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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[project]
name = "molfeat"
description = "molfeat - the hub for all your molecular featurizers"
dynamic = ["version"]
authors = [{ name = "Emmanuel Noutahi", email = "[email protected]" }]
readme = "README.md"
license = { text = "Apache" }
requires-python = ">3.8"
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"Intended Audience :: Healthcare Industry",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Information Analysis",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
]
dependencies = [
"tqdm",
"loguru",
"joblib",
"filelock",
"fsspec >=2021.9",
"s3fs >=2021.9",
"gcsfs >=2021.9",
"pandas",
"numpy",
"scipy",
"torch>=1.13",
"datamol >=0.8.0",
"pyyaml",
"platformdirs",
"matplotlib",
"h5py",
"pyarrow",
"pydantic >=2.0.0",
"platformdirs",
"scikit-learn",
"packaging",
"pmapper",
"mordredcommunity",
"python-dotenv",
"rdkit",
]
[project.optional-dependencies]
dgl = ["dgl>=1.1.1,<=2.0.0", "dgllife>=0.3.2"]
graphormer = ["graphormer-pretrained"]
transformer = ["tokenizers <0.13.2", "transformers", "sentencepiece"]
fcd = ["fcd_torch"]
viz = ["nglview", "ipywidgets"]
pyg = ["pytorch_geometric >=2.4.0"]
all = [
"dgl",
"dgllife",
"graphormer-pretrained",
"tokenizers <0.13.2",
"transformers",
"fcd_torch",
"nglview",
"ipywidgets",
"pytorch_geometric >=2.4.0"
]
test = ["pytest >=6.0","pytest-dotenv", "pytest-cov", "pytest-xdist", "black >=22", "ruff"]
docs = ["mkdocs", "mike", "mdx_truly_sane_lists", "mkdocs-material >=7.1.1", "mkdocs-jupyter >=0.24.8", "mkdocstrings", "mkdocstrings-python", "markdown-include"]
dev = ["molfeat[test]", "molfeat[all]", "molfeat[docs]", "pre-commit"]
[project.urls]
Website = "https://molfeat.datamol.io"
"Source Code" = "https://github.com/datamol-io/molfeat"
"Bug Tracker" = "https://github.com/datamol-io/molfeat/issues"
Documentation = "https://molfeat-docs.datamol.io/"
[tool.setuptools]
include-package-data = true
zip-safe = false
license-files = ["LICENSE"]
[tool.setuptools_scm]
fallback_version = "dev"
[tool.setuptools.packages.find]
where = ["."]
include = ["molfeat", "molfeat.*"]
exclude = []
namespaces = true
[tool.setuptools.package-data]
"molfeat.data" = ["**/*"]
[tool.black]
line-length = 100
target-version = ['py39', 'py310']
include = '\.pyi?$'
[tool.ruff]
ignore = [
"E501", # Never enforce `E501` (line length violations).
"E731", # Do not assign a lambda expression, use a def
]
line-length = 110
target-version = "py311"
[tool.ruff.per-file-ignores]
"__init__.py" = [
"F401", # imported but unused
"E402", # Module level import not at top of file
]
[tool.ruff.pycodestyle]
max-doc-length = 150
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "--verbose --cov-report xml --cov-report term --color yes"
testpaths = ["tests"]
norecursedirs = "tests/helpers"
[tool.coverage.run]
omit = ["setup.py", "tests/*"]
[tool.coverage.xml]
output = "cov.xml"