corresponding to the output PDF."""
         if self._targetgrid is None:
             return self.xgrid
         return self._targetgrid
@@ -370,8 +371,23 @@ def opname(q2: float) -> str:
         """Operator file name from :math:`Q^2` value."""
         return f"operators/{q2:8.2f}"
 
-    def __getitem__(self, q2: float):
-        # TODO: autoload
+    def __getitem__(self, q2: float) -> Operator:
+        """Retrieve operator for given :math:`Q^2`.
+
+        If the operator is not already in memory, it will be automatically
+        loaded.
+
+        Parameters
+        ----------
+        q2: float
+            :math:`Q^2` value labeling the operator to be retrieved
+
+        Returns
+        -------
+        Operator
+            the retrieved operator
+
+        """
         op = self._operators[q2]
         if op is not None:
             return op
@@ -401,6 +417,20 @@ def __getitem__(self, q2: float):
         return op
 
     def __setitem__(self, q2: float, op: Operator, compress: bool = True):
+        """Set operator for given :math:`Q^2`.
+
+        The operator is automatically dumped on disk, .
+
+        Parameters
+        ----------
+        q2: float
+            :math:`Q^2` value labeling the operator to be set
+        op: Operator
+            the retrieved operator
+        compress: bool
+            whether to save the operator compressed or not (default: `True`)
+
+        """
         if not isinstance(op, Operator):
             raise ValueError("Only an Operator can be added to an EKO")
 
@@ -468,17 +498,29 @@ def __delitem__(self, q2: float):
 
     @contextlib.contextmanager
     def operator(self, q2: float):
+        """Retrieve operator and discard immediately.
+
+        To be used as a contextmanager: the operator is automatically loaded as
+        usual, but after the context manager it is dropped from memory.
+
+        Parameters
+        ----------
+        q2: float
+            :math:`Q^2` value labeling the operator to be retrieved
+
+        """
         try:
             yield self[q2]
         finally:
             del self[q2]
 
     @property
-    def Q2grid(self):
+    def Q2grid(self) -> npt.NDArray:
+        """Provide the list of :math:`Q^2` as an array."""
         return np.array(list(self._operators))
 
     def __iter__(self):
-        """Iterate over keys (i.e. Q2 values)
+        """Iterate over keys (i.e. Q2 values).
 
         Yields
         ------
@@ -511,9 +553,45 @@ def items(self):
             del self[q2]
 
     def __contains__(self, q2: float) -> bool:
+        """Check whether :math:`Q^2` operators are present.
+
+        'Present' means, in this case, they are conceptually part of the
+        :class:`EKO`. But it is telling nothing about being loaded in memory or
+        not.
+
+        Returns
+        -------
+        bool
+            the result of checked condition
+
+        """
         return q2 in self._operators
 
-    def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
+    def approx(
+        self, q2: float, rtol: float = 1e-6, atol: float = 1e-10
+    ) -> Optional[float]:
+        """Look for close enough :math:`Q^2` value in the :class:`EKO`.
+
+        Parameters
+        ----------
+        q2: float
+            value of :math:`Q2` in which neighborhood to look
+        rtol: float
+            relative tolerance
+        atol: float
+            absolute tolerance
+
+        Returns
+        -------
+        float or None
+            retrieved value of :math:`Q^2`, if a single one is found
+
+        Raises
+        ------
+        ValueError
+            if multiple values are find in the neighborhood
+
+        """
         q2s = self.Q2grid
         close = q2s[np.isclose(q2, q2s, rtol=rtol, atol=atol)]
 
@@ -525,7 +603,6 @@ def approx(self, q2, rtol=1e-6, atol=1e-10) -> Optional[float]:
 
     def unload(self):
         """Fully unload the operators in memory."""
-
         for q2 in self:
             del self[q2]
 
@@ -563,16 +640,48 @@ def deepcopy(self, path: os.PathLike):
         return new
 
     @staticmethod
-    def bootstrap(tdir: os.PathLike, theory: dict, operator: dict):
-        tdir = pathlib.Path(tdir)
-        (tdir / THEORYFILE).write_text(yaml.dump(theory), encoding="utf-8")
-        (tdir / OPERATORFILE).write_text(yaml.dump(operator), encoding="utf-8")
-        (tdir / RECIPESDIR).mkdir()
-        (tdir / PARTSDIR).mkdir()
-        (tdir / OPERATORSDIR).mkdir()
+    def bootstrap(dirpath: os.PathLike, theory: dict, operator: dict):
+        """Create directory structure.
+
+        Parameters
+        ----------
+        dirpath: os.PathLike
+            path to create the directory into
+        theory: dict
+            theory card to be dumped
+        operator: dict
+            operator card to be dumped
+
+        """
+        dirpath = pathlib.Path(dirpath)
+        (dirpath / THEORYFILE).write_text(yaml.dump(theory), encoding="utf-8")
+        (dirpath / OPERATORFILE).write_text(yaml.dump(operator), encoding="utf-8")
+        (dirpath / RECIPESDIR).mkdir()
+        (dirpath / PARTSDIR).mkdir()
+        (dirpath / OPERATORSDIR).mkdir()
 
     @staticmethod
     def extract(path: os.PathLike, filename: str) -> str:
+        """Extract file from disk assets.
+
+        Note
+        ----
+        At the moment, it only support text files (since it is returning the
+        content as a string)
+
+        Parameters
+        ----------
+        path: os.PathLike
+            path to the disk dump
+        filename: str
+            relative path inside the archive of the file to extract
+
+        Returns
+        -------
+        str
+            file content
+
+        """
         path = pathlib.Path(path)
 
         with tarfile.open(path, "r") as tar:
@@ -587,17 +696,20 @@ def extract(path: os.PathLike, filename: str) -> str:
 
     @property
     def theory(self) -> dict:
+        """Provide theory card, retrieving from the dump."""
         # TODO: make an actual attribute, move load to `theory_card`, and the
         # type of the attribute will be `eko.runcards.TheoryCard`
         return yaml.safe_load(self.extract(self.path, THEORYFILE))
 
     @property
     def theory_card(self) -> dict:
+        """Provide theory card, retrieving from the dump."""
         # TODO: return `eko.runcards.TheoryCard`
         return self.theory
 
     @property
     def operator_card(self) -> dict:
+        """Provide operator card, retrieving from the dump."""
         # TODO: return `eko.runcards.OperatorCard`
         return yaml.safe_load(self.extract(self.path, OPERATORFILE))
 
@@ -732,6 +844,19 @@ def new(cls, theory: dict, operator: dict, path: Optional[os.PathLike] = None):
 
     @classmethod
     def load(cls, path: os.PathLike):
+        """Load dump into an :class:`EKO` object.
+
+        Parameters
+        ----------
+        path:: os.PathLike
+            path to the dump to load
+
+        Returns
+        -------
+        EKO
+            the loaded instance
+
+        """
         path = pathlib.Path(path)
         if not tarfile.is_tarfile(path):
             raise ValueError("EKO: the corresponding file is not a valid tar archive")
@@ -744,7 +869,16 @@ def load(cls, path: os.PathLike):
         return eko
 
     @property
-    def raw(self):
+    def raw(self) -> dict:
+        """Provide raw representation of the full content.
+
+        Returns
+        -------
+        dict
+            nested dictionary, storing all the values in the structure, but the
+            operators themselves
+
+        """
         return dict(
             path=str(self.path),
             Q0=float(np.sqrt(self.Q02)),
@@ -754,9 +888,6 @@ def raw(self):
             debug=self.debug.raw,
         )
 
-    def close(self):
-        for q2 in self.Q2grid:
-            del self[q2]
-
     def __del__(self):
-        self.close()
+        """Destroy the memory structure gracefully."""
+        self.unload()

From af88b47d386c7ad5d419971aa982ff368cf66fbc Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 13:24:52 +0200
Subject: [PATCH 135/148] Add more struct tests

---
 tests/eko/test_output_struct.py | 76 ++++++++++++++++++++++++++++++++-
 1 file changed, 75 insertions(+), 1 deletion(-)

diff --git a/tests/eko/test_output_struct.py b/tests/eko/test_output_struct.py
index c850766a0..f66977e14 100644
--- a/tests/eko/test_output_struct.py
+++ b/tests/eko/test_output_struct.py
@@ -1,8 +1,82 @@
 # -*- coding: utf-8 -*-
-from eko import output
+import io
+from dataclasses import dataclass
+
+import numpy as np
+import numpy.typing as npt
+import pytest
+import yaml
+
+from eko import interpolation, output
 from eko.output import struct
 
 
+@dataclass
+class MyDictLike(struct.DictLike):
+    l: npt.NDArray
+    f: float
+    x: interpolation.XGrid
+    t: tuple
+    s: str
+
+
+def test_DictLike():
+    d = MyDictLike.from_dict(
+        dict(
+            l=np.arange(5.0),
+            f=np.arange(5.0)[-1],
+            x=interpolation.XGrid([0.1, 1.0]),
+            t=(1.0, 2.0),
+            s="s",
+        )
+    )
+    assert d.f == 4.0
+    dd = MyDictLike.from_dict(d.raw)
+    assert dd.f == 4.0
+    # check we can dump and reload
+    stream = io.StringIO()
+    yaml.safe_dump(d.raw, stream)
+    stream.seek(0)
+    ddd = yaml.safe_load(stream)
+    assert "l" in ddd
+    np.testing.assert_allclose(ddd["l"], np.arange(5.0))
+
+
+class TestOperator:
+    def test_value_only(self):
+        v = np.random.rand(2, 2)
+        opv = struct.Operator(operator=v)
+        assert opv.error is None
+        for compress in (True, False):
+            stream = io.BytesIO()
+            opv.save(stream, compress)
+            stream.seek(0)
+            opv_ = struct.Operator.load(stream, compress)
+            np.testing.assert_allclose(opv.operator, opv_.operator)
+            np.testing.assert_allclose(v, opv_.operator)
+            assert opv_.error is None
+
+    def test_value_and_error(self):
+        v, e = np.random.rand(2, 2, 2)
+        opve = struct.Operator(operator=v, error=e)
+        for compress in (True, False):
+            stream = io.BytesIO()
+            opve.save(stream, compress)
+            stream.seek(0)
+            opve_ = struct.Operator.load(stream, compress)
+            np.testing.assert_allclose(opve.operator, opve_.operator)
+            np.testing.assert_allclose(v, opve_.operator)
+            np.testing.assert_allclose(opve.error, opve_.error)
+            np.testing.assert_allclose(e, opve_.error)
+
+    def test_load_error(self, monkeypatch):
+        # We might consider dropping this exception since np.load will always return a array (or fail on it's own)
+        stream = io.BytesIO()
+        monkeypatch.setattr(np, "load", lambda _: None)
+        with pytest.raises(ValueError):
+            struct.Operator.load(stream, False)
+
+
 class TestLegacy:
     def test_items(self, fake_output):
         """Test autodump, autoload, and manual unload."""

From bc89ac6081fd11df0f9ec022f509e31adb57b00d Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 15:01:06 +0200
Subject: [PATCH 136/148] Add rotations tests

---
 tests/eko/test_output_struct.py | 48 +++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/tests/eko/test_output_struct.py b/tests/eko/test_output_struct.py
index f66977e14..9738fecb8 100644
--- a/tests/eko/test_output_struct.py
+++ b/tests/eko/test_output_struct.py
@@ -77,6 +77,54 @@ def test_load_error(self, monkeypatch):
             struct.Operator.load(stream, False)
 
 
+class TestRotations:
+    def test_fallback(self):
+        pids = np.array([1, 2])
+        xg = interpolation.XGrid([0.1, 1.0])
+        r = struct.Rotations(xgrid=xg, pids=pids)
+        np.testing.assert_allclose(r.pids, pids)
+        np.testing.assert_allclose(r.targetpids, pids)
+        np.testing.assert_allclose(r.inputpids, pids)
+        assert r.xgrid == xg
+        assert r.targetgrid == xg
+        assert r.inputgrid == xg
+
+    def test_overwrite(self):
+        pids = np.array([1, 2])
+        tpids = np.array([3, 4])
+        ipids = np.array([5, 6])
+        xg = interpolation.XGrid([0.1, 1.0])
+        txg = interpolation.XGrid([0.2, 1.0])
+        ixg = interpolation.XGrid([0.3, 1.0])
+        r = struct.Rotations(
+            xgrid=xg,
+            pids=pids,
+            _targetgrid=txg,
+            _inputgrid=ixg,
+            _targetpids=tpids,
+            _inputpids=ipids,
+        )
+        np.testing.assert_allclose(r.pids, pids)
+        np.testing.assert_allclose(r.targetpids, tpids)
+        np.testing.assert_allclose(r.inputpids, ipids)
+        assert r.xgrid == xg
+        assert r.targetgrid == txg
+        assert r.inputgrid == ixg
+
+    def test_init(self):
+        pids = np.array([1, 2])
+        xg = interpolation.XGrid([0.1, 1.0])
+        txg = np.array([0.2, 1.0])
+        ixg = {"grid": [0.3, 1.0], "log": True}
+        r = struct.Rotations(xgrid=xg, pids=pids, _targetgrid=txg, _inputgrid=ixg)
+        assert isinstance(r.xgrid, interpolation.XGrid)
+        assert isinstance(r.targetgrid, interpolation.XGrid)
+        assert isinstance(r.inputgrid, interpolation.XGrid)
+        assert r.xgrid == xg
+        assert r.targetgrid == interpolation.XGrid(txg)
+        assert r.inputgrid == interpolation.XGrid.load(ixg)
+
+
 class TestLegacy:
     def test_items(self, fake_output):
         """Test autodump, autoload, and manual unload."""

From f8eb45607422edf275451b383f783dc77dedf5ec Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 16:44:20 +0200
Subject: [PATCH 137/148] Complete most tests

---
 src/eko/compatibility.py        |   7 +-
 src/eko/output/struct.py        |  33 +++------
 src/eko/runner.py               |   4 +-
 tests/eko/test_compatibility.py |   7 +-
 tests/eko/test_output_struct.py | 124 +++++++++++++++++++++++++++++++-
 tests/eko/test_runner.py        |   1 +
 6 files changed, 140 insertions(+), 36 deletions(-)

diff --git a/src/eko/compatibility.py b/src/eko/compatibility.py
index baa76fbff..86a89f9ca 100644
--- a/src/eko/compatibility.py
+++ b/src/eko/compatibility.py
@@ -32,7 +32,7 @@ def update(theory: dict, operators: Optional[dict]):
     if "alphaqed" in new_theory:
         new_theory["alphaem"] = new_theory.pop("alphaqed")
     if "QED" in new_theory:
-        new_theory["order"] = (new_theory.pop("PTO") + 1, new_theory.pop("QED"))
+        new_theory["order"] = [new_theory.pop("PTO") + 1, new_theory.pop("QED")]
 
     if operators is not None and "configs" not in operators:
         new_operators["configs"] = {}
@@ -51,14 +51,15 @@ def update(theory: dict, operators: Optional[dict]):
 
         max_order = operators["ev_op_max_order"]
         if isinstance(max_order, int):
-            new_operators["configs"]["ev_op_max_order"] = (
+            new_operators["configs"]["ev_op_max_order"] = [
                 max_order,
                 new_theory["order"][1],
-            )
+            ]
 
         new_operators["rotations"]["xgrid"] = operators["interpolation_xgrid"]
         for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
             new_operators["rotations"][f"{basis}"] = operators[basis]
+        new_operators["Q0"] = new_theory["Q0"]
 
     return new_theory, new_operators
 
diff --git a/src/eko/output/struct.py b/src/eko/output/struct.py
index eb9d20fa8..239336f3e 100644
--- a/src/eko/output/struct.py
+++ b/src/eko/output/struct.py
@@ -363,13 +363,11 @@ def __post_init__(self):
         """Validate class members."""
         if self.path.suffix != ".tar":
             raise ValueError("Not a valid path for an EKO")
-        if not tarfile.is_tarfile(self.path):
-            raise ValueError("EKO: the corresponding file is not a valid tar archive")
 
     @staticmethod
     def opname(q2: float) -> str:
         """Operator file name from :math:`Q^2` value."""
-        return f"operators/{q2:8.2f}"
+        return f"{OPERATORSDIR}/{q2:8.2f}"
 
     def __getitem__(self, q2: float) -> Operator:
         """Retrieve operator for given :math:`Q^2`.
@@ -379,7 +377,7 @@ def __getitem__(self, q2: float) -> Operator:
 
         Parameters
         ----------
-        q2: float
+        q2 : float
             :math:`Q^2` value labeling the operator to be retrieved
 
         Returns
@@ -388,9 +386,10 @@ def __getitem__(self, q2: float) -> Operator:
             the retrieved operator
 
         """
-        op = self._operators[q2]
-        if op is not None:
-            return op
+        if q2 in self._operators:
+            op = self._operators[q2]
+            if op is not None:
+                return op
 
         with tarfile.open(self.path) as tar:
             names = list(
@@ -399,18 +398,11 @@ def __getitem__(self, q2: float) -> Operator:
 
             if len(names) == 0:
                 raise ValueError(f"Q2 value '{q2}' not available in '{self.path}'")
-            if len(names) > 1:
-                raise ValueError(
-                    f"Q2 value '{q2}' occurs multiple times in '{self.path}'"
-                )
 
             name = names[0]
             compressed = name.endswith(".lz4")
             stream = tar.extractfile(name)
 
-            if stream is None:
-                raise ValueError
-
             op = Operator.load(stream, compressed=compressed)
 
         self._operators[q2] = op
@@ -686,10 +678,6 @@ def extract(path: os.PathLike, filename: str) -> str:
 
         with tarfile.open(path, "r") as tar:
             fd = tar.extractfile(filename)
-            if fd is None:
-                raise ValueError(
-                    f"The member '{filename}' is not a readable file inside EKO tar"
-                )
             content = fd.read().decode()
 
         return content
@@ -763,6 +751,9 @@ def detached(cls, theory: dict, operator: dict, path: pathlib.Path):
 
         """
         bases = operator["rotations"]
+        for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
+            bases[f"_{basis}"] = bases[basis]
+            del bases[basis]
         bases["pids"] = np.array(br.flavor_basis_pids)
         for k in ("xgrid", "_inputgrid", "_targetgrid"):
             if operator["rotations"][k] is None:
@@ -834,10 +825,6 @@ def new(cls, theory: dict, operator: dict, path: Optional[os.PathLike] = None):
 
             shutil.rmtree(td)
 
-        for basis in ("inputgrid", "targetgrid", "inputpids", "targetpids"):
-            operator["rotations"][f"_{basis}"] = operator["rotations"][basis]
-            del operator["rotations"][basis]
-
         eko = cls.detached(theory, operator, path=path)
         logger.info(f"New operator created at path '{path}'")
         return eko
@@ -882,7 +869,7 @@ def raw(self) -> dict:
         return dict(
             path=str(self.path),
             Q0=float(np.sqrt(self.Q02)),
-            Q2grid=self.Q2grid,
+            Q2grid=self.Q2grid.tolist(),
             configs=self.configs.raw,
             rotations=self.rotations.raw,
             debug=self.debug.raw,
diff --git a/src/eko/runner.py b/src/eko/runner.py
index 8c3a364d5..37f37a3e6 100644
--- a/src/eko/runner.py
+++ b/src/eko/runner.py
@@ -82,9 +82,7 @@ def __init__(self, theory_card: dict, operators_card: dict):
             self.post_process[key] = rot.get(key, None)
             new_operators["rotations"][key] = None
 
-        self.out = EKO.new(
-            theory=theory_card, operator=dict(Q0=np.sqrt(tc.q2_ref), **new_operators)
-        )
+        self.out = EKO.new(theory=theory_card, operator=new_operators)
 
     def get_output(self) -> EKO:
         """Run evolution and generate output operator.
diff --git a/tests/eko/test_compatibility.py b/tests/eko/test_compatibility.py
index 8bc46d3f0..1a9de4d0b 100644
--- a/tests/eko/test_compatibility.py
+++ b/tests/eko/test_compatibility.py
@@ -1,12 +1,7 @@
 # -*- coding: utf-8 -*-
 from eko import compatibility
 
-theory1 = {
-    "alphas": 0.1180,
-    "alphaqed": 0.007496,
-    "PTO": 2,
-    "QED": 0,
-}
+theory1 = {"alphas": 0.1180, "alphaqed": 0.007496, "PTO": 2, "QED": 0, "Q0": 1.0}
 
 
 def test_compatibility():
diff --git a/tests/eko/test_output_struct.py b/tests/eko/test_output_struct.py
index 9738fecb8..ea8324c2d 100644
--- a/tests/eko/test_output_struct.py
+++ b/tests/eko/test_output_struct.py
@@ -7,8 +7,10 @@
 import pytest
 import yaml
 
-from eko import interpolation, output
+from eko import compatibility, interpolation, output
 from eko.output import struct
+from ekobox import operators_card as oc
+from ekobox import theory_card as tc
 
 
 @dataclass
@@ -125,6 +127,126 @@ def test_init(self):
         assert r.inputgrid == interpolation.XGrid.load(ixg)
 
 
+class TestEKO:
+    def _default_cards(self):
+        t = tc.generate(0, 1.0)
+        o = oc.generate([10.0])
+        return compatibility.update(t, o)
+
+    def test_new_error(self, tmp_path):
+        nt, no = self._default_cards()
+        # try to write to a file different from bla
+        no_tar_path = tmp_path / "Blub.bla"
+        with pytest.raises(ValueError):
+            struct.EKO.new(nt, no, no_tar_path)
+        # try to overwrite an existing file
+        exists_path = tmp_path / "Blub.tar"
+        exists_path.write_text("Blub", encoding="utf-8")
+        with pytest.raises(FileExistsError):
+            struct.EKO.new(nt, no, exists_path)
+
+    def test_load_error(self, tmp_path):
+        # try to read from a non-tar path
+        no_tar_path = tmp_path / "Blub.tar"
+        no_tar_path.write_text("Blub", encoding="utf-8")
+        with pytest.raises(ValueError):
+            struct.EKO.load(no_tar_path)
+
+    def test_properties(self):
+        eko = struct.EKO.new(*self._default_cards())
+        assert "mc" in eko.theory_card
+        assert "debug" in eko.operator_card
+        np.testing.assert_allclose(eko.Q2grid, np.array([10.0]))
+        assert 10.0 in eko
+        default_grid = interpolation.XGrid(eko.operator_card["rotations"]["xgrid"])
+        assert eko.xgrid == default_grid
+        for use_target in (True, False):
+            assert eko.interpolator(False, use_target).xgrid == default_grid
+        xg = interpolation.XGrid([0.1, 1.0])
+        eko.xgrid = xg
+        assert eko.xgrid == xg
+        assert "debug" in eko.raw
+        # check we can dump and reload
+        stream = io.StringIO()
+        yaml.safe_dump(eko.raw, stream)
+        stream.seek(0)
+        raw_eko = yaml.safe_load(stream)
+        assert "debug" in raw_eko
+
+    def test_ops(self):
+        v = np.random.rand(2, 2)
+        opv = struct.Operator(operator=v)
+        eko = struct.EKO.new(*self._default_cards())
+        # try setting not an operator
+        with pytest.raises(ValueError):
+            eko[10.0] = "bla"
+        # approx
+        eko[10.0] = opv
+        assert eko.approx(20.0) is None
+        assert eko.approx(11.0, atol=2) == 10.0
+        eko[11.0] = opv
+        with pytest.raises(ValueError):
+            eko.approx(10.5, atol=2)
+        # iterate
+        for q2, q2eko in zip((10.0, 11.0), eko):
+            assert q2 == q2eko
+            np.testing.assert_allclose(v, eko[q2].operator)
+        for q2, (q2eko, op) in zip((10.0, 11.0), eko.items()):
+            assert q2 == q2eko
+            np.testing.assert_allclose(v, op.operator)
+        # getter
+        with pytest.raises(ValueError):
+            eko[12.0]
+        with eko.operator(10.0) as op:
+            np.testing.assert_allclose(v, op.operator)
+        # overwrite
+        vv = np.random.rand(2, 2)
+        opvv = struct.Operator(operator=vv)
+        eko[11.0] = opvv
+        np.testing.assert_allclose(vv, eko[11.0].operator)
+
+    def test_interpolator(self):
+        nt, no = self._default_cards()
+        txg = np.geomspace(0.1, 1.0, 5)
+        ixg = np.geomspace(0.01, 1.0, 5)
+        no["rotations"]["targetgrid"] = txg
+        no["rotations"]["inputgrid"] = ixg
+        eko = struct.EKO.new(nt, no)
+        assert eko.interpolator(False, True).xgrid == interpolation.XGrid(txg)
+        assert eko.interpolator(False, False).xgrid == interpolation.XGrid(ixg)
+
+    def test_copy(self, tmp_path):
+        v = np.random.rand(2, 2)
+        opv = struct.Operator(operator=v)
+        eko1 = struct.EKO.new(*self._default_cards())
+        eko1[10.0] = opv
+        np.testing.assert_allclose(eko1[10.0].operator, v)
+        p = tmp_path / "eko2.tar"
+        eko2 = eko1.deepcopy(p)
+        np.testing.assert_allclose(eko1[10.0].operator, v)
+        np.testing.assert_allclose(eko2[10.0].operator, v)
+        vv = np.random.rand(2, 2)
+        opvv = struct.Operator(operator=vv)
+        eko2[10.0] = opvv
+        np.testing.assert_allclose(eko1[10.0].operator, v)
+        np.testing.assert_allclose(eko2[10.0].operator, vv)
+        # try loading again
+        eko2_ = struct.EKO.load(p)
+        assert eko2.raw == eko2_.raw
+
+    def test_extract(self, tmp_path):
+        p = tmp_path / "test.tar"
+        eko = struct.EKO.new(*self._default_cards(), p)
+        # check theory file
+        t = struct.EKO.extract(p, struct.THEORYFILE)
+        assert isinstance(t, str)
+        tt = yaml.safe_load(io.StringIO(t))
+        assert tt == eko.theory_card
+        # try a wrong file
+        with pytest.raises(KeyError):
+            t = struct.EKO.extract(p, "Blub.bla")
+
+
 class TestLegacy:
     def test_items(self, fake_output):
         """Test autodump, autoload, and manual unload."""
diff --git a/tests/eko/test_runner.py b/tests/eko/test_runner.py
index 796556b95..c1d491022 100644
--- a/tests/eko/test_runner.py
+++ b/tests/eko/test_runner.py
@@ -38,6 +38,7 @@
 }
 operators_card = {
     "Q2grid": [10, 100],
+    "Q0": np.sqrt(2),
     "configs": {
         "interpolation_polynomial_degree": 1,
         "interpolation_is_log": True,

From 44b581cc497008e0c0da33162cb94e26a818a584 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 17:09:49 +0200
Subject: [PATCH 138/148] Fix numba and LHA

---
 benchmarks/lha_paper_bench.py          | 4 ++--
 src/eko/evolution_operator/__init__.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/benchmarks/lha_paper_bench.py b/benchmarks/lha_paper_bench.py
index 451c638d1..f2ee934e3 100644
--- a/benchmarks/lha_paper_bench.py
+++ b/benchmarks/lha_paper_bench.py
@@ -112,8 +112,8 @@ def run_lha(self, theory_updates):
             [
                 {
                     "Q2grid": [1e4],
-                    "configs": {"ev_op_iterations": 10},
-                    "xgrid": make_lambert_grid(60).tolist(),
+                    "ev_op_iterations": 10,
+                    "interpolation_xgrid": make_lambert_grid(60).tolist(),
                 }
             ],
             ["ToyLH"],
diff --git a/src/eko/evolution_operator/__init__.py b/src/eko/evolution_operator/__init__.py
index 4d2a17678..be5f8a690 100644
--- a/src/eko/evolution_operator/__init__.py
+++ b/src/eko/evolution_operator/__init__.py
@@ -265,7 +265,7 @@ def __init__(
         self._mellin_cut = mellin_cut
         self.is_threshold = is_threshold
         self.op_members = {}
-        self.order = config["order"]
+        self.order = tuple(config["order"])
 
     @property
     def n_pools(self):
@@ -376,7 +376,7 @@ def quad_ker(self, label, logx, areas):
             nf=self.nf,
             L=np.log(self.fact_to_ren),
             ev_op_iterations=self.config["ev_op_iterations"],
-            ev_op_max_order=self.config["ev_op_max_order"],
+            ev_op_max_order=tuple(self.config["ev_op_max_order"]),
             sv_mode=self.sv_mode,
             is_threshold=self.is_threshold,
         )

From 4e6c8a3e317ef0b2e0f9373b6b868ae579651dc5 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 17:22:24 +0200
Subject: [PATCH 139/148] Recover test_ev_operator

---
 tests/eko/test_ev_operator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/eko/test_ev_operator.py b/tests/eko/test_ev_operator.py
index f3e1b6935..1e10b4058 100644
--- a/tests/eko/test_ev_operator.py
+++ b/tests/eko/test_ev_operator.py
@@ -161,7 +161,7 @@ def test_quad_ker(monkeypatch):
     "configs": {
         "interpolation_polynomial_degree": 1,
         "interpolation_is_log": True,
-        "ev_op_max_order": 1,
+        "ev_op_max_order": [1, 1],
         "ev_op_iterations": 1,
         "backward_inversion": "exact",
         "n_integration_cores": 1,

From 7f38cad48d9c12f56943f379be48106cd3e805a6 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 29 Jul 2022 17:29:14 +0200
Subject: [PATCH 140/148] Add tests for runcards objects

---
 src/eko/runcards.py        | 49 +++++++++++++++++++++++++++++++++++++-
 tests/eko/test_runcards.py | 32 +++++++++++++++++++++++++
 2 files changed, 80 insertions(+), 1 deletion(-)
 create mode 100644 tests/eko/test_runcards.py

diff --git a/src/eko/runcards.py b/src/eko/runcards.py
index b9be63c4c..44dc47618 100644
--- a/src/eko/runcards.py
+++ b/src/eko/runcards.py
@@ -1,12 +1,59 @@
 # -*- coding: utf-8 -*-
+"""Structures to hold runcard information.
+
+.. todo::
+    Inherit from :class:`eko.output.struct.DictLike`, to get
+    :meth:`eko.output.struct.DictLike.raw` for free and avoid duplication.
+
+"""
 from dataclasses import dataclass
 
 
 @dataclass
 class TheoryCard:
-    pto: int
+    """Represent theory card content."""
+
+    order: tuple[int, int]
+    """Perturbatiive order tuple, ``(QCD, QED)``."""
+
+    @classmethod
+    def load(cls, card: dict):
+        """Load from runcard raw content.
+
+        Parameters
+        ----------
+        card: dict
+            content of the theory runcard
+
+        Returns
+        -------
+        TheoryCard
+            the loaded instance
+
+        """
+        return cls(order=tuple(card["order"]))
 
 
 @dataclass
 class OperatorCard:
+    """Represent operator card content."""
+
     xgrid: list
+    """Grid defining internal interpolation basis."""
+
+    @classmethod
+    def load(cls, card: dict):
+        """Load from runcard raw content.
+
+        Parameters
+        ----------
+        card: dict
+            content of the theory runcard
+
+        Returns
+        -------
+        TheoryCard
+            the loaded instance
+
+        """
+        return cls(xgrid=card["xgrid"])
diff --git a/tests/eko/test_runcards.py b/tests/eko/test_runcards.py
new file mode 100644
index 000000000..e8123ec2d
--- /dev/null
+++ b/tests/eko/test_runcards.py
@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+from eko import runcards as rc
+
+fake_theory = dict(order=(2, 0))
+
+fake_operator = dict(xgrid=[1e-3, 1e-2, 1e-1, 1.0])
+
+
+class TestTheory:
+    def test_init(self):
+        t = rc.TheoryCard(order=fake_theory["order"])
+
+        assert t.order == fake_theory["order"]
+
+    def test_load(self):
+        t0 = rc.TheoryCard(order=fake_theory["order"])
+        t1 = rc.TheoryCard.load(fake_theory)
+
+        assert t0 == t1
+
+
+class TestOperator:
+    def test_init(self):
+        o = rc.OperatorCard(xgrid=fake_operator["xgrid"])
+
+        assert o.xgrid == fake_operator["xgrid"]
+
+    def test_load(self):
+        o0 = rc.OperatorCard(xgrid=fake_operator["xgrid"])
+        o1 = rc.OperatorCard.load(fake_operator)
+
+        assert o0 == o1

From 67bd77d0de248fd2e0d9235d4bd62fc06962584e Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Fri, 29 Jul 2022 17:33:07 +0200
Subject: [PATCH 141/148] Fix legacy typing compatibility

---
 src/eko/runcards.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/eko/runcards.py b/src/eko/runcards.py
index 44dc47618..0c46b51ed 100644
--- a/src/eko/runcards.py
+++ b/src/eko/runcards.py
@@ -7,13 +7,14 @@
 
 """
 from dataclasses import dataclass
+from typing import Tuple
 
 
 @dataclass
 class TheoryCard:
     """Represent theory card content."""
 
-    order: tuple[int, int]
+    order: Tuple[int, int]
     """Perturbatiive order tuple, ``(QCD, QED)``."""
 
     @classmethod

From 2090ddd1bb2259a7ac8b80261b56de1b707a88cd Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Fri, 29 Jul 2022 17:44:16 +0200
Subject: [PATCH 142/148] Revert HERA20 fix

---
 benchmarks/HERA20_bench.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/benchmarks/HERA20_bench.py b/benchmarks/HERA20_bench.py
index 79f17c92b..a09d83f3d 100644
--- a/benchmarks/HERA20_bench.py
+++ b/benchmarks/HERA20_bench.py
@@ -22,7 +22,7 @@
 }
 
 # LHAPDF x-range is smaller
-base_op = {"xgrid": interpolation.make_lambert_grid(50, 1.0e-6)}
+base_op = {"interpolation_xgrid": interpolation.make_lambert_grid(50, 1.0e-6)}
 
 
 class BenchmarkHERA20(Runner):

From f5a730a7e07fb339c91da1562cf19ca43648a0c4 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Sat, 30 Jul 2022 08:59:16 +0200
Subject: [PATCH 143/148] Poetry update

---
 poetry.lock | 551 +++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 416 insertions(+), 135 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5fd358c7a..5c8257aec 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -81,17 +81,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.4.0"
+version = "22.1.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.5"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "babel"
@@ -232,7 +232,7 @@ optional = true
 python-versions = "*"
 
 [package.extras]
-test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
+test = ["hypothesis (==3.55.3)", "flake8 (==3.7.8)"]
 
 [[package]]
 name = "coverage"
@@ -293,7 +293,7 @@ graph = ["objgraph (>=1.7.2)"]
 
 [[package]]
 name = "distlib"
-version = "0.3.4"
+version = "0.3.5"
 description = "Distribution utilities"
 category = "dev"
 optional = false
@@ -317,7 +317,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "executing"
-version = "0.8.3"
+version = "0.9.1"
 description = "Get the currently executing AST node of a frame, and other information"
 category = "main"
 optional = false
@@ -337,7 +337,7 @@ pyrepl = ">=0.8.2"
 
 [[package]]
 name = "fastjsonschema"
-version = "2.15.3"
+version = "2.16.1"
 description = "Fastest Python implementation of JSON schema"
 category = "main"
 optional = false
@@ -393,7 +393,7 @@ docs = ["sphinx"]
 
 [[package]]
 name = "identify"
-version = "2.5.1"
+version = "2.5.2"
 description = "File identification library for Python"
 category = "dev"
 optional = false
@@ -436,7 +436,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 
 [[package]]
 name = "importlib-resources"
-version = "5.8.0"
+version = "5.9.0"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
@@ -446,8 +446,8 @@ python-versions = ">=3.7"
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "iniconfig"
@@ -561,7 +561,7 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.7.2"
+version = "4.8.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -622,7 +622,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.3"
+version = "1.4.4"
 description = "A fast implementation of the Cassowary constraint solver"
 category = "main"
 optional = true
@@ -975,8 +975,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
+testing = ["pytest-benchmark", "pytest"]
+dev = ["tox", "pre-commit"]
 
 [[package]]
 name = "pre-commit"
@@ -1089,7 +1089,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "pylint"
-version = "2.14.4"
+version = "2.14.5"
 description = "python code static checker"
 category = "dev"
 optional = false
@@ -1179,7 +1179,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
+testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
 
 [[package]]
 name = "pytest-env"
@@ -1283,14 +1283,14 @@ jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
 
 [[package]]
 name = "scipy"
-version = "1.8.1"
+version = "1.9.0"
 description = "SciPy: Scientific Library for Python"
 category = "main"
 optional = false
-python-versions = ">=3.8,<3.11"
+python-versions = ">=3.8,<3.12"
 
 [package.dependencies]
-numpy = ">=1.17.3,<1.25.0"
+numpy = ">=1.18.5,<1.25.0"
 
 [[package]]
 name = "setuptools-scm"
@@ -1378,7 +1378,7 @@ docutils = "<0.18"
 sphinx = ">=1.6"
 
 [package.extras]
-dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version"]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -1525,8 +1525,8 @@ python-versions = ">=3.6"
 webencodings = ">=0.4"
 
 [package.extras]
-doc = ["sphinx", "sphinx-rtd-theme"]
-test = ["pytest", "pytest-cov", "pytest-flake8", "pytest-isort", "coverage"]
+test = ["coverage", "pytest-isort", "pytest-flake8", "pytest-cov", "pytest"]
+doc = ["sphinx-rtd-theme", "sphinx"]
 
 [[package]]
 name = "toml"
@@ -1581,7 +1581,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "urllib3"
-version = "1.26.10"
+version = "1.26.11"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
@@ -1594,21 +1594,20 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.15.1"
+version = "20.16.2"
 description = "Virtual Python Environment builder"
 category = "dev"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.6"
 
 [package.dependencies]
 distlib = ">=0.3.1,<1"
 filelock = ">=3.2,<4"
 platformdirs = ">=2,<3"
-six = ">=1.9.0,<2"
 
 [package.extras]
 docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"]
-testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)"]
+testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "packaging (>=20.0)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)"]
 
 [[package]]
 name = "wcwidth"
@@ -1686,7 +1685,10 @@ appnope = [
     {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
     {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
 ]
-astroid = []
+astroid = [
+    {file = "astroid-2.11.7-py3-none-any.whl", hash = "sha256:86b0a340a512c65abf4368b80252754cda17c02cdbbd3f587dddf98112233e7b"},
+    {file = "astroid-2.11.7.tar.gz", hash = "sha256:bb24615c77f4837c707669d16907331374ae8a964650a66999da3f5ca68dc946"},
+]
 asttokens = [
     {file = "asttokens-2.0.5-py2.py3-none-any.whl", hash = "sha256:0844691e88552595a6f4a4281a9f7f79b8dd45ca4ccea82e5e05b4bbdb76705c"},
     {file = "asttokens-2.0.5.tar.gz", hash = "sha256:9a54c114f02c7a9480d56550932546a3f1fe71d8a02f1bc7ccd0ee3ee35cf4d5"},
@@ -1694,10 +1696,12 @@ asttokens = [
 asv = [
     {file = "asv-0.4.2.tar.gz", hash = "sha256:9134f56b7a2f465420f17b5bb0dee16047a70f01029c996b7ab3f197de2d0779"},
 ]
-atomicwrites = []
+atomicwrites = [
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+    {file = "scipy-1.9.0-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:8d541db2d441ef87afb60c4a2addb00c3af281633602a4967e733ef4b7050504"},
+    {file = "scipy-1.9.0-cp38-cp38-macosx_12_0_universal2.macosx_10_9_x86_64.whl", hash = "sha256:97a1f1e51ea30782d7baa8d0c52f72c3f9f05cb609cf1b990664231c5102bccd"},
+    {file = "scipy-1.9.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:16207622570af10f9e6a2cdc7da7a9660678852477adbcd056b6d1057a036fef"},
+    {file = "scipy-1.9.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bb687d245b6963673c639f318eea7e875d1ba147a67925586abed3d6f39bb7d8"},
+    {file = "scipy-1.9.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:73b704c5eea9be811919cae4caacf3180dd9212d9aed08477c1d2ba14900a9de"},
+    {file = "scipy-1.9.0-cp38-cp38-win32.whl", hash = "sha256:12005d30894e4fe7b247f7233ba0801a341f887b62e2eb99034dd6f2a8a33ad6"},
+    {file = "scipy-1.9.0-cp38-cp38-win_amd64.whl", hash = "sha256:fc58c3fcb8a724b703ffbc126afdca5a8353d4d5945d5c92db85617e165299e7"},
+    {file = "scipy-1.9.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:01c2015e132774feefe059d5354055fec6b751d7a7d70ad2cf5ce314e7426e2a"},
+    {file = "scipy-1.9.0-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:f7c3c578ff556333f3890c2df6c056955d53537bb176698359088108af73a58f"},
+    {file = "scipy-1.9.0-cp39-cp39-macosx_12_0_universal2.macosx_10_9_x86_64.whl", hash = "sha256:e2ac088ea4aa61115b96b47f5f3d94b3fa29554340b6629cd2bfe6b0521ee33b"},
+    {file = "scipy-1.9.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:5d1b9cf3771fd921f7213b4b886ab2606010343bb36259b544a816044576d69e"},
+    {file = "scipy-1.9.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d3a326673ac5afa9ef5613a61626b9ec15c8f7222b4ecd1ce0fd8fcba7b83c59"},
+    {file = "scipy-1.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:693b3fe2e7736ce0dbc72b4d933798eb6ca8ce51b8b934e3f547cc06f48b2afb"},
+    {file = "scipy-1.9.0-cp39-cp39-win32.whl", hash = "sha256:7bad16b91918bf3288089a78a4157e04892ea6475fb7a1d9bcdf32c30c8a3dba"},
+    {file = "scipy-1.9.0-cp39-cp39-win_amd64.whl", hash = "sha256:bd490f77f35800d5620f4d9af669e372d9a88db1f76ef219e1609cc4ecdd1a24"},
+    {file = "scipy-1.9.0.tar.gz", hash = "sha256:c0dfd7d2429452e7e94904c6a3af63cbaa3cf51b348bd9d35b42db7e9ad42791"},
+]
+setuptools-scm = [
+    {file = "setuptools_scm-7.0.5-py3-none-any.whl", hash = "sha256:7930f720905e03ccd1e1d821db521bff7ec2ac9cf0ceb6552dd73d24a45d3b02"},
+    {file = "setuptools_scm-7.0.5.tar.gz", hash = "sha256:031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844"},
+]
 six = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -2613,17 +2870,38 @@ tomli = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
-tomlkit = []
-tornado = []
+tomlkit = [
+    {file = "tomlkit-0.11.1-py3-none-any.whl", hash = "sha256:1c5bebdf19d5051e2e1de6cf70adfc5948d47221f097fcff7a3ffc91e953eaf5"},
+    {file = "tomlkit-0.11.1.tar.gz", hash = "sha256:61901f81ff4017951119cd0d1ed9b7af31c821d6845c8c477587bbdcd5e5854e"},
+]
+tornado = [
+    {file = "tornado-6.2-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:20f638fd8cc85f3cbae3c732326e96addff0a15e22d80f049e00121651e82e72"},
+    {file = "tornado-6.2-cp37-abi3-macosx_10_9_x86_64.whl", hash = "sha256:87dcafae3e884462f90c90ecc200defe5e580a7fbbb4365eda7c7c1eb809ebc9"},
+    {file = "tornado-6.2-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ba09ef14ca9893954244fd872798b4ccb2367c165946ce2dd7376aebdde8e3ac"},
+    {file = "tornado-6.2-cp37-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:b8150f721c101abdef99073bf66d3903e292d851bee51910839831caba341a75"},
+    {file = "tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d3a2f5999215a3a06a4fc218026cd84c61b8b2b40ac5296a6db1f1451ef04c1e"},
+    {file = "tornado-6.2-cp37-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:5f8c52d219d4995388119af7ccaa0bcec289535747620116a58d830e7c25d8a8"},
+    {file = "tornado-6.2-cp37-abi3-musllinux_1_1_i686.whl", hash = "sha256:6fdfabffd8dfcb6cf887428849d30cf19a3ea34c2c248461e1f7d718ad30b66b"},
+    {file = "tornado-6.2-cp37-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:1d54d13ab8414ed44de07efecb97d4ef7c39f7438cf5e976ccd356bebb1b5fca"},
+    {file = "tornado-6.2-cp37-abi3-win32.whl", hash = "sha256:5c87076709343557ef8032934ce5f637dbb552efa7b21d08e89ae7619ed0eb23"},
+    {file = "tornado-6.2-cp37-abi3-win_amd64.whl", hash = "sha256:e5f923aa6a47e133d1cf87d60700889d7eae68988704e20c75fb2d65677a8e4b"},
+    {file = "tornado-6.2.tar.gz", hash = "sha256:9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13"},
+]
 traitlets = [
     {file = "traitlets-5.3.0-py3-none-any.whl", hash = "sha256:65fa18961659635933100db8ca120ef6220555286949774b9cfc106f941d1c7a"},
     {file = "traitlets-5.3.0.tar.gz", hash = "sha256:0bb9f1f9f017aa8ec187d8b1b2a7a6626a2a1d877116baba52a129bfa124f8e2"},
 ]
-typing-extensions = []
-urllib3 = []
+typing-extensions = [
+    {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"},
+    {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"},
+]
+urllib3 = [
+    {file = "urllib3-1.26.11-py2.py3-none-any.whl", hash = "sha256:c33ccba33c819596124764c23a97d25f32b28433ba0dedeb77d873a38722c9bc"},
+    {file = "urllib3-1.26.11.tar.gz", hash = "sha256:ea6e8fb210b19d950fab93b60c9009226c63a28808bc8386e05301e25883ac0a"},
+]
 virtualenv = [
-    {file = "virtualenv-20.15.1-py2.py3-none-any.whl", hash = "sha256:b30aefac647e86af6d82bfc944c556f8f1a9c90427b2fb4e3bfbf338cb82becf"},
-    {file = "virtualenv-20.15.1.tar.gz", hash = "sha256:288171134a2ff3bfb1a2f54f119e77cd1b81c29fc1265a2356f3e8d14c7d58c4"},
+    {file = "virtualenv-20.16.2-py2.py3-none-any.whl", hash = "sha256:635b272a8e2f77cb051946f46c60a54ace3cb5e25568228bd6b57fc70eca9ff3"},
+    {file = "virtualenv-20.16.2.tar.gz", hash = "sha256:0ef5be6d07181946891f5abc8047fda8bc2f0b4b9bf222c64e6e8963baee76db"},
 ]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
@@ -2702,4 +2980,7 @@ wrapt = [
     {file = "wrapt-1.14.1-cp39-cp39-win_amd64.whl", hash = "sha256:dee60e1de1898bde3b238f18340eec6148986da0455d8ba7848d50470a7a32fb"},
     {file = "wrapt-1.14.1.tar.gz", hash = "sha256:380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d"},
 ]
-zipp = []
+zipp = [
+    {file = "zipp-3.8.1-py3-none-any.whl", hash = "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009"},
+    {file = "zipp-3.8.1.tar.gz", hash = "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2"},
+]

From 8b8e3e367335ac84a3bd4bf6458cde9cfde8e85a Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 5 Sep 2022 12:28:49 +0200
Subject: [PATCH 144/148] Revert logger.info to lazy evaluation

---
 src/eko/evolution_operator/__init__.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/eko/evolution_operator/__init__.py b/src/eko/evolution_operator/__init__.py
index be5f8a690..23d88b6cb 100644
--- a/src/eko/evolution_operator/__init__.py
+++ b/src/eko/evolution_operator/__init__.py
@@ -436,8 +436,11 @@ def run_op_integration(
                 temp_dict[label] = res[:2]
             column.append(temp_dict)
         logger.info(
-            f"{self.log_label}: computing operators: - {k+1}/{self.grid_size}"
-            f" took: {(time.perf_counter() - start_time):6f} s"
+            "%s: computing operators - %u/%u took: %6f s",
+            self.log_label,
+            k + 1,
+            self.grid_size,
+            (time.perf_counter() - start_time),
         )
         return column
 

From 3f7dc23d605b77ef0344d6ad077b2dc79b73a3e8 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 5 Sep 2022 12:30:45 +0200
Subject: [PATCH 145/148] Try fix poetry

---
 poetry.lock | 449 ++++++----------------------------------------------
 1 file changed, 50 insertions(+), 399 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 01a168061..b3412f5e2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -232,7 +232,7 @@ optional = true
 python-versions = "*"
 
 [package.extras]
-test = ["hypothesis (==3.55.3)", "flake8 (==3.7.8)"]
+test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
 
 [[package]]
 name = "coverage"
@@ -317,7 +317,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "executing"
-version = "0.8.3"
+version = "0.10.0"
 description = "Get the currently executing AST node of a frame, and other information"
 category = "main"
 optional = false
@@ -393,7 +393,7 @@ docs = ["sphinx"]
 
 [[package]]
 name = "identify"
-version = "2.5.1"
+version = "2.5.3"
 description = "File identification library for Python"
 category = "dev"
 optional = false
@@ -561,7 +561,7 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.7.2"
+version = "4.14.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -1001,8 +1001,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-testing = ["pytest-benchmark", "pytest"]
-dev = ["tox", "pre-commit"]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
@@ -1208,7 +1208,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
+testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "pytest-env"
@@ -1406,7 +1406,7 @@ docutils = "<0.18"
 sphinx = ">=1.6"
 
 [package.extras]
-dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client"]
+dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -1554,8 +1554,8 @@ python-versions = ">=3.6"
 webencodings = ">=0.4"
 
 [package.extras]
-test = ["coverage", "pytest-isort", "pytest-flake8", "pytest-cov", "pytest"]
-doc = ["sphinx-rtd-theme", "sphinx"]
+doc = ["sphinx", "sphinx-rtd-theme"]
+test = ["pytest", "pytest-cov", "pytest-flake8", "pytest-isort", "coverage"]
 
 [[package]]
 name = "toml"
@@ -1610,7 +1610,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "urllib3"
-version = "1.26.10"
+version = "1.26.12"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
@@ -1623,21 +1623,20 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.15.1"
+version = "20.16.3"
 description = "Virtual Python Environment builder"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-distlib = ">=0.3.1,<1"
-filelock = ">=3.2,<4"
-platformdirs = ">=2,<3"
-six = ">=1.9.0,<2"
+distlib = ">=0.3.5,<1"
+filelock = ">=3.4.1,<4"
+platformdirs = ">=2.4,<3"
 
 [package.extras]
-docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"]
-testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)"]
+docs = ["proselint (>=0.13)", "sphinx (>=5.1.1)", "sphinx-argparse (>=0.3.1)", "sphinx-rtd-theme (>=1)", "towncrier (>=21.9)"]
+testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "wcwidth"
@@ -1716,18 +1715,12 @@ appnope = [
     {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
 ]
 astroid = []
-asttokens = [
-    {file = "asttokens-2.0.5-py2.py3-none-any.whl", hash = "sha256:0844691e88552595a6f4a4281a9f7f79b8dd45ca4ccea82e5e05b4bbdb76705c"},
-    {file = "asttokens-2.0.5.tar.gz", hash = "sha256:9a54c114f02c7a9480d56550932546a3f1fe71d8a02f1bc7ccd0ee3ee35cf4d5"},
-]
+asttokens = []
 asv = [
     {file = "asv-0.4.2.tar.gz", hash = "sha256:9134f56b7a2f465420f17b5bb0dee16047a70f01029c996b7ab3f197de2d0779"},
 ]
 atomicwrites = []
-attrs = [
-    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
-    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
-]
+attrs = []
 babel = [
     {file = "Babel-2.10.3-py3-none-any.whl", hash = "sha256:ff56f4892c1c4bf0d814575ea23471c230d544203c7748e8c68f0089478d48eb"},
     {file = "Babel-2.10.3.tar.gz", hash = "sha256:7614553711ee97490f732126dc077f8d0ae084ebc6a96e23db1482afabdb2c51"},
@@ -1744,80 +1737,12 @@ beautifulsoup4 = [
     {file = "beautifulsoup4-4.11.1-py3-none-any.whl", hash = "sha256:58d5c3d29f5a36ffeb94f02f0d786cd53014cf9b3b3951d42e0080d8a9498d30"},
     {file = "beautifulsoup4-4.11.1.tar.gz", hash = "sha256:ad9aa55b65ef2808eb405f46cf74df7fcb7044d5cbc26487f96eb2ef2e436693"},
 ]
-bleach = [
-    {file = "bleach-5.0.1-py3-none-any.whl", hash = "sha256:085f7f33c15bd408dd9b17a4ad77c577db66d76203e5984b1bd59baeee948b2a"},
-    {file = "bleach-5.0.1.tar.gz", hash = "sha256:0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c"},
-]
+bleach = []
 certifi = [
     {file = "certifi-2022.6.15-py3-none-any.whl", hash = "sha256:fe86415d55e84719d75f8b69414f6438ac3547d2078ab91b67e779ef69378412"},
     {file = "certifi-2022.6.15.tar.gz", hash = "sha256:84c85a9078b11105f04f3036a9482ae10e4621616db313fe045dd24743a0820d"},
 ]
-cffi = [
-    {file = "cffi-1.15.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:a66d3508133af6e8548451b25058d5812812ec3798c886bf38ed24a98216fab2"},
-    {file = "cffi-1.15.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:470c103ae716238bbe698d67ad020e1db9d9dba34fa5a899b5e21577e6d52ed2"},
-    {file = "cffi-1.15.1-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:9ad5db27f9cabae298d151c85cf2bad1d359a1b9c686a275df03385758e2f914"},
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From be82c99d4e6d0bc21f3fc72c3c7599ca57ab7706 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 5 Sep 2022 13:09:09 +0200
Subject: [PATCH 146/148] Cast couplings order for numba

---
 src/eko/couplings.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/eko/couplings.py b/src/eko/couplings.py
index b6c0d00ea..2d3ec307e 100644
--- a/src/eko/couplings.py
+++ b/src/eko/couplings.py
@@ -381,7 +381,7 @@ def __init__(
             raise NotImplementedError("a_s beyond N3LO is not implemented")
         if order[1] not in [0, 1, 2]:
             raise NotImplementedError("a_em beyond NLO is not implemented")
-        self.order = order
+        self.order = tuple(order)
         if method not in ["expanded", "exact"]:
             raise ValueError(f"Unknown method {method}")
         self.method = method

From fdd02fd27542574de79af8c9d9f80083959ed60b Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 19 Sep 2022 11:10:40 +0200
Subject: [PATCH 147/148] Remove unlink in load_tar

---
 src/eko/output/legacy.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/eko/output/legacy.py b/src/eko/output/legacy.py
index 089280dc6..b1ec9de2c 100644
--- a/src/eko/output/legacy.py
+++ b/src/eko/output/legacy.py
@@ -279,8 +279,6 @@ def load_tar(tarname: Union[str, os.PathLike]) -> struct.EKO:
                 stream.seek(0)
                 grids[pathlib.Path(fp.stem).stem] = np.load(stream)
 
-            fp.unlink()
-
         q2grid = metadata["Q2grid"]
         for q2, slices in zip(q2grid, zip(*grids.values())):
             operator_grid[q2] = dict(zip(grids.keys(), slices))

From 47e30e518ae0aa1b34bd8d2b2d0bb7d0b7b479de Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 19 Sep 2022 14:21:16 +0200
Subject: [PATCH 148/148] Update docs

---
 doc/source/overview/tutorials/output.ipynb | 181 ++++-----------------
 1 file changed, 28 insertions(+), 153 deletions(-)

diff --git a/doc/source/overview/tutorials/output.ipynb b/doc/source/overview/tutorials/output.ipynb
index 79bddaec3..13c10b68e 100644
--- a/doc/source/overview/tutorials/output.ipynb
+++ b/doc/source/overview/tutorials/output.ipynb
@@ -55,7 +55,7 @@
    "id": "f26bf77f-9999-42d0-8ebf-2c1607214ea7",
    "metadata": {},
    "source": [
-    "Now that we have it, we can actually use one of the available formats to dump it."
+    "The computed operator is now it's own type (that no longer inherits from dictionary as in previous eko versions):"
    ]
   },
   {
@@ -63,39 +63,20 @@
    "execution_count": 3,
    "id": "daae3811-e7a6-4a7c-9f55-eef8ea1564b8",
    "metadata": {},
-   "outputs": [],
-   "source": [
-    "evolution_operator.dump_tar(\"myeko.tar\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "a0d115e4-43cd-4f83-bcb5-922dcbfc56d4",
-   "metadata": {},
-   "source": [
-    "Once dumped, we can always use the paired method to load it, at any later time."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "b62dc52e-ff36-4621-a772-502ff495456f",
-   "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "eko.output.Output"
+       "eko.output.struct.EKO"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "myeko = eko.output.Output.load_tar(\"myeko.tar\")\n",
-    "type(myeko)"
+    "type(evolution_operator)"
    ]
   },
   {
@@ -103,12 +84,12 @@
    "id": "91b17b27-e423-43fe-87f2-a1eaff027c7a",
    "metadata": {},
    "source": [
-    "Now, let's inspect the content of the operator."
+    "Now, let's inspect the content of the operator: e.g. you can extract the theory and operator card"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "e5c5b8af-d478-48ca-bb61-9a0de680252a",
    "metadata": {},
    "outputs": [
@@ -116,113 +97,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Q2grid\n",
-      "eko_version\n",
-      "inputgrid\n",
-      "inputpids\n",
-      "interpolation_is_log\n",
-      "interpolation_polynomial_degree\n",
-      "interpolation_xgrid\n",
-      "q2_ref\n",
-      "targetgrid\n",
-      "targetpids\n"
+      "{'CKM': '0.97428 0.22530 0.003470 0.22520 0.97345 0.041000 0.00862 0.04030 0.999152', 'Comments': 'LO baseline for small-x res', 'DAMP': 0, 'EScaleVar': 1, 'FNS': 'FFNS', 'GF': 1.1663787e-05, 'HQ': 'POLE', 'IB': 0, 'IC': 0, 'ID': 0, 'MP': 0.938, 'MW': 80.398, 'MZ': 91.1876, 'MaxNfAs': 6, 'MaxNfPdf': 6, 'ModEv': 'EXA', 'ModSV': None, 'NfFF': 3, 'PTO': 0, 'Q0': 1.0, 'QED': 0, 'Qedref': 1.777, 'Qmb': 4.5, 'Qmc': 2.0, 'Qmt': 173.07, 'Qref': 91.2, 'SIN2TW': 0.23126, 'SxOrd': 'LL', 'SxRes': 0, 'TMC': 0, 'XIF': 1.0, 'XIR': 1.0, 'alphaqed': 0.007496251999999999, 'alphas': 0.11800000000000001, 'fact_to_ren_scale_ratio': 1.0, 'global_nx': 0, 'kDISbThr': 1.0, 'kDIScThr': 1.0, 'kDIStThr': 1.0, 'kbThr': 1.0, 'kcThr': 1.0, 'ktThr': 1.0, 'mb': 4.5, 'mc': 2.0, 'mt': 173.07, 'nf0': None, 'nfref': None}\n",
+      "{'Q0': 1.0, 'Q2grid': [100], 'backward_inversion': 'expanded', 'configs': {'backward_inversion': 'expanded', 'ev_op_iterations': 10, 'ev_op_max_order': [10, 0], 'interpolation_is_log': True, 'interpolation_polynomial_degree': 4, 'n_integration_cores': 0}, 'debug': {'skip_non_singlet': False, 'skip_singlet': False}, 'debug_skip_non_singlet': False, 'debug_skip_singlet': False, 'ev_op_iterations': 10, 'ev_op_max_order': 10, 'inputgrid': None, 'inputpids': None, 'interpolation_is_log': True, 'interpolation_polynomial_degree': 4, 'interpolation_xgrid': [0.001, 0.01, 0.1, 0.5, 1.0], 'n_integration_cores': 0, 'rotations': {'inputgrid': None, 'inputpids': None, 'targetgrid': None, 'targetpids': None, 'xgrid': [0.001, 0.01, 0.1, 0.5, 1.0]}, 'targetgrid': None, 'targetpids': None}\n"
      ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "'0.0.0'"
-      ]
-     },
-     "execution_count": 5,
-     "metadata": {},
-     "output_type": "execute_result"
     }
    ],
    "source": [
-    "print(*myeko.keys(), sep=\"\\n\")\n",
-    "myeko[\"eko_version\"]"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "3d610d9f-b2cb-4ddf-ab02-a47d9c9638c3",
-   "metadata": {},
-   "source": [
-    "In the last step, we proved that an `eko.output.Output` object essentially behaves like a dictionary. Indeed, it is a dictionary."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "fcca9db4-a266-4abb-8aea-2390fc3aaa72",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "isinstance(myeko, dict)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "7b1baedd-8a95-4b5c-a1a0-03716534ecf3",
-   "metadata": {},
-   "source": [
-    "At the moment we have only seen one attribute in action: an `Output` object records the version of `eko` that has generated.\n",
-    "Let's have a look at some other ones."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "593038bf-d8db-46ce-8a19-fbb2ae1908b6",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "INTERNAL\n",
-      "log? True, degree? 4\n",
-      "[0.001 0.01  0.1   0.5   1.   ]\n",
-      "\n",
-      "INPUT\n",
-      "grid: (5,) float64\n",
-      "pids: 14 <class 'int'>\n",
-      "Q0^2: 1.0 GeV^2\n",
-      "TARGET\n",
-      "grid: (5,) float64\n",
-      "pids: 14 <class 'int'>\n",
-      "\n",
-      "All grid the same? True\n"
-     ]
-    }
-   ],
-   "source": [
-    "interpl = myeko[\"interpolation_is_log\"]\n",
-    "interpd = myeko[\"interpolation_polynomial_degree\"]\n",
-    "interpg = myeko[\"interpolation_xgrid\"]\n",
-    "print(f\"INTERNAL\\nlog? {interpl}, degree? {interpd}\\n{interpg}\\n\")\n",
-    "\n",
-    "ig = myeko[\"inputgrid\"]\n",
-    "ip = myeko[\"inputpids\"]\n",
-    "q0 = myeko[\"q2_ref\"]\n",
-    "print(f\"INPUT\\ngrid: {ig.shape} {ig.dtype}\\npids: {len(ip)} {type(ip[0])}\\nQ0^2: {q0} GeV^2\")\n",
-    "tg = myeko[\"targetgrid\"]\n",
-    "tp = myeko[\"targetpids\"]\n",
-    "print(f\"TARGET\\ngrid: {tg.shape} {tg.dtype}\\npids: {len(tp)} {type(tp[0])}\")\n",
-    "\n",
-    "print(\"\\nAll grid the same?\", (interpg == ig).all() and (interpg == tg).all())"
+    "# obtain theory card\n",
+    "print(evolution_operator.theory_card)\n",
+    "# or operator card\n",
+    "print(evolution_operator.operator_card)"
    ]
   },
   {
@@ -231,29 +115,28 @@
    "metadata": {},
    "source": [
     "So an `Output` object has some internal parameters, related to the interpolation used for the calculation, and then some external attributes, related to the final operator delivered.\n",
-    "But actually, we have not accessed yet the actual operator."
+    "But actually, we have not accessed yet the actual operator - let's first find out again which final scales we computed:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
    "id": "c82e6733-946f-4210-a6fa-95f995ee5be5",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "dict_keys([100.0])"
+       "array([100])"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "opgrid = myeko[\"Q2grid\"]\n",
-    "opgrid.keys()"
+    "evolution_operator.Q2grid"
    ]
   },
   {
@@ -261,13 +144,13 @@
    "id": "075734fa-8108-44ff-9070-cb4e5baab072",
    "metadata": {},
    "source": [
-    "Even the operator grid is a dictionary, mapping $Q^2$ values to the operator evolving to that scale (from the unique starting scale $Q_0^2$).\n",
-    "In the present case there is a unique final scale, but in the general one there might be many."
+    "Remember that the unique starting scale is $Q_0^2$. In the present case there is a unique final scale, but in the general one there might be many.\n",
+    "Now, let's use this operator! The recommended way to load an operator is by using a context manager:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 6,
    "id": "15262aee-1cfa-40f3-b072-b53ec5517784",
    "metadata": {},
    "outputs": [
@@ -275,23 +158,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "dict_keys(['operators', 'errors'])\n",
-      "\n",
-      "OPERATOR\n",
-      "(14, 5, 14, 5) float64\n",
-      "\n",
-      "ERROR\n",
-      "(14, 5, 14, 5) float64\n"
+      "operator: (14, 5, 14, 5)\n",
+      "error: (14, 5, 14, 5)\n"
      ]
     }
    ],
    "source": [
-    "print(opgrid[100.].keys())\n",
-    "op = opgrid[100.][\"operators\"]\n",
-    "operr = opgrid[100.][\"errors\"]\n",
-    "\n",
-    "print(f\"\\nOPERATOR\\n{op.shape} {op.dtype}\")\n",
-    "print(f\"\\nERROR\\n{operr.shape} {operr.dtype}\")"
+    "with evolution_operator.operator(100) as op:\n",
+    "    print(f\"operator: {op.operator.shape}\")\n",
+    "    print(f\"error: {op.error.shape}\")"
    ]
   },
   {
@@ -300,7 +175,7 @@
    "metadata": {},
    "source": [
     "This is the final product we expected from the beginning: the evolution operator, delivered as a numerical array.\n",
-    "It is actually composed by 3 elements:\n",
+    "It is actually composed by two elements:\n",
     "\n",
     "- the **operator** itself,  whose dimensions are `(flavor_out, x_out, flavor_in, x_in)`\n",
     "- the *error* on each operator element, propagated from the integration error on the numerical Mellin inversion (no other source is taken into account)"
@@ -313,7 +188,7 @@
    "source": [
     "How to use this object is now completely up to the user, but a few helpers are included in another package: `ekobox`!\n",
     "\n",
-    "This package will be explored in a separate tutorial."
+    "This package will be explored in [a separate tutorial](./pdf.ipynb)."
    ]
   }
  ],
@@ -333,7 +208,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,