Use pyproject.toml instead of setup.py/setup.cfg

.circleci/install_triggers

@@ -1,5 +1,3 @@
 ^\.circleci/
 ^environment\.yml$
 ^pyproject.toml$
-^setup\.py$
-^setup\.cfg$

doc/contributing.rst

@@ -443,7 +443,7 @@ previous command. To only run tests from a single file, run the command
    pytest tests/unit/test_some_file.py
 
 If you would like to avoid loading the default pytest configuration from
-`setup.cfg <https://github.com/ESMValGroup/ESMValCore/blob/main/setup.cfg>`_
+`pyproject.toml <https://github.com/ESMValGroup/ESMValCore/blob/main/pyproject.toml>`_
 because this can be a bit slow for running just a few tests, use
 
 .. code-block:: bash
@@ -660,7 +660,7 @@ the following files:
 - ``environment.yml``
   contains all the development dependencies; these are all from
   `conda-forge <https://conda-forge.org/>`_
-- ``setup.py``
+- ``pyproject.toml``
   contains all Python dependencies, regardless of their installation source
 
 Note that packages may have a different name on

environment.yml

@@ -12,7 +12,7 @@ dependencies:
   - dask-jobqueue
   - distributed
   - esgf-pyclient >=0.3.1
-  - esmpy !=8.1.0
+  - esmpy
   - filelock
   - fiona
   - fire

esmvalcore/_main.py

@@ -33,14 +33,10 @@
 import logging
 import os
 import sys
+from importlib.metadata import entry_points
 from pathlib import Path
 from typing import Optional
 
-if (sys.version_info.major, sys.version_info.minor) < (3, 10):
-    from importlib_metadata import entry_points
-else:
-    from importlib.metadata import entry_points  # type: ignore
-
 import fire
 
 # set up logging
@@ -583,6 +579,7 @@ def _get_config_info(cli_config_dir):
                 zip(
                     config_dirs,
                     _get_all_config_sources(cli_config_dir),
+                    strict=False,
                 )
             )
 

esmvalcore/_recipe/check.py

@@ -171,7 +171,7 @@ def _group_years(years):
     ends.append(year)
 
     ranges = []
-    for start, end in zip(starts, ends):
+    for start, end in zip(starts, ends, strict=False):
         ranges.append(f"{start}" if start == end else f"{start}-{end}")
 
     return ", ".join(ranges)

esmvalcore/_recipe/from_datasets.py

@@ -219,7 +219,7 @@ def _group_ensemble_names(ensemble_names: Iterable[str]) -> list[str]:
     groups = []
     for ensemble_range in ensemble_ranges:
         txt = ""
-        for name, value in zip("ripf", ensemble_range):
+        for name, value in zip("ripf", ensemble_range, strict=False):
             txt += name
             if value[0] == value[1]:
                 txt += f"{value[0]}"

esmvalcore/_task.py

@@ -109,9 +109,12 @@ def _get_resource_usage(process, start_time, children=True):
             continue
 
         # Create and yield log entry
-        entries = [sum(entry) for entry in zip(*cache.values())]
+        entries = [sum(entry) for entry in zip(*cache.values(), strict=False)]
         entries.insert(0, time.time() - start_time)
-        entries = [round(entry, p) for entry, p in zip(entries, precision)]
+        entries = [
+            round(entry, p)
+            for entry, p in zip(entries, precision, strict=False)
+        ]
         entries.insert(0, datetime.datetime.utcnow())
         max_memory = max(max_memory, entries[4])
         yield (fmt.format(*entries), max_memory)
@@ -609,9 +612,10 @@ def _run(self, input_files):
 
         returncode = None
 
-        with resource_usage_logger(process.pid, self.resource_log), open(
-            self.log, "ab"
-        ) as log:
+        with (
+            resource_usage_logger(process.pid, self.resource_log),
+            open(self.log, "ab") as log,
+        ):
             last_line = [""]
             while returncode is None:
                 returncode = process.poll()

esmvalcore/preprocessor/_multimodel.py

@@ -82,13 +82,13 @@ def _unify_time_coordinates(cubes):
             # monthly data
             dates = [
                 datetime(year, month, 15, 0, 0, 0)
-                for year, month in zip(years, months)
+                for year, month in zip(years, months, strict=False)
             ]
         elif 0 not in np.diff(days):
             # daily data
             dates = [
                 datetime(year, month, day, 0, 0, 0)
-                for year, month, day in zip(years, months, days)
+                for year, month, day in zip(years, months, days, strict=False)
             ]
             if coord.units != t_unit:
                 logger.warning(

esmvalcore/preprocessor/_time.py

@@ -672,7 +672,10 @@ def spans_full_season(cube: Cube) -> list[bool]:
         seasons = cube.coord("clim_season").points
         tar_days = [(len(sea) * 29, len(sea) * 31) for sea in seasons]
 
-        return [dt[0] <= dn <= dt[1] for dn, dt in zip(num_days, tar_days)]
+        return [
+            dt[0] <= dn <= dt[1]
+            for dn, dt in zip(num_days, tar_days, strict=False)
+        ]
 
     full_seasons = spans_full_season(result)
     result = result[full_seasons]

esmvalcore/preprocessor/_volume.py

@@ -510,7 +510,10 @@ def extract_transect(
         )
 
     for dim_name, dim_cut, coord in zip(
-        ["latitude", "longitude"], [latitude, longitude], [lats, lons]
+        ["latitude", "longitude"],
+        [latitude, longitude],
+        [lats, lons],
+        strict=False,
     ):
         # ####
         # Look for the first coordinate.

pyproject.toml

@@ -1,34 +1,174 @@
 [build-system]
-requires = ["setuptools >= 40.6.0", "wheel", "setuptools_scm>=6.2"]
+requires = [
+    "setuptools >= 40.6.0",
+    "setuptools_scm>=6.2",
+]
 build-backend = "setuptools.build_meta"
 
+[project]
+authors = [
+    {name = "ESMValTool Development Team", email = "esmvaltool-dev@listserv.dfn.de"}
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+    "Topic :: Scientific/Engineering :: GIS",
+    "Topic :: Scientific/Engineering :: Hydrology",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dynamic = [
+    "readme",
+    "version",
+]
+dependencies = [
+    "cartopy",
+    "cf-units",
+    "dask[array,distributed]!=2024.8.0",  # ESMValCore/issues/2503
+    "dask-jobqueue",
+    "esgf-pyclient>=0.3.1",
+    "esmf-regrid>=0.11.0",
+    "esmpy",  # not on PyPI
+    "filelock",
+    "fiona",
+    "fire",
+    "geopy",
+    "humanfriendly",
+    "iris-grib>=0.20.0",  # github.com/ESMValGroup/ESMValCore/issues/2535
+    "isodate>=0.7.0",
+    "jinja2",
+    "nc-time-axis",  # needed by iris.plot
+    "nested-lookup",
+    "netCDF4",
+    "numpy!=1.24.3,<2.0.0",  # avoid pulling 2.0.0rc1
+    "packaging",
+    "pandas",
+    "pillow",
+    "prov",
+    "psutil",
+    "py-cordex",
+    "pybtex",
+    "pyyaml",
+    "requests",
+    "scipy>=1.6",
+    "scitools-iris>=3.10.0",
+    "shapely>=2.0.0",
+    "stratify>=0.3",
+    "yamale",
+]
+description = "A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts"
+license = {text = "Apache License, Version 2.0"}
+name = "ESMValCore"
+requires-python = ">=3.10"
+
+[project.optional-dependencies]
+test = [
+    "pytest>6.0.0",
+    "pytest-cov>=2.10.1",
+    "pytest-env",
+    "pytest-html!=2.1.0",
+    "pytest-metadata>=1.5.1",
+    "pytest-mock",
+    "pytest-xdist",
+    "ESMValTool_sample_data==0.0.3",
+]
+doc = [
+    "autodocsumm>=0.2.2",
+    "ipython",
+    "nbsphinx",
+    "sphinx>=6.1.3",
+    "pydata_sphinx_theme",
+]
+develop = [
+    "esmvalcore[test,doc]",
+    "pre-commit",
+    "pylint",
+    "pydocstyle",
+    "vprof",
+]
+
+[project.scripts]
+esmvaltool = "esmvalcore._main:run"
+
+[project.urls]
+Code = "https://github.com/ESMValGroup/ESMValCore"
+Community = "https://github.com/ESMValGroup/Community"
+Documentation = "https://docs.esmvaltool.org"
+Homepage = "https://esmvaltool.org"
+Issues = "https://github.com/ESMValGroup/ESMValCore/issues"
+
+[tool.setuptools]
+include-package-data = true
+license-files = ["LICENSE"]
+packages = ["esmvalcore"]
+zip-safe = false
+
+[tool.setuptools.dynamic]
+readme = {file = "README.md", content-type = "text/markdown"}
+
 [tool.setuptools_scm]
 version_scheme = "release-branch-semver"
 
-[tool.codespell]
-skip = "*.ipynb,esmvalcore/config/extra_facets/ipslcm-mappings.yml"
-ignore-words-list = "vas,hist,oce"
+# Configure tests
 
-[tool.pylint.main]
-jobs = 1  # Running more than one job in parallel crashes prospector.
-ignore-paths = [
-    "doc/conf.py",  # Sphinx configuration file
+[tool.pytest.ini_options]
+addopts = [
+    "-ra",
+    "--strict-config",
+    "--strict-markers",
+    "--doctest-modules",
+    "--ignore=esmvalcore/cmor/tables/",
+    "--cov-report=xml:test-reports/coverage.xml",
+    "--cov-report=html:test-reports/coverage_html",
+    "--html=test-reports/report.html",
 ]
-[tool.pylint.basic]
-good-names = [
-    "_",            # Used by convention for unused variables
-    "i", "j", "k",  # Used by convention for indices
-    "logger",       # Our preferred name for the logger
+log_cli_level = "INFO"
+env = {MPLBACKEND = "Agg"}
+log_level = "WARNING"
+minversion = "6"
+markers = [
+    "installation: Test requires installation of dependencies",
+    "use_sample_data: Run functional tests using real data",
 ]
-[tool.pylint.format]
-max-line-length = 79
-[tool.pylint."messages control"]
-disable = [
-    "import-error",      # Needed because Codacy does not install dependencies
-    "file-ignored",      # Disable messages about disabling checks
-    "line-too-long",     # Disable line-too-long as this is taken care of by the formatter.
-    "locally-disabled",  # Disable messages about disabling checks
+testpaths = ["tests"]
+xfail_strict = true
+
+[tool.coverage.run]
+parallel = true
+source = ["esmvalcore"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
 ]
+
+# Configure type checks
+
+[tool.mypy]
+# See https://mypy.readthedocs.io/en/stable/config_file.html
+ignore_missing_imports = true
+enable_error_code = [
+    "truthy-bool",
+]
+
+# Configure linters
+
+[tool.codespell]
+skip = "*.ipynb,esmvalcore/config/extra_facets/ipslcm-mappings.yml"
+ignore-words-list = "vas,hist,oce"
+
 [tool.ruff]
 line-length = 79
 [tool.ruff.lint]
@@ -59,3 +199,31 @@ ignore = [
 known-first-party = ["esmvalcore"]
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
+
+# Configure linters that are run by Prospector
+# TODO: remove once we have enabled all ruff rules for the tools provided by
+# Prospector, see https://github.com/ESMValGroup/ESMValCore/issues/2528.
+
+[tool.pylint.main]
+jobs = 1  # Running more than one job in parallel crashes prospector.
+ignore-paths = [
+    "doc/conf.py",  # Sphinx configuration file
+]
+[tool.pylint.basic]
+good-names = [
+    "_",            # Used by convention for unused variables
+    "i", "j", "k",  # Used by convention for indices
+    "logger",       # Our preferred name for the logger
+]
+[tool.pylint.format]
+max-line-length = 79
+[tool.pylint."messages control"]
+disable = [
+    "import-error",      # Needed because Codacy does not install dependencies
+    "file-ignored",      # Disable messages about disabling checks
+    "line-too-long",     # Disable line-too-long as this is taken care of by the formatter.
+    "locally-disabled",  # Disable messages about disabling checks
+]
+
+[tool.pydocstyle]
+convention = "numpy"