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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 = "graphium"
description = "Graphium: Scaling molecular GNNs to infinity."
dynamic = ["version"]
authors = [
{ name = "Dominique Beaini", email = "dominique@valencediscovery.com" },
]
readme = "README.md"
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",
"Programming Language :: Python :: 3.11",
]
dependencies = [
"typer",
"loguru",
"omegaconf >=2.0.0",
"tqdm",
"platformdirs",
# scientific
"numpy",
"scipy >=1.4",
"pandas >=1.0",
"scikit-learn",
"fastparquet",
# viz
"matplotlib >=3.0.1",
"seaborn",
# cloud IO
"fsspec >=2021.6",
"s3fs >=2021.6",
"gcsfs >=2021.6",
# ML packages
"lightning >=2.0",
"torchmetrics >=0.7.0,<0.11",
"ogb",
"torch-geometric >=2.0",
"wandb",
"mup",
"torch_sparse >=0.6",
"torch_cluster >=1.5",
"torch_scatter >=2.0",
# chemistry
"datamol >=0.10",
]
[project.scripts]
graphium = "graphium.cli.main:app"
graphium-train = "graphium.cli.train_finetune_test:cli"
[project.urls]
Website = "https://graphium.datamol.io/"
"Source Code" = "https://github.com/datamol-io/graphium"
"Bug Tracker" = "https://github.com/datamol-io/graphium/issues"
Documentation = "https://graphium-docs.datamol.io/"
[tool.setuptools]
include-package-data = true
[tool.setuptools_scm]
fallback_version = "dev"
[tool.setuptools.packages.find]
where = ["."]
include = ["graphium", "graphium.*", "expts", "expts.*"]
exclude = []
namespaces = true
[tool.setuptools.package-data]
"graphium" = ["**/*.csv", "**/*.parquet", "**/*.yaml"]
[tool.black]
line-length = 110
target-version = ['py310', 'py311']
include = '\.pyi?$'
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "--verbose --durations=10 -n 1 --cov=graphium --cov-fail-under=60 --cov-report xml --cov-report term"
testpaths = ["tests"]
filterwarnings = [
"ignore::DeprecationWarning:ray.*:",
"ignore::DeprecationWarning:numba.*:",
"ignore::DeprecationWarning:lightning_fabric.*:",
"ignore::DeprecationWarning:pytorch_lightning.*:",
"ignore::DeprecationWarning:pkg_resources.*:",
]
markers = [
"ipu: marks tests that are specific to the IPU (deselect with '-m \"not ipu\"')",
]
[tool.coverage.run]
source = ["graphium/"]
disable_warnings = ["no-data-collected"]
data_file = ".coverage/coverage"
[tool.coverage.report]
omit = ["graphium/__init__.py", "graphium/_version.py"]
[tool.coverage.xml]
output = "coverage.xml"