chemap/pyproject.toml at main · matchms/chemap · GitHub

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[project]
name = "chemap"
version = "0.3.5"
description = "Library for computing molecular fingerprint based similarities as well as dimensionality reduction based chemical space visualizations. "
authors = [
  { name="Florian Huber", email="florian.huber@hs-duesseldorf.de" },
  { name="Julian Pollmann", email="julian.pollmann@hs-duesseldorf.de" },
]
license = "MIT"
readme = "README.md"
requires-python = ">=3.11,<3.14"
classifiers = [
    "Programming Language :: Python :: 3",
    "Operating System :: OS Independent",
]

dependencies = [
    "map4>=1.1.3",
    "numba>=0.61.2",
    "numpy>=2.1.0",
    "pandas>=2.2.1",
    "scipy>=1.14.2",
    "matplotlib>=3.10.1",
    "rdkit>=2024.9.6",
    "scikit-fingerprints>=1.15.0",
    "tqdm>=4.67.1",
    "pooch>=1.8.2",
    "joblib>=1.3.2",
]

[project.optional-dependencies]
# GPU-accelerated UMAP via RAPIDS cuML (choose the CUDA version that matches your system)
gpu-cu12 = [
  "cuml-cu12>=25.6.0; platform_system=='Linux'",
  "cupy-cuda12x>=13.0.0; platform_system=='Linux'",
]

gpu-cu13 = [
  "cuml-cu13>=26.0.0; platform_system=='Linux'",
  "cupy-cuda13x>=13.0.0; platform_system=='Linux'",
]

# Alternative: CPU UMAP
cpu = [
  "umap-learn>=0.5.8",
  "pynndescent>=0.5.13",
]

# Development extras
[dependency-groups]
dev = [
    "decorator>=5.1.1",
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "yapf>=0.40.1",
    "testfixtures>=7.1.0",
    "twine>=6.1.0",
    "poetry-bumpversion>=0.3.1",
    "pre-commit>=4.2.0",
    "ruff>=0.11.4",
]

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[tool.uv]
conflicts = [
  [
    { extra = "cpu" },
    { extra = "gpu-cu12" },
    { extra = "gpu-cu13" },
  ],
]

[tool.ruff]
line-length = 120
output-format = "grouped"

[tool.ruff.format]
docstring-code-format = true
line-ending = "lf"

[tool.ruff.lint]
# TODO: add some rules in future, eg. W291/292
extend-select = ["D", "E", "I"]
ignore = [
    "D100",
    "D101",
    "D102",
    "D103",
    "D104",
    "D105",
    "D107",
    "D200",
    "D201",
    "D202",
    "D203",
    "D204",
    "D205",
    "D209",
    "D210",
    "D212",
    "D213",
    "D4",
]

[tool.ruff.lint.isort]
known-first-party = ["chemap"]
lines-after-imports = 2
no-lines-before = ["future", "standard-library", "third-party", "first-party", "local-folder"]
section-order = ["future", "standard-library", "third-party", "first-party", "local-folder"]

# disable pydoc for tests
[tool.ruff.lint.per-file-ignores]
"tests/**" = ["D"]

[tool.pytest.ini_options]
testpaths = [
    "tests",
    "integration-tests",
]