From 379bebf10d594e5d39afb95c6f13e23c67d837eb Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 18:28:24 -0400
Subject: [PATCH 01/26] add format docs

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 .gitignore          |  3 ++
 docs/formats.rst    |  8 +++++
 docs/make_format.py | 85 ++++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 95 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 41ee080cf..874dccb73 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,4 +24,7 @@ _version.py
 __pycache__
 docs/_build
 docs/formats.csv
+docs/drivers.csv
+docs/minimizers.csv
 docs/api/
+docs/formats/
\ No newline at end of file
diff --git a/docs/formats.rst b/docs/formats.rst
index c0ff5b8f9..2e5477f2a 100644
--- a/docs/formats.rst
+++ b/docs/formats.rst
@@ -6,3 +6,11 @@ dpdata supports the following formats:
 .. csv-table:: Supported Formats
    :file: formats.csv
    :header-rows: 1
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+   :hidden:
+
+   formats/*
diff --git a/docs/make_format.py b/docs/make_format.py
index a208b21ed..d2ce9259c 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -1,6 +1,10 @@
 import csv
-from collections import defaultdict
+from collections import OrderedDict, defaultdict
+import os
+from inspect import Parameter, Signature, signature
+from typing import Literal
 
+from sphinx.ext.napoleon.docstring import NumpyDocstring
 # ensure all plugins are loaded!
 from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
@@ -96,6 +100,84 @@ def check_supported(fmt: Format):
     "to_multi_systems": ":func:`MultiSystems.to() <dpdata.system.MultiSystems.to>`",
 }
 
+method_classes = {
+    "from_system": "System",
+    "to_system": "System",
+    "from_labeled_system": "LabeledSystem",
+    "to_labeled_system": "LabeledSystem",
+    "from_bond_order_system": "BondOrderSystem",
+    "to_bond_order_system": "BondOrderSystem",
+    "from_multi_systems": "MultiSystems",
+    "to_multi_systems": "MultiSystems",
+}
+
+
+def generate_sub_format_pages(formats: dict):
+    """Generate sub format pages."""
+    os.makedirs("formats", exist_ok=True)
+    for format, alias in formats.items():
+        # format: Format, alias: list[str]
+        buff = []
+        for aa in alias:
+            buff.append("%s format" % aa)
+            buff.append("=" * len(buff[-1]))
+            buff.append("")
+        
+        docstring = format.__doc__
+        if docstring is not None:
+            rst = str(NumpyDocstring(docstring))
+            buff.append(rst)
+            buff.append("")
+        
+        buff.append("Conversation")
+        buff.append("------------")
+        methods = check_supported(format)
+        for method in methods:
+            buff.append("")
+            sig = signature(getattr(format, method))
+            parameters = dict(sig.parameters)
+            # del self
+            del parameters[list(parameters)[0]]
+            # del data
+            if method.startswith("to_"):
+                del parameters[list(parameters)[0]]
+            if "args" in parameters:
+                del parameters["args"]
+            if "kwargs" in parameters:
+                del parameters["kwargs"]
+            sig = Signature(list(parameters.values()))
+            sig = str(sig)
+            if method.startswith("from_") and method != "from_multi_systems":
+                for aa in alias:
+                    parameters['fmt'] = Parameter('fmt', Parameter.POSITIONAL_OR_KEYWORD, default=None, annotation=Literal[aa])
+                    sig_fmt = Signature(list(parameters.values()))
+                    sig_fmt = str(sig_fmt)
+                    buff.append(""".. py:function:: %s.from%s""" % (method_classes[method], sig_fmt))
+                    buff.append("""   :noindex:""")
+                for aa in alias:
+                    buff.append(""".. py:function:: %s.from_%s%s""" % (method_classes[method], aa.replace("/", "_").replace(".", ""), sig))
+                    buff.append("""   :noindex:""")
+                buff.append("")
+                buff.append("""   Convert this format to :func:`%s`.""" % (method_classes[method]))
+            elif method.startswith("to_"):
+                for aa in alias:
+                    parameters = {'fmt': Parameter('fmt', Parameter.POSITIONAL_OR_KEYWORD, annotation=Literal[aa]), **parameters}
+                    sig_fmt = Signature(list(parameters.values()))
+                    sig_fmt = str(sig_fmt)
+                    buff.append(""".. py:function:: %s.to%s""" % (method_classes[method], sig_fmt))
+                    buff.append("""   :noindex:""")
+                for aa in alias:
+                    buff.append(""".. py:function:: %s.to_%s%s""" % (method_classes[method], aa.replace("/", "_").replace(".", ""), sig))
+                    buff.append("""   :noindex:""")
+                buff.append("")
+                buff.append("""   Convert :func:`%s` to this format.""" % (method_classes[method]))
+            buff.append("")
+            buff.append("")
+
+        with open("formats/%s.rst" % format.__name__, "w") as rstfile:
+            rstfile.write("\n".join(buff))
+
+
 if __name__ == "__main__":
     formats = get_formats()
     with open("formats.csv", "w", newline="") as csvfile:
@@ -151,3 +233,4 @@ def check_supported(fmt: Format):
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
                 }
             )
+    generate_sub_format_pages(formats)
\ No newline at end of file

From 07dfde3f0121f63d2c67e4ab0ff5f448d78ce9b5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 28 Jul 2023 22:29:19 +0000
Subject: [PATCH 02/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .gitignore          |  2 +-
 docs/make_format.py | 59 ++++++++++++++++++++++++++++++++++++---------
 2 files changed, 48 insertions(+), 13 deletions(-)

diff --git a/.gitignore b/.gitignore
index 874dccb73..cd48a3e25 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,4 +27,4 @@ docs/formats.csv
 docs/drivers.csv
 docs/minimizers.csv
 docs/api/
-docs/formats/
\ No newline at end of file
+docs/formats/
diff --git a/docs/make_format.py b/docs/make_format.py
index d2ce9259c..c656d32ce 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -1,10 +1,11 @@
 import csv
-from collections import OrderedDict, defaultdict
 import os
+from collections import defaultdict
 from inspect import Parameter, Signature, signature
 from typing import Literal
 
 from sphinx.ext.napoleon.docstring import NumpyDocstring
+
 # ensure all plugins are loaded!
 from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
@@ -122,13 +123,13 @@ def generate_sub_format_pages(formats: dict):
             buff.append("%s format" % aa)
             buff.append("=" * len(buff[-1]))
             buff.append("")
-        
+
         docstring = format.__doc__
         if docstring is not None:
             rst = str(NumpyDocstring(docstring))
             buff.append(rst)
             buff.append("")
-        
+
         buff.append("Conversation")
         buff.append("------------")
         methods = check_supported(format)
@@ -149,28 +150,62 @@ def generate_sub_format_pages(formats: dict):
             sig = str(sig)
             if method.startswith("from_") and method != "from_multi_systems":
                 for aa in alias:
-                    parameters['fmt'] = Parameter('fmt', Parameter.POSITIONAL_OR_KEYWORD, default=None, annotation=Literal[aa])
+                    parameters["fmt"] = Parameter(
+                        "fmt",
+                        Parameter.POSITIONAL_OR_KEYWORD,
+                        default=None,
+                        annotation=Literal[aa],
+                    )
                     sig_fmt = Signature(list(parameters.values()))
                     sig_fmt = str(sig_fmt)
-                    buff.append(""".. py:function:: %s.from%s""" % (method_classes[method], sig_fmt))
+                    buff.append(
+                        f""".. py:function:: {method_classes[method]}.from{sig_fmt}"""
+                    )
                     buff.append("""   :noindex:""")
                 for aa in alias:
-                    buff.append(""".. py:function:: %s.from_%s%s""" % (method_classes[method], aa.replace("/", "_").replace(".", ""), sig))
+                    buff.append(
+                        """.. py:function:: {}.from_{}{}""".format(
+                            method_classes[method],
+                            aa.replace("/", "_").replace(".", ""),
+                            sig,
+                        )
+                    )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                buff.append("""   Convert this format to :func:`%s`.""" % (method_classes[method]))
+                buff.append(
+                    """   Convert this format to :func:`%s`."""
+                    % (method_classes[method])
+                )
             elif method.startswith("to_"):
                 for aa in alias:
-                    parameters = {'fmt': Parameter('fmt', Parameter.POSITIONAL_OR_KEYWORD, annotation=Literal[aa]), **parameters}
+                    parameters = {
+                        "fmt": Parameter(
+                            "fmt",
+                            Parameter.POSITIONAL_OR_KEYWORD,
+                            annotation=Literal[aa],
+                        ),
+                        **parameters,
+                    }
                     sig_fmt = Signature(list(parameters.values()))
                     sig_fmt = str(sig_fmt)
-                    buff.append(""".. py:function:: %s.to%s""" % (method_classes[method], sig_fmt))
+                    buff.append(
+                        f""".. py:function:: {method_classes[method]}.to{sig_fmt}"""
+                    )
                     buff.append("""   :noindex:""")
                 for aa in alias:
-                    buff.append(""".. py:function:: %s.to_%s%s""" % (method_classes[method], aa.replace("/", "_").replace(".", ""), sig))
+                    buff.append(
+                        """.. py:function:: {}.to_{}{}""".format(
+                            method_classes[method],
+                            aa.replace("/", "_").replace(".", ""),
+                            sig,
+                        )
+                    )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                buff.append("""   Convert :func:`%s` to this format.""" % (method_classes[method]))
+                buff.append(
+                    """   Convert :func:`%s` to this format."""
+                    % (method_classes[method])
+                )
             buff.append("")
             buff.append("")
 
@@ -233,4 +268,4 @@ def generate_sub_format_pages(formats: dict):
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
                 }
             )
-    generate_sub_format_pages(formats)
\ No newline at end of file
+    generate_sub_format_pages(formats)

From 281de64caee0f1cd5e168c795ea474f1bc779273 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 19:26:40 -0400
Subject: [PATCH 03/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/index.rst      |  2 +-
 docs/make_format.py | 46 ++++++++++++++++++++++++++++++++++-----------
 2 files changed, 36 insertions(+), 12 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index c25592c17..57feda8b9 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -7,7 +7,7 @@ Welcome to dpdata's documentation!
 ==================================
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    :caption: Contents:
 
    Overview <self>
diff --git a/docs/make_format.py b/docs/make_format.py
index c656d32ce..d45e4471f 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -4,7 +4,7 @@
 from inspect import Parameter, Signature, signature
 from typing import Literal
 
-from sphinx.ext.napoleon.docstring import NumpyDocstring
+from numpydoc.docscrape_sphinx import SphinxDocString
 
 # ensure all plugins are loaded!
 from dpdata.driver import Driver, Minimizer
@@ -123,10 +123,12 @@ def generate_sub_format_pages(formats: dict):
             buff.append("%s format" % aa)
             buff.append("=" * len(buff[-1]))
             buff.append("")
+        buff.append("Class: %s" % get_cls_link(format))
+        buff.append("")
 
         docstring = format.__doc__
         if docstring is not None:
-            rst = str(NumpyDocstring(docstring))
+            rst = str(SphinxDocString(docstring))
             buff.append(rst)
             buff.append("")
 
@@ -134,8 +136,16 @@ def generate_sub_format_pages(formats: dict):
         buff.append("------------")
         methods = check_supported(format)
         for method in methods:
+            if method.startswith("from_"):
+                buff.append("Convert from this format to %s" % method_classes[method])
+                buff.append("`" * len(buff[-1]))
+            elif method.startswith("to_"):
+                buff.append("Convert from %s to this format" % method_classes[method])
+                buff.append("`" * len(buff[-1]))
             buff.append("")
-            sig = signature(getattr(format, method))
+            method_obj = getattr(format, method)
+            docstring = method_obj.__doc__
+            sig = signature(method_obj)
             parameters = dict(sig.parameters)
             # del self
             del parameters[list(parameters)[0]]
@@ -172,10 +182,17 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                buff.append(
-                    """   Convert this format to :func:`%s`."""
-                    % (method_classes[method])
-                )
+                if docstring is not None:
+                    doc_obj = SphinxDocString(docstring)
+                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("args", "kwargs")]
+                    rst = str(doc_obj)
+                    buff.append(rst)
+                    buff.append("")
+                else:
+                    buff.append(
+                        """   Convert this format to :func:`%s`."""
+                        % (method_classes[method])
+                    )
             elif method.startswith("to_"):
                 for aa in alias:
                     parameters = {
@@ -202,10 +219,17 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                buff.append(
-                    """   Convert :func:`%s` to this format."""
-                    % (method_classes[method])
-                )
+                if docstring is not None:
+                    doc_obj = SphinxDocString(docstring)
+                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("data", "args", "kwargs")]
+                    rst = str(doc_obj)
+                    buff.append(rst)
+                    buff.append("")
+                else:
+                    buff.append(
+                        """   Convert :func:`%s` to this format."""
+                        % (method_classes[method])
+                    )
             buff.append("")
             buff.append("")
 

From d2d1bdd9d4837303136df611145839c1d1b0594c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 28 Jul 2023 23:26:59 +0000
Subject: [PATCH 04/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index d45e4471f..6d4357e97 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -184,7 +184,11 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("")
                 if docstring is not None:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("args", "kwargs")]
+                    doc_obj["Parameters"] = [
+                        xx
+                        for xx in doc_obj["Parameters"]
+                        if xx.name not in ("args", "kwargs")
+                    ]
                     rst = str(doc_obj)
                     buff.append(rst)
                     buff.append("")
@@ -221,7 +225,11 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("")
                 if docstring is not None:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("data", "args", "kwargs")]
+                    doc_obj["Parameters"] = [
+                        xx
+                        for xx in doc_obj["Parameters"]
+                        if xx.name not in ("data", "args", "kwargs")
+                    ]
                     rst = str(doc_obj)
                     buff.append(rst)
                     buff.append("")

From 67941b9841aac10c0ff3fbb8fe086b1e05fa266b Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 19:47:49 -0400
Subject: [PATCH 05/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/formats.rst    |  1 -
 docs/make_format.py | 49 +++++++++++++++++++--------------------------
 2 files changed, 21 insertions(+), 29 deletions(-)

diff --git a/docs/formats.rst b/docs/formats.rst
index 2e5477f2a..41ca90916 100644
--- a/docs/formats.rst
+++ b/docs/formats.rst
@@ -11,6 +11,5 @@ dpdata supports the following formats:
 .. toctree::
    :maxdepth: 1
    :glob:
-   :hidden:
 
    formats/*
diff --git a/docs/make_format.py b/docs/make_format.py
index 6d4357e97..14120a988 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -158,20 +158,21 @@ def generate_sub_format_pages(formats: dict):
                 del parameters["kwargs"]
             sig = Signature(list(parameters.values()))
             sig = str(sig)
-            if method.startswith("from_") and method != "from_multi_systems":
-                for aa in alias:
-                    parameters["fmt"] = Parameter(
-                        "fmt",
-                        Parameter.POSITIONAL_OR_KEYWORD,
-                        default=None,
-                        annotation=Literal[aa],
-                    )
-                    sig_fmt = Signature(list(parameters.values()))
-                    sig_fmt = str(sig_fmt)
-                    buff.append(
-                        f""".. py:function:: {method_classes[method]}.from{sig_fmt}"""
-                    )
-                    buff.append("""   :noindex:""")
+            if method.startswith("from_"):
+                if method != "from_multi_systems":
+                    for aa in alias:
+                        parameters["fmt"] = Parameter(
+                            "fmt",
+                            Parameter.POSITIONAL_OR_KEYWORD,
+                            default=None,
+                            annotation=Literal[aa],
+                        )
+                        sig_fmt = Signature(list(parameters.values()))
+                        sig_fmt = str(sig_fmt)
+                        buff.append(
+                            f""".. py:function:: {method_classes[method]}.from{sig_fmt}"""
+                        )
+                        buff.append("""   :noindex:""")
                 for aa in alias:
                     buff.append(
                         """.. py:function:: {}.from_{}{}""".format(
@@ -182,14 +183,10 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if docstring is not None:
+                if docstring is not None and method in format.__dict__:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [
-                        xx
-                        for xx in doc_obj["Parameters"]
-                        if xx.name not in ("args", "kwargs")
-                    ]
-                    rst = str(doc_obj)
+                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("*args", "**kwargs")]
+                    rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")
                 else:
@@ -223,14 +220,10 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if docstring is not None:
+                if docstring is not None and method in format.__dict__:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [
-                        xx
-                        for xx in doc_obj["Parameters"]
-                        if xx.name not in ("data", "args", "kwargs")
-                    ]
-                    rst = str(doc_obj)
+                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("data", "*args", "**kwargs")]
+                    rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")
                 else:

From ea04b8bfe9fbcc5d3cb8b23bf169b4183923f2cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 28 Jul 2023 23:53:57 +0000
Subject: [PATCH 06/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 14120a988..afa923c77 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -185,7 +185,11 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("")
                 if docstring is not None and method in format.__dict__:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("*args", "**kwargs")]
+                    doc_obj["Parameters"] = [
+                        xx
+                        for xx in doc_obj["Parameters"]
+                        if xx.name not in ("*args", "**kwargs")
+                    ]
                     rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")
@@ -222,7 +226,11 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("")
                 if docstring is not None and method in format.__dict__:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [xx for xx in doc_obj["Parameters"] if xx.name not in ("data", "*args", "**kwargs")]
+                    doc_obj["Parameters"] = [
+                        xx
+                        for xx in doc_obj["Parameters"]
+                        if xx.name not in ("data", "*args", "**kwargs")
+                    ]
                     rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")

From b179fb7e0a83b0cc3071b5f0ef759a3bc83a4165 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 20:29:20 -0400
Subject: [PATCH 07/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/index.rst      |  2 +-
 docs/make_format.py | 49 +++++++++++++++++++++++++++++++--------------
 2 files changed, 35 insertions(+), 16 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index 57feda8b9..c25592c17 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -7,7 +7,7 @@ Welcome to dpdata's documentation!
 ==================================
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: Contents:
 
    Overview <self>
diff --git a/docs/make_format.py b/docs/make_format.py
index afa923c77..8befb9ac4 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -5,10 +5,13 @@
 from typing import Literal
 
 from numpydoc.docscrape_sphinx import SphinxDocString
+from numpydoc.docscrape import Parameter as numpydoc_Parameter
 
 # ensure all plugins are loaded!
 from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
+from dpdata.system import System, LabeledSystem, MultiSystems
+from dpdata.bond_order_system import BondOrderSystem
 
 
 def get_formats() -> dict:
@@ -69,7 +72,7 @@ def get_cls_link(cls: object) -> str:
 
 
 def check_supported(fmt: Format):
-    methods = set()
+    methods = []
     for mtd in [
         "from_system",
         "to_system",
@@ -81,12 +84,12 @@ def check_supported(fmt: Format):
         "to_multi_systems",
     ]:
         if detect_overridden(fmt, mtd):
-            methods.add(mtd)
+            methods.append(mtd)
             if mtd == "to_system":
-                methods.add("to_labeled_system")
+                methods.append("to_labeled_system")
     if fmt.MultiMode != fmt.MultiModes.NotImplemented:
-        methods.add("from_multi_systems")
-        methods.add("to_multi_systems")
+        methods.append("from_multi_systems")
+        methods.append("to_multi_systems")
     return methods
 
 
@@ -112,6 +115,17 @@ def check_supported(fmt: Format):
     "to_multi_systems": "MultiSystems",
 }
 
+method_obj = {
+    "from_system": System,
+    "to_system": System,
+    "from_labeled_system": LabeledSystem,
+    "to_labeled_system": LabeledSystem,
+    "from_bond_order_system": BondOrderSystem,
+    "to_bond_order_system": BondOrderSystem,
+    "from_multi_systems": MultiSystems,
+    "to_multi_systems": MultiSystems,
+}
+
 
 def generate_sub_format_pages(formats: dict):
     """Generate sub format pages."""
@@ -159,6 +173,8 @@ def generate_sub_format_pages(formats: dict):
             sig = Signature(list(parameters.values()))
             sig = str(sig)
             if method.startswith("from_"):
+                sig = Signature(list(parameters.values()), return_annotation=method_obj[method])
+                sig = str(sig_fmt)
                 if method != "from_multi_systems":
                     for aa in alias:
                         parameters["fmt"] = Parameter(
@@ -167,15 +183,15 @@ def generate_sub_format_pages(formats: dict):
                             default=None,
                             annotation=Literal[aa],
                         )
-                        sig_fmt = Signature(list(parameters.values()))
+                        sig_fmt = Signature(list(parameters.values()), return_annotation=method_obj[method])
                         sig_fmt = str(sig_fmt)
                         buff.append(
-                            f""".. py:function:: {method_classes[method]}.from{sig_fmt}"""
+                            f""".. py:function:: dpdata.{method_classes[method]}.from{sig_fmt}"""
                         )
                         buff.append("""   :noindex:""")
                 for aa in alias:
                     buff.append(
-                        """.. py:function:: {}.from_{}{}""".format(
+                        """.. py:function:: dpdata.{}.from_{}{}""".format(
                             method_classes[method],
                             aa.replace("/", "_").replace(".", ""),
                             sig,
@@ -190,6 +206,8 @@ def generate_sub_format_pages(formats: dict):
                         for xx in doc_obj["Parameters"]
                         if xx.name not in ("*args", "**kwargs")
                     ]
+                    doc_obj["Yields"] = []
+                    doc_obj["Returns"] = [numpydoc_Parameter("", method_classes[method], "converted system")]
                     rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")
@@ -211,12 +229,12 @@ def generate_sub_format_pages(formats: dict):
                     sig_fmt = Signature(list(parameters.values()))
                     sig_fmt = str(sig_fmt)
                     buff.append(
-                        f""".. py:function:: {method_classes[method]}.to{sig_fmt}"""
+                        f""".. py:function:: dpdata.{method_classes[method]}.to{sig_fmt}"""
                     )
                     buff.append("""   :noindex:""")
                 for aa in alias:
                     buff.append(
-                        """.. py:function:: {}.to_{}{}""".format(
+                        """.. py:function:: dpdata.{}.to_{}{}""".format(
                             method_classes[method],
                             aa.replace("/", "_").replace(".", ""),
                             sig,
@@ -226,11 +244,12 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("")
                 if docstring is not None and method in format.__dict__:
                     doc_obj = SphinxDocString(docstring)
-                    doc_obj["Parameters"] = [
-                        xx
-                        for xx in doc_obj["Parameters"]
-                        if xx.name not in ("data", "*args", "**kwargs")
-                    ]
+                    if len(doc_obj["Parameters"]) > 0:
+                        doc_obj["Parameters"] = [
+                            xx
+                            for xx in doc_obj["Parameters"][1:]
+                            if xx.name not in ("*args", "**kwargs")
+                        ]
                     rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")

From eb4ee2a17ab4969161d41e868e6f6936c88d255a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 00:32:06 +0000
Subject: [PATCH 08/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 8befb9ac4..74b6a7340 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -4,14 +4,15 @@
 from inspect import Parameter, Signature, signature
 from typing import Literal
 
-from numpydoc.docscrape_sphinx import SphinxDocString
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
+from numpydoc.docscrape_sphinx import SphinxDocString
+
+from dpdata.bond_order_system import BondOrderSystem
 
 # ensure all plugins are loaded!
 from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
-from dpdata.system import System, LabeledSystem, MultiSystems
-from dpdata.bond_order_system import BondOrderSystem
+from dpdata.system import LabeledSystem, MultiSystems, System
 
 
 def get_formats() -> dict:
@@ -173,7 +174,9 @@ def generate_sub_format_pages(formats: dict):
             sig = Signature(list(parameters.values()))
             sig = str(sig)
             if method.startswith("from_"):
-                sig = Signature(list(parameters.values()), return_annotation=method_obj[method])
+                sig = Signature(
+                    list(parameters.values()), return_annotation=method_obj[method]
+                )
                 sig = str(sig_fmt)
                 if method != "from_multi_systems":
                     for aa in alias:
@@ -183,7 +186,10 @@ def generate_sub_format_pages(formats: dict):
                             default=None,
                             annotation=Literal[aa],
                         )
-                        sig_fmt = Signature(list(parameters.values()), return_annotation=method_obj[method])
+                        sig_fmt = Signature(
+                            list(parameters.values()),
+                            return_annotation=method_obj[method],
+                        )
                         sig_fmt = str(sig_fmt)
                         buff.append(
                             f""".. py:function:: dpdata.{method_classes[method]}.from{sig_fmt}"""
@@ -207,7 +213,11 @@ def generate_sub_format_pages(formats: dict):
                         if xx.name not in ("*args", "**kwargs")
                     ]
                     doc_obj["Yields"] = []
-                    doc_obj["Returns"] = [numpydoc_Parameter("", method_classes[method], "converted system")]
+                    doc_obj["Returns"] = [
+                        numpydoc_Parameter(
+                            "", method_classes[method], "converted system"
+                        )
+                    ]
                     rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")

From e8d5ecc2faec13f3e4bccdeba9bfa910925395a4 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 20:52:25 -0400
Subject: [PATCH 09/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 33 +++++++++++++++++++++++----------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 74b6a7340..bdbf5d7c7 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -1,7 +1,7 @@
 import csv
 import os
 from collections import defaultdict
-from inspect import Parameter, Signature, signature
+from inspect import Parameter, Signature, signature, cleandoc
 from typing import Literal
 
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
@@ -116,7 +116,7 @@ def check_supported(fmt: Format):
     "to_multi_systems": "MultiSystems",
 }
 
-method_obj = {
+method_cls_obj = {
     "from_system": System,
     "to_system": System,
     "from_labeled_system": LabeledSystem,
@@ -143,6 +143,7 @@ def generate_sub_format_pages(formats: dict):
 
         docstring = format.__doc__
         if docstring is not None:
+            docstring = cleandoc(docstring)
             rst = str(SphinxDocString(docstring))
             buff.append(rst)
             buff.append("")
@@ -160,8 +161,11 @@ def generate_sub_format_pages(formats: dict):
             buff.append("")
             method_obj = getattr(format, method)
             docstring = method_obj.__doc__
+            if docstring is not None:
+                docstring = cleandoc(docstring)
             sig = signature(method_obj)
             parameters = dict(sig.parameters)
+            return_annotation = sig.return_annotation
             # del self
             del parameters[list(parameters)[0]]
             # del data
@@ -171,13 +175,12 @@ def generate_sub_format_pages(formats: dict):
                 del parameters["args"]
             if "kwargs" in parameters:
                 del parameters["kwargs"]
-            sig = Signature(list(parameters.values()))
+            if method == "to_multi_systems" or method.startswith("from_"):
+                sig = Signature(list(parameters.values()), return_annotation=method_cls_obj[method])
+            else:
+                sig = Signature(list(parameters.values()), return_annotation=return_annotation)
             sig = str(sig)
             if method.startswith("from_"):
-                sig = Signature(
-                    list(parameters.values()), return_annotation=method_obj[method]
-                )
-                sig = str(sig_fmt)
                 if method != "from_multi_systems":
                     for aa in alias:
                         parameters["fmt"] = Parameter(
@@ -188,7 +191,7 @@ def generate_sub_format_pages(formats: dict):
                         )
                         sig_fmt = Signature(
                             list(parameters.values()),
-                            return_annotation=method_obj[method],
+                            return_annotation=method_cls_obj[method],
                         )
                         sig_fmt = str(sig_fmt)
                         buff.append(
@@ -215,7 +218,7 @@ def generate_sub_format_pages(formats: dict):
                     doc_obj["Yields"] = []
                     doc_obj["Returns"] = [
                         numpydoc_Parameter(
-                            "", method_classes[method], "converted system"
+                            "", method_classes[method], ["converted system"]
                         )
                     ]
                     rst = "   " + str(doc_obj)
@@ -236,7 +239,10 @@ def generate_sub_format_pages(formats: dict):
                         ),
                         **parameters,
                     }
-                    sig_fmt = Signature(list(parameters.values()))
+                    if method == "to_multi_systems":
+                        sig_fmt = Signature(list(parameters.values()), return_annotation=method_cls_obj[method])
+                    else:
+                        sig_fmt = Signature(list(parameters.values()), return_annotation=return_annotation)
                     sig_fmt = str(sig_fmt)
                     buff.append(
                         f""".. py:function:: dpdata.{method_classes[method]}.to{sig_fmt}"""
@@ -260,6 +266,13 @@ def generate_sub_format_pages(formats: dict):
                             for xx in doc_obj["Parameters"][1:]
                             if xx.name not in ("*args", "**kwargs")
                         ]
+                    if method == "to_multi_systems":
+                        doc_obj["Yields"] = []
+                        doc_obj["Returns"] = [
+                            numpydoc_Parameter(
+                                "", method_classes[method], ["this system"]
+                            )
+                        ]
                     rst = "   " + str(doc_obj)
                     buff.append(rst)
                     buff.append("")

From eb7f30cb1cde7f62d730c4d0a30b39a47db2aaa5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 00:53:12 +0000
Subject: [PATCH 10/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index bdbf5d7c7..1c612a098 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -1,7 +1,7 @@
 import csv
 import os
 from collections import defaultdict
-from inspect import Parameter, Signature, signature, cleandoc
+from inspect import Parameter, Signature, cleandoc, signature
 from typing import Literal
 
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
@@ -176,9 +176,13 @@ def generate_sub_format_pages(formats: dict):
             if "kwargs" in parameters:
                 del parameters["kwargs"]
             if method == "to_multi_systems" or method.startswith("from_"):
-                sig = Signature(list(parameters.values()), return_annotation=method_cls_obj[method])
+                sig = Signature(
+                    list(parameters.values()), return_annotation=method_cls_obj[method]
+                )
             else:
-                sig = Signature(list(parameters.values()), return_annotation=return_annotation)
+                sig = Signature(
+                    list(parameters.values()), return_annotation=return_annotation
+                )
             sig = str(sig)
             if method.startswith("from_"):
                 if method != "from_multi_systems":
@@ -240,9 +244,15 @@ def generate_sub_format_pages(formats: dict):
                         **parameters,
                     }
                     if method == "to_multi_systems":
-                        sig_fmt = Signature(list(parameters.values()), return_annotation=method_cls_obj[method])
+                        sig_fmt = Signature(
+                            list(parameters.values()),
+                            return_annotation=method_cls_obj[method],
+                        )
                     else:
-                        sig_fmt = Signature(list(parameters.values()), return_annotation=return_annotation)
+                        sig_fmt = Signature(
+                            list(parameters.values()),
+                            return_annotation=return_annotation,
+                        )
                     sig_fmt = str(sig_fmt)
                     buff.append(
                         f""".. py:function:: dpdata.{method_classes[method]}.to{sig_fmt}"""

From 80e6485dec3e0e171c02f882a4ae85dc2a55c71b Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 20:55:57 -0400
Subject: [PATCH 11/26] install rdkit

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 5b555ad59..087d6ff9a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,6 +54,7 @@ docs = [
     'm2r2',
     'deepmodeling-sphinx>=0.1.1',
     'sphinx-argparse',
+    'rdkit',
 ]
 
 [tool.setuptools.packages.find]

From 95175d9ebf4e84a5c48376cd03ece1ca040a84a3 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:14:58 -0400
Subject: [PATCH 12/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 86 +++++++++++++++++++++++++++------------------
 1 file changed, 51 insertions(+), 35 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 1c612a098..23cad83c8 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -134,6 +134,8 @@ def generate_sub_format_pages(formats: dict):
     for format, alias in formats.items():
         # format: Format, alias: list[str]
         buff = []
+        buff.append(".. _%s:" % format.__name__)
+        buff.append("")
         for aa in alias:
             buff.append("%s format" % aa)
             buff.append("=" * len(buff[-1]))
@@ -152,6 +154,9 @@ def generate_sub_format_pages(formats: dict):
         buff.append("------------")
         methods = check_supported(format)
         for method in methods:
+            buff.append("")
+            buff.append(".. _%s_%s:" % (format.__name__, method))
+            buff.append("")
             if method.startswith("from_"):
                 buff.append("Convert from this format to %s" % method_classes[method])
                 buff.append("`" * len(buff[-1]))
@@ -212,27 +217,33 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if docstring is not None and method in format.__dict__:
-                    doc_obj = SphinxDocString(docstring)
+                if docstring is None or method not in format.__dict__:
+                    docstring = """   Convert this format to :func:`%s`.""" % (method_classes[method])
+                doc_obj = SphinxDocString(docstring)
+                if len(doc_obj["Parameters"]) > 0:
                     doc_obj["Parameters"] = [
                         xx
                         for xx in doc_obj["Parameters"]
                         if xx.name not in ("*args", "**kwargs")
                     ]
-                    doc_obj["Yields"] = []
-                    doc_obj["Returns"] = [
-                        numpydoc_Parameter(
-                            "", method_classes[method], ["converted system"]
-                        )
-                    ]
-                    rst = "   " + str(doc_obj)
-                    buff.append(rst)
-                    buff.append("")
                 else:
-                    buff.append(
-                        """   Convert this format to :func:`%s`."""
-                        % (method_classes[method])
+                    if method == "from_multi_systems":
+                        doc_obj["Parameters"] = [
+                            numpydoc_Parameter(
+                                "directory",
+                                "str",
+                                ["directory of systems"],
+                            )
+                        ]
+                doc_obj["Yields"] = []
+                doc_obj["Returns"] = [
+                    numpydoc_Parameter(
+                        "", method_classes[method], ["converted system"]
                     )
+                ]
+                rst = "   " + str(doc_obj)
+                buff.append(rst)
+                buff.append("")
             elif method.startswith("to_"):
                 for aa in alias:
                     parameters = {
@@ -268,29 +279,34 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if docstring is not None and method in format.__dict__:
-                    doc_obj = SphinxDocString(docstring)
-                    if len(doc_obj["Parameters"]) > 0:
-                        doc_obj["Parameters"] = [
-                            xx
-                            for xx in doc_obj["Parameters"][1:]
-                            if xx.name not in ("*args", "**kwargs")
-                        ]
+                if docstring is None or method not in format.__dict__:
+                    docstring = "Convert :func:`%s` to this format." % (method_classes[method])
+                doc_obj = SphinxDocString(docstring)
+                if len(doc_obj["Parameters"]) > 0:
+                    doc_obj["Parameters"] = [
+                        xx
+                        for xx in doc_obj["Parameters"][1:]
+                        if xx.name not in ("*args", "**kwargs")
+                    ]
+                else:
                     if method == "to_multi_systems":
-                        doc_obj["Yields"] = []
-                        doc_obj["Returns"] = [
+                        doc_obj["Parameters"] = [
                             numpydoc_Parameter(
-                                "", method_classes[method], ["this system"]
+                                "directory",
+                                "str",
+                                ["directory to save systems"],
                             )
                         ]
-                    rst = "   " + str(doc_obj)
-                    buff.append(rst)
-                    buff.append("")
-                else:
-                    buff.append(
-                        """   Convert :func:`%s` to this format."""
-                        % (method_classes[method])
-                    )
+                if method == "to_multi_systems":
+                    doc_obj["Yields"] = []
+                    doc_obj["Returns"] = [
+                        numpydoc_Parameter(
+                            "", method_classes[method], ["this system"]
+                        )
+                    ]
+                rst = "   " + str(doc_obj)
+                buff.append(rst)
+                buff.append("")
             buff.append("")
             buff.append("")
 
@@ -312,10 +328,10 @@ def generate_sub_format_pages(formats: dict):
         for kk, vv in formats.items():
             writer.writerow(
                 {
-                    "Class": get_cls_link(kk),
+                    "Class": ":ref:`%s`" % kk.__name__,
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
                     "Supported Functions": "\n".join(
-                        method_links[mtd] for mtd in check_supported(kk)
+                        ":ref:`%s_%s`" % (kk.__name__, mtd) for mtd in check_supported(kk)
                     ),
                 }
             )

From 7fe8237289aae8d25a1543a6b4dd24ecb4a550c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 01:15:13 +0000
Subject: [PATCH 13/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 23cad83c8..828426df2 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -155,7 +155,7 @@ def generate_sub_format_pages(formats: dict):
         methods = check_supported(format)
         for method in methods:
             buff.append("")
-            buff.append(".. _%s_%s:" % (format.__name__, method))
+            buff.append(f".. _{format.__name__}_{method}:")
             buff.append("")
             if method.startswith("from_"):
                 buff.append("Convert from this format to %s" % method_classes[method])
@@ -218,7 +218,9 @@ def generate_sub_format_pages(formats: dict):
                     buff.append("""   :noindex:""")
                 buff.append("")
                 if docstring is None or method not in format.__dict__:
-                    docstring = """   Convert this format to :func:`%s`.""" % (method_classes[method])
+                    docstring = """   Convert this format to :func:`%s`.""" % (
+                        method_classes[method]
+                    )
                 doc_obj = SphinxDocString(docstring)
                 if len(doc_obj["Parameters"]) > 0:
                     doc_obj["Parameters"] = [
@@ -237,9 +239,7 @@ def generate_sub_format_pages(formats: dict):
                         ]
                 doc_obj["Yields"] = []
                 doc_obj["Returns"] = [
-                    numpydoc_Parameter(
-                        "", method_classes[method], ["converted system"]
-                    )
+                    numpydoc_Parameter("", method_classes[method], ["converted system"])
                 ]
                 rst = "   " + str(doc_obj)
                 buff.append(rst)
@@ -280,7 +280,9 @@ def generate_sub_format_pages(formats: dict):
                     buff.append("""   :noindex:""")
                 buff.append("")
                 if docstring is None or method not in format.__dict__:
-                    docstring = "Convert :func:`%s` to this format." % (method_classes[method])
+                    docstring = "Convert :func:`%s` to this format." % (
+                        method_classes[method]
+                    )
                 doc_obj = SphinxDocString(docstring)
                 if len(doc_obj["Parameters"]) > 0:
                     doc_obj["Parameters"] = [
@@ -300,9 +302,7 @@ def generate_sub_format_pages(formats: dict):
                 if method == "to_multi_systems":
                     doc_obj["Yields"] = []
                     doc_obj["Returns"] = [
-                        numpydoc_Parameter(
-                            "", method_classes[method], ["this system"]
-                        )
+                        numpydoc_Parameter("", method_classes[method], ["this system"])
                     ]
                 rst = "   " + str(doc_obj)
                 buff.append(rst)
@@ -331,7 +331,8 @@ def generate_sub_format_pages(formats: dict):
                     "Class": ":ref:`%s`" % kk.__name__,
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
                     "Supported Functions": "\n".join(
-                        ":ref:`%s_%s`" % (kk.__name__, mtd) for mtd in check_supported(kk)
+                        f":ref:`{kk.__name__}_{mtd}`"
+                        for mtd in check_supported(kk)
                     ),
                 }
             )

From e54e8c25172d154f8c966a7b4ac494931a7dcf8a Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:20:32 -0400
Subject: [PATCH 14/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 828426df2..b74e20311 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -218,7 +218,7 @@ def generate_sub_format_pages(formats: dict):
                     buff.append("""   :noindex:""")
                 buff.append("")
                 if docstring is None or method not in format.__dict__:
-                    docstring = """   Convert this format to :func:`%s`.""" % (
+                    docstring = """   Convert this format to :class:`%s`.""" % (
                         method_classes[method]
                     )
                 doc_obj = SphinxDocString(docstring)
@@ -280,7 +280,7 @@ def generate_sub_format_pages(formats: dict):
                     buff.append("""   :noindex:""")
                 buff.append("")
                 if docstring is None or method not in format.__dict__:
-                    docstring = "Convert :func:`%s` to this format." % (
+                    docstring = "Convert :class:`%s` to this format." % (
                         method_classes[method]
                     )
                 doc_obj = SphinxDocString(docstring)

From d824add832dc1b3c69a88e0ea423febc35836370 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 01:20:47 +0000
Subject: [PATCH 15/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index b74e20311..0162bd91a 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -331,8 +331,7 @@ def generate_sub_format_pages(formats: dict):
                     "Class": ":ref:`%s`" % kk.__name__,
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
                     "Supported Functions": "\n".join(
-                        f":ref:`{kk.__name__}_{mtd}`"
-                        for mtd in check_supported(kk)
+                        f":ref:`{kk.__name__}_{mtd}`" for mtd in check_supported(kk)
                     ),
                 }
             )

From 36feeee89f37cbd9015312792a593ad2b7df2e0d Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:25:20 -0400
Subject: [PATCH 16/26] fix from

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 0162bd91a..039f850bb 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -204,7 +204,7 @@ def generate_sub_format_pages(formats: dict):
                         )
                         sig_fmt = str(sig_fmt)
                         buff.append(
-                            f""".. py:function:: dpdata.{method_classes[method]}.from{sig_fmt}"""
+                            f""".. py:function:: dpdata.{method_classes[method]}{sig_fmt}"""
                         )
                         buff.append("""   :noindex:""")
                 for aa in alias:

From 4aa0f357da153394275c53af841bc756976ecf2a Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:33:10 -0400
Subject: [PATCH 17/26] to_label_system falls back to to_system

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/make_format.py b/docs/make_format.py
index 039f850bb..ba42cabdb 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -165,6 +165,8 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("`" * len(buff[-1]))
             buff.append("")
             method_obj = getattr(format, method)
+            if method == "to_label_system" and method not in format.__dict__ and "to_system" in format.__dict__:
+                method_obj = getattr(format, "to_system")
             docstring = method_obj.__doc__
             if docstring is not None:
                 docstring = cleandoc(docstring)

From 000ebb74aa5df72f7219fb03c858d35d01952dc3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 01:33:24 +0000
Subject: [PATCH 18/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index ba42cabdb..7a449d2ff 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -165,7 +165,11 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("`" * len(buff[-1]))
             buff.append("")
             method_obj = getattr(format, method)
-            if method == "to_label_system" and method not in format.__dict__ and "to_system" in format.__dict__:
+            if (
+                method == "to_label_system"
+                and method not in format.__dict__
+                and "to_system" in format.__dict__
+            ):
                 method_obj = getattr(format, "to_system")
             docstring = method_obj.__doc__
             if docstring is not None:

From 985141327e6f704f748ec915fc487f0e5ec6fc30 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:40:04 -0400
Subject: [PATCH 19/26] fix typo

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 7a449d2ff..b67b89db4 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -165,11 +165,7 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("`" * len(buff[-1]))
             buff.append("")
             method_obj = getattr(format, method)
-            if (
-                method == "to_label_system"
-                and method not in format.__dict__
-                and "to_system" in format.__dict__
-            ):
+            if method == "to_labeled_system" and method not in format.__dict__ and "to_system" in format.__dict__:
                 method_obj = getattr(format, "to_system")
             docstring = method_obj.__doc__
             if docstring is not None:

From 880cfdd8f935d006f8b56bbdcb5ba0b31c570000 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 01:40:42 +0000
Subject: [PATCH 20/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index b67b89db4..4261b4d7c 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -165,7 +165,11 @@ def generate_sub_format_pages(formats: dict):
                 buff.append("`" * len(buff[-1]))
             buff.append("")
             method_obj = getattr(format, method)
-            if method == "to_labeled_system" and method not in format.__dict__ and "to_system" in format.__dict__:
+            if (
+                method == "to_labeled_system"
+                and method not in format.__dict__
+                and "to_system" in format.__dict__
+            ):
                 method_obj = getattr(format, "to_system")
             docstring = method_obj.__doc__
             if docstring is not None:

From 7392eb2252bd8ae00a25a89e54a6114b4a8ef505 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:50:08 -0400
Subject: [PATCH 21/26] skip

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 4261b4d7c..7e9778112 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -285,7 +285,9 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if docstring is None or method not in format.__dict__:
+                if method == "to_labeled_system" and method not in format.__dict__ and "to_system" in format.__dict__:
+                    pass
+                elif docstring is None or method not in format.__dict__:
                     docstring = "Convert :class:`%s` to this format." % (
                         method_classes[method]
                     )

From 393ee76f3564c0f95e4512b00aee5ad2f3da8fe2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 01:50:25 +0000
Subject: [PATCH 22/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 7e9778112..e9441b56d 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -285,7 +285,11 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if method == "to_labeled_system" and method not in format.__dict__ and "to_system" in format.__dict__:
+                if (
+                    method == "to_labeled_system"
+                    and method not in format.__dict__
+                    and "to_system" in format.__dict__
+                ):
                     pass
                 elif docstring is None or method not in format.__dict__:
                     docstring = "Convert :class:`%s` to this format." % (

From cb84ee466bd775b7550a9973a49a7c4f9b6f8956 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 21:54:58 -0400
Subject: [PATCH 23/26] fix

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index e9441b56d..262cfd2e0 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -285,13 +285,9 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if (
-                    method == "to_labeled_system"
+                if docstring is None or (method not in format.__dict__ and not (method == "to_labeled_system"
                     and method not in format.__dict__
-                    and "to_system" in format.__dict__
-                ):
-                    pass
-                elif docstring is None or method not in format.__dict__:
+                    and "to_system" in format.__dict__)):
                     docstring = "Convert :class:`%s` to this format." % (
                         method_classes[method]
                     )

From ea4817ca5dff94b8d58e977db7cb882efa04d66f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 01:55:31 +0000
Subject: [PATCH 24/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 262cfd2e0..beec3091d 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -285,9 +285,14 @@ def generate_sub_format_pages(formats: dict):
                     )
                     buff.append("""   :noindex:""")
                 buff.append("")
-                if docstring is None or (method not in format.__dict__ and not (method == "to_labeled_system"
-                    and method not in format.__dict__
-                    and "to_system" in format.__dict__)):
+                if docstring is None or (
+                    method not in format.__dict__
+                    and not (
+                        method == "to_labeled_system"
+                        and method not in format.__dict__
+                        and "to_system" in format.__dict__
+                    )
+                ):
                     docstring = "Convert :class:`%s` to this format." % (
                         method_classes[method]
                     )

From 4e1c9ced92bb4b92904f47a32d487e2bbabb0eda Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 28 Jul 2023 22:07:56 -0400
Subject: [PATCH 25/26] kk

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 docs/make_format.py | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index beec3091d..1420d77b7 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -73,7 +73,7 @@ def get_cls_link(cls: object) -> str:
 
 
 def check_supported(fmt: Format):
-    methods = []
+    methods = {}
     for mtd in [
         "from_system",
         "to_system",
@@ -85,24 +85,24 @@ def check_supported(fmt: Format):
         "to_multi_systems",
     ]:
         if detect_overridden(fmt, mtd):
-            methods.append(mtd)
+            methods[mtd] = None
             if mtd == "to_system":
-                methods.append("to_labeled_system")
+                methods["to_labeled_system"] = None
     if fmt.MultiMode != fmt.MultiModes.NotImplemented:
-        methods.append("from_multi_systems")
-        methods.append("to_multi_systems")
-    return methods
+        methods["from_multi_systems"] = None
+        methods["to_multi_systems"] = None
+    return list(methods.keys())
 
 
 method_links = {
-    "from_system": ":func:`System() <dpdata.system.System>`",
-    "to_system": ":func:`System.to() <dpdata.system.System.to>`",
-    "from_labeled_system": ":func:`LabeledSystem() <dpdata.system.LabeledSystem>`",
-    "to_labeled_system": ":func:`LabeledSystem.to() <dpdata.system.System.to>`",
-    "from_bond_order_system": ":func:`BondOrderSystem() <dpdata.bond_order_system.BondOrderSystem>`",
-    "to_bond_order_system": ":func:`BondOrderSystem.to() <dpdata.system.System.to>`",
-    "from_multi_systems": ":func:`MultiSystems.load_systems_from_file() <dpdata.system.MultiSystems.load_systems_from_file>`",
-    "to_multi_systems": ":func:`MultiSystems.to() <dpdata.system.MultiSystems.to>`",
+    "from_system": ":ref:`System() <{}_{}>`",
+    "to_system": ":ref:`System.to() <{}_{}>`",
+    "from_labeled_system": ":ref:`LabeledSystem() <{}_{}>`",
+    "to_labeled_system": ":ref:`LabeledSystem.to() <{}_{}>`",
+    "from_bond_order_system": ":ref:`BondOrderSystem() <{}_{}>`",
+    "to_bond_order_system": ":ref:`BondOrderSystem.to() <{}_{}>`",
+    "from_multi_systems": ":ref:`MultiSystems.load_systems_from_file() <{}_{}>`",
+    "to_multi_systems": ":ref:`MultiSystems.to() <{}_{}>`",
 }
 
 method_classes = {
@@ -150,8 +150,8 @@ def generate_sub_format_pages(formats: dict):
             buff.append(rst)
             buff.append("")
 
-        buff.append("Conversation")
-        buff.append("------------")
+        buff.append("Conversions")
+        buff.append("-----------")
         methods = check_supported(format)
         for method in methods:
             buff.append("")
@@ -331,9 +331,9 @@ def generate_sub_format_pages(formats: dict):
     formats = get_formats()
     with open("formats.csv", "w", newline="") as csvfile:
         fieldnames = [
-            "Class",
+            "Format",
             "Alias",
-            "Supported Functions",
+            "Supported Conversions",
         ]
         writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
 
@@ -341,10 +341,10 @@ def generate_sub_format_pages(formats: dict):
         for kk, vv in formats.items():
             writer.writerow(
                 {
-                    "Class": ":ref:`%s`" % kk.__name__,
+                    "Format": ":ref:`%s`" % kk.__name__,
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
-                    "Supported Functions": "\n".join(
-                        f":ref:`{kk.__name__}_{mtd}`" for mtd in check_supported(kk)
+                    "Supported Conversions": "\n".join(
+                        method_links[mtd].format(kk.__name__, mtd) for mtd in check_supported(kk)
                     ),
                 }
             )

From 3e667e81b4206730f8ec1743217e726c8b66baff Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jul 2023 02:08:17 +0000
Subject: [PATCH 26/26] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/make_format.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/make_format.py b/docs/make_format.py
index 1420d77b7..62dd08793 100644
--- a/docs/make_format.py
+++ b/docs/make_format.py
@@ -344,7 +344,8 @@ def generate_sub_format_pages(formats: dict):
                     "Format": ":ref:`%s`" % kk.__name__,
                     "Alias": "\n".join("``%s``" % vvv for vvv in vv),
                     "Supported Conversions": "\n".join(
-                        method_links[mtd].format(kk.__name__, mtd) for mtd in check_supported(kk)
+                        method_links[mtd].format(kk.__name__, mtd)
+                        for mtd in check_supported(kk)
                     ),
                 }
             )