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Migrate to pyproject.toml for everything except for extensions.
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@shyuep
shyuep committed Jun 14, 2024
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299 changes: 227 additions & 72 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,167 @@
[build-system]
requires = [
"Cython>=0.29.23",
# pin NumPy version used in the build
"oldest-supported-numpy",
"setuptools>=65.0.0",
"Cython>=0.29.23",
# pin NumPy version used in the build
"oldest-supported-numpy",
"setuptools>=65.0.0",
]
build-backend = "setuptools.build_meta"


[project]
name = "pymatgen"
authors = [
{ name = "Pymatgen Development Team", email = "[email protected]" },
]
description = """
Python Materials Genomics is a robust materials analysis code that defines core object representations for structures
and molecules with support for many electronic structure codes. It is currently the core analysis code powering the
Materials Project (https://materialsproject.org)."""
readme = "README.md"
requires-python = ">=3.9"
keywords = [
"ABINIT",
"analysis",
"crystal",
"diagrams",
"electronic",
"gaussian",
"materials",
"nwchem",
"phase",
"project",
"qchem",
"science",
"structure",
"VASP",
]
license = { text = "MIT" }
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Chemistry",
"Topic :: Scientific/Engineering :: Information Analysis",
"Topic :: Scientific/Engineering :: Physics",
"Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
"matplotlib>=3.8",
"monty>=2024.5.24",
"networkx>=2.2",
"numpy>=1.25.0",
"palettable>=3.1.1",
"pandas>=2",
"plotly>=4.5.0",
"pybtex>=0.24.0",
"requests>=2.32",
"ruamel.yaml>=0.17.0",
"scipy>=1.13.0",
"spglib>=2.0.2",
"sympy>=1.2",
"tabulate>=0.9",
"tqdm>=4.60",
"uncertainties>=3.1.4",
"joblib>=1",
]
version = "2024.6.10"

[project.urls]
Homepage = "https://pymatgen.org"
Documentation = "https://pymatgen.org"
Repository = "https://github.com/materialsproject/pymatgen"
Issues = "https://github.com/materialsproject/pymatgen/issues"
Pypi = "https://pypi.org/project/pymatgen"

[project.optional-dependencies]
ase = ["ase>=3.23.0"]
# don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"]
vis = ["vtk>=6.0.0"]
abinit = ["netcdf4>=1.6.5"]
mlp = ["matgl>=1.1.1", "chgnet>=0.3.8"]
electronic_structure = ["fdint>=2.0.2"]
dev = [
"mypy>=1.10.0",
"pre-commit>=3",
"pytest-cov>=4",
"pytest-split>=0.8",
"pytest>8",
"ruff>=0.4",
]
ci = [
"pytest>=8",
"pytest-cov>=4",
"pytest-split>=0.8",
]
docs = [
"sphinx",
"sphinx_rtd_theme",
"doc2dash",
]
optional = [
"ase>=3.23.0",
# TODO restore BoltzTraP2 when install fixed, hopefully following merge of
# https://gitlab.com/sousaw/BoltzTraP2/-/merge_requests/18
# caused CI failure due to ModuleNotFoundError: No module named 'packaging'
# "BoltzTraP2>=22.3.2; platform_system!='Windows'",
"chemview>=0.6",
"chgnet>=0.3.8",
"f90nml>=1.1.2",
"galore>=0.6.1",
"h5py>=3.11.0",
"jarvis-tools>=2020.7.14",
"matgl>=1.1.1",
"netCDF4>=1.6.5",
"phonopy>=2.23",
"seekpath>=2.0.1",
# don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
"tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
# "hiphive>=0.6",
# "openbabel>=3.1.1; platform_system=='Linux'",
]
numba = ["numba>=0.55"]

[tool.setuptools.packages.find]
where = ["."]
include = ["pymatgen.*"]

[tool.setuptools.package-data]
"pymatgen.analysis" = ["*.yaml", "*.json", "*.csv"]
"pymatgen.analysis.chemenv" = [
"coordination_environments/coordination_geometries_files/*.json",
"coordination_environments/coordination_geometries_files/*.txt",
"coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json",
]
"pymatgen.analysis.structure_prediction" = ["*.yaml", "data/*.json"]
"pymatgen.analysis.diffraction" = ["*.json"]
"pymatgen.analysis.magnetism" = ["default_magmoms.yaml"]
"pymatgen.analysis.solar" = ["am1.5G.dat"]
"pymatgen.entries" = ["*.json.gz", "*.yaml", "data/*.json"]
"pymatgen.core" = ["*.json"]
"pymatgen" = ["py.typed"]
"pymatgen.io.vasp" = ["*.yaml", "*.json", "*.json.gz", "*.json.bz2"]
"pymatgen.io.feff" = ["*.yaml"]
"pymatgen.io.cp2k" = ["*.yaml"]
"pymatgen.io.lobster" = ["lobster_basis/*.yaml"]
"pymatgen.command_line" = ["*"]
"pymatgen.util" = ["structures/*.json", "*.json"]
"pymatgen.vis" = ["*.yaml"]
"pymatgen.io.lammps" = ["CoeffsDataType.yaml", "templates/*.template"]
"pymatgen.symmetry" = ["*.yaml", "*.json", "*.sqlite"]

[project.scripts]
pmg = "pymatgen.cli.pmg:main"
feff_plot_cross_section = "pymatgen.cli.feff_plot_cross_section:main"
feff_plot_dos = "pymatgen.cli.feff_plot_dos:main"
get_environment = "pymatgen.cli.get_environment:main"

[tool.versioningit.vcs]
method = "git"
default-tag = "0.0.1"
Expand All @@ -25,55 +180,55 @@ line-length = 120

[tool.ruff.lint]
select = [
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"D", # pydocstyle
"E", # pycodestyle error
"EXE", # flake8-executable
"F", # pyflakes
"FA", # flake8-future-annotations
"FBT003", # boolean-positional-value-in-call
"FLY", # flynt
"I", # isort
"ICN", # flake8-import-conventions
"ISC", # flake8-implicit-str-concat
"PD", # pandas-vet
"PERF", # perflint
"PIE", # flake8-pie
"PL", # pylint
"PLR0402",
"PLR1714",
"PLR5501",
"PT", # flake8-pytest-style
"PYI", # flakes8-pyi
"Q", # flake8-quotes
"RET", # flake8-return
"RSE", # flake8-raise
"RUF", # Ruff-specific rules
"SIM", # flake8-simplify
"SLOT", # flake8-slots
"TCH", # flake8-type-checking
"TID", # flake8-tidy-imports
"UP", # pyupgrade
"W", # pycodestyle warning
"YTT", # flake8-2020
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"D", # pydocstyle
"E", # pycodestyle error
"EXE", # flake8-executable
"F", # pyflakes
"FA", # flake8-future-annotations
"FBT003", # boolean-positional-value-in-call
"FLY", # flynt
"I", # isort
"ICN", # flake8-import-conventions
"ISC", # flake8-implicit-str-concat
"PD", # pandas-vet
"PERF", # perflint
"PIE", # flake8-pie
"PL", # pylint
"PLR0402",
"PLR1714",
"PLR5501",
"PT", # flake8-pytest-style
"PYI", # flakes8-pyi
"Q", # flake8-quotes
"RET", # flake8-return
"RSE", # flake8-raise
"RUF", # Ruff-specific rules
"SIM", # flake8-simplify
"SLOT", # flake8-slots
"TCH", # flake8-type-checking
"TID", # flake8-tidy-imports
"UP", # pyupgrade
"W", # pycodestyle warning
"YTT", # flake8-2020
]
ignore = [
"B023", # Function definition does not bind loop variable
"B028", # No explicit stacklevel keyword argument found
"B904", # Within an except clause, raise exceptions with ...
"C408", # unnecessary-collection-call
"D105", # Missing docstring in magic method
"D205", # 1 blank line required between summary line and description
"D212", # Multi-line docstring summary should start at the first line
"PD901", # pandas-df-variable-name
"PERF203", # try-except-in-loop
"PERF401", # manual-list-comprehension
"PLR", # pylint refactor
"PLW2901", # Outer for loop variable overwritten by inner assignment target
"PT013", # pytest-incorrect-pytest-import
"PTH", # prefer pathlib to os.path
"SIM105", # Use contextlib.suppress() instead of try-except-pass
"B023", # Function definition does not bind loop variable
"B028", # No explicit stacklevel keyword argument found
"B904", # Within an except clause, raise exceptions with ...
"C408", # unnecessary-collection-call
"D105", # Missing docstring in magic method
"D205", # 1 blank line required between summary line and description
"D212", # Multi-line docstring summary should start at the first line
"PD901", # pandas-df-variable-name
"PERF203", # try-except-in-loop
"PERF401", # manual-list-comprehension
"PLR", # pylint refactor
"PLW2901", # Outer for loop variable overwritten by inner assignment target
"PT013", # pytest-incorrect-pytest-import
"PTH", # prefer pathlib to os.path
"SIM105", # Use contextlib.suppress() instead of try-except-pass
]
pydocstyle.convention = "google"
isort.required-imports = ["from __future__ import annotations"]
Expand All @@ -97,31 +252,31 @@ addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mod
[tool.coverage.run]
parallel = true
omit = [
"pymatgen/cli/feff_plot_cross_section.py",
"pymatgen/cli/feff_plot_dos.py",
"pymatgen/cli/pmg_config.py",
"pymatgen/cli/pmg_plot.py",
"pymatgen/cli/pmg_potcar.py",
"pymatgen/cli/pmg_query.py",
"pymatgen/dao.py",
"pymatgen/cli/feff_plot_cross_section.py",
"pymatgen/cli/feff_plot_dos.py",
"pymatgen/cli/pmg_config.py",
"pymatgen/cli/pmg_plot.py",
"pymatgen/cli/pmg_potcar.py",
"pymatgen/cli/pmg_query.py",
"pymatgen/dao.py",
]

[tool.coverage.report]
exclude_also = [
"@deprecated",
"@np.deprecate",
"def __repr__",
"except ImportError:",
"if 0:",
"if TYPE_CHECKING:",
"if __name__ == .__main__.:",
"if self.debug:",
"if settings.DEBUG",
"if typing.TYPE_CHECKING:",
"pragma: no cover",
"raise AssertionError",
"raise NotImplementedError",
"show_plot",
"@deprecated",
"@np.deprecate",
"def __repr__",
"except ImportError:",
"if 0:",
"if TYPE_CHECKING:",
"if __name__ == .__main__.:",
"if self.debug:",
"if settings.DEBUG",
"if typing.TYPE_CHECKING:",
"pragma: no cover",
"raise AssertionError",
"raise NotImplementedError",
"show_plot",
]

[tool.mypy]
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