squidpy/hatch.toml at main · scverse/squidpy · GitHub

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[envs.default]
installer = "uv"
dependency-groups = ["dev"]

[envs.docs]
dependency-groups = ["docs"]
scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
scripts.clean = "git clean -fdX -- {args:docs}"

[envs.data]
scripts.download = "python ./.scripts/ci/download_data.py {args}"

[envs.hatch-test]
dependency-groups = ["test"]
extra-dependencies = ["diff-cover"]
matrix = [
  { deps = ["stable"], python = ["3.11", "3.12", "3.13"] },
  { deps = ["pre"], python = ["3.13"] },
]
overrides.matrix.deps.env-vars = [
  { key = "UV_PRERELEASE", value = "allow", if = ["pre"] },
]
# default commands (only `cov-report` is overridden)
scripts.run = "pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
scripts.run-cov = "coverage run -m pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
scripts.cov-combine = ["coverage combine"]
scripts.cov-report = [
    "coverage report",
    "coverage xml -o coverage.xml",
    "diff-cover --compare-branch origin/main coverage.xml",
]
# extra commands
scripts.cov-erase = "coverage erase"
scripts.download = "python ./.scripts/ci/download_data.py {args}"

[envs.notebooks]
extra-dependencies = [
    "ipykernel",
    "jupytext",
    "nbconvert",
    "leidenalg",
    "watermark",
    "napari-spatialdata",
]
extras = ["docs"]
scripts.setup-squidpy-kernel = "python -m ipykernel install --user --name=squidpy"
scripts.run-notebooks = "python ./.scripts/ci/run_notebooks.py docs/notebooks"