pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = [ "hatch-vcs", "hatchling" ]

[project]
name = "squidpy"
description = "Spatial Single Cell Analysis in Python"
readme = "README.md"
keywords = [
  "bio-informatics",
  "image analysis",
  "single-cell",
  "spatial data analysis",
  "spatial transcriptomics",
]
license = "BSD-3-Clause"
maintainers = [
  { name = "Selman Ozleyen", email = "selman.ozleyen@helmholtz-munich.de" },
  { name = "Tim Treis", email = "tim.treis@scverse.org" },
]
authors = [
  { name = "scverse" },
]
requires-python = ">=3.12"
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Environment :: Console",
  "Framework :: Jupyter",
  "Intended Audience :: Science/Research",
  "Natural Language :: English",
  "Operating System :: MacOS :: MacOS X",
  "Operating System :: POSIX :: Linux",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Topic :: Scientific/Engineering :: Visualization",
  "Typing :: Typed",
]
dynamic = [
  "version", # allow version to be set by git tags
]
dependencies = [
  "aiohttp>=3.8.1",
  "anndata>=0.9",
  "centrosome>=1.2.3",
  "cp-measure>=0.2,<0.3",
  "cycler>=0.11",
  "dask[array,distributed]>=2021.2",    # distributed is the only scheduler that forks for GIL-bound featurization
  "dask-image>=0.5",
  "docrep>=0.3.1",
  "fast-array-utils>=1.5",              # `types.HasArrayNamespace`
  "fsspec>=2021.11",
  "imagecodecs>=2025.8.2,<2026",
  "legacy-api-wrap>=1.5",               # keyword-only args keep accepting old positional calls (#1288)
  "matplotlib>=3.3",
  "matplotlib-scalebar>=0.8",
  "networkx>=2.6",
  "numba>=0.56.4",
  "numba-progress>=1.1",
  "numpy>=1.23",
  "omnipath>=1.0.7",
  "pandas>=2.1",
  "pillow>=8",
  "pooch>=1.6",
  "pyyaml>=6",
  "scanpy>=1.9.3",
  "scikit-image>=0.26",
  # due to https://github.com/scikit-image/scikit-image/issues/6850 breaks rescale ufunc
  "scikit-learn>=0.24",
  # dataset registry + downloader now live in scverse-misc
  "scverse-misc[datasets]>=0.1.1,<0.2",
  "spatialdata>=0.7.2",                 # 0.7.2 dropped xarray-schema (pkg_resources break, #1115)
  "spatialdata-plot>=0.4.1",
  "statsmodels>=0.12",
  "threadpoolctl>=3",                   # clamp BLAS/OpenMP per worker in tiled featurization
  # https://github.com/scverse/squidpy/issues/526
  "tifffile!=2022.4.22",
  "tqdm>=4.50.2",
  "validators>=0.18.2",
  "xarray>=2024.10",
  "zarr>=3",
]
optional-dependencies.leiden = [
  "leidenalg",
  "spatialleiden>=0.4",
]
urls."Bug Tracker" = "https://github.com/scverse/squidpy/issues"
urls.Documentation = "https://squidpy.readthedocs.io"
urls.Home-page = "https://github.com/scverse/squidpy"
urls.Source = "https://github.com/scverse/squidpy"

[dependency-groups]
dev = [
  "hatch>=1.9",
  "ipykernel",
  "ipywidgets",
  "jupyterlab",
  "jupytext",
  "notebook",
  "pre-commit>=3",
  "ruff",
]
test = [
  "coverage[toml]>=7",
  # Image-comparison baselines are matplotlib-version-sensitive; matplotlib 3.11.0 (released
  # 2026-06-12) shifts scatter/alpha rendering past the RMS tolerance. Cap for tests only
  # (the runtime dependency stays open) until the baselines are regenerated against 3.11.
  "matplotlib<3.11",
  "pytest>=7",
  # Just for VS Code
  "pytest-cov>=4",
  "pytest-mock>=3.5",
  "pytest-rerunfailures",
  "pytest-timeout>=2.1",
  "pytest-xdist>=3",
  "scanpy[leiden]",
]
docs = [
  "docutils<0.22",                    # Pin to avoid sphinx-tabs KeyError with backrefs
  "ipython",
  "ipywidgets>=8",
  "myst-nb>=0.17.1",
  "nbsphinx>=0.8.1",
  "scverse-misc[sphinx]>=0.1.2,<0.2",
  "sphinx>=5.3",
  "sphinx-autodoc-annotation",
  "sphinx-autodoc-typehints>=1.10.3",
  "sphinx-copybutton>=0.5",
  "sphinx-design",
  "sphinx-rtd-theme",
  "sphinx-tabs",
  "sphinxcontrib-bibtex>=2.3",
  "sphinxcontrib-spelling>=7.6.2",
]

[tool.setuptools]
package-dir = { "" = "src" }
include-package-data = true

[tool.setuptools_scm]

[tool.hatch]
version.source = "vcs"
metadata.allow-direct-references = true
build.hooks.vcs.version-file = "_version.py"
build.targets.wheel.packages = [ "src/squidpy" ]

[tool.pixi]
workspace.channels = [ "conda-forge" ]
workspace.platforms = [ "linux-64", "osx-arm64" ]
dependencies.python = ">=3.12"
pypi-dependencies.squidpy = { path = ".", editable = true }
tasks.format = "ruff format ."
tasks.kernel-install = 'python -m ipykernel install --user --name pixi-dev --display-name "squidpy (dev)"'
tasks.lab = "jupyter lab"
tasks.lint = "ruff check ."
tasks.pre-commit = "pre-commit run"
tasks.pre-commit-install = "pre-commit install"
tasks.test = "pytest -v --color=yes --tb=short --durations=10"
feature.py312.dependencies.python = "3.12.*"
feature.py314.dependencies.python = "3.14.*"
environments.default = { features = [ "py314" ], solve-group = "py314" }
environments.dev-py312 = { features = [ "dev", "test", "py312" ], solve-group = "py312" }
environments.dev-py314 = { features = [ "dev", "test", "py314" ], solve-group = "py314" }
environments.docs-py312 = { features = [ "docs", "py312" ], solve-group = "py312" }
environments.docs-py314 = { features = [ "docs", "py314" ], solve-group = "py314" }
environments.test-py314 = { features = [ "test", "py314" ], solve-group = "py314" }

[tool.ruff]
line-length = 120
exclude = [
  ".git",
  ".tox",
  "__pycache__",
  "build",
  "dist",
  "docs/_build",
  "setup.py",
]
format.docstring-code-format = true
lint.select = [
  "B",   # flake8-bugbear
  "BLE", # flake8-blind-except
  "C4",  # flake8-comprehensions
  "E",   # pycodestyle
  "F",   # pyflakes
  "I",   # isort
  # below are not autofixed
  "UP",  # pyupgrade
  "W",   # pycodestyle
]
# too many positional arguments: most arguments are keyword-only (#1288)
lint.extend-select = [ "PLR0917" ]
lint.ignore = [
  # B008 Do not perform function calls in argument defaults.
  "B008",
  # B024 Do not use `__class__` for string comparisons.
  "B024",
  # D100 Missing docstring in public module
  "D100",
  # Missing docstring in public package
  "D104",
  # Missing docstring in magic method
  "D105",
  # D107 Missing docstring in __init__,
  "D107",
  # Missing blank line before section
  "D411",
  # line too long -> we accept long comment lines; formatter gets rid of long code lines
  "E501",
  # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
  "E731",
  # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
  "E741",
  # PEP 695 generics (`class C[T]` / `def f[T]`) -> deferred to a dedicated rewrite.
  # `GraphMatrixT`/`CoordT` are a shared TypeVar pair: defined in `gr.neighbors`, used by a
  # module-level `Callable` alias, imported by `gr._build`, and re-exported from the public
  # `squidpy.gr` API. ruff cannot autofix the cross-module use (`SpatialNeighborsResult`, which
  # imports the TypeVar) and its fix for the local use (`GraphBuilder`) leaves the still-required
  # exported TypeVars in place, creating dual same-name definitions. Converting correctly means
  # deciding whether to keep exporting `GraphMatrixT` -- a public-API change, not a version bump.
  "UP046",
  "UP047",
  ## Flake8 rules not supported by ruff:
  # RST201 Block quote ends without a blank line; unexpected unindent.
  # "RST201",
  # RST301 Unexpected indentation.
  # "RST301",
  # RST306 Unknown target name.
  # "RST306",
  # RST203 Definition list ends without a blank line; unexpected unindent.
  # "RST203",
  # line break before a binary operator -> black does not adhere to PEP8
  # "W503",
  # line break occured after a binary operator -> black does not adhere to PEP8
  # "W504",
  # whitespace before : -> black does not adhere to PEP8
  # "E203",
  # whitespace before : -> black does not adhere to PEP8
  # "E203",
  # missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
  # "E231",
  # continuation line over-indented for hanging indent -> black does not adhere to PEP8
  # "E126",
  # inline comment should start with '#' -> Scanpy allows them for specific explanations
  # "E266",
  # format string does contain unindexed parameters
  # "P101",
  # indentation is not a multiple of 4
  # "E111",
  # "E114",
]
lint.explicit-preview-rules = true  # only the preview rules selected by name, i.e. PLR0917
lint.per-file-ignores."*/__init__.py" = [ "D104", "F401" ]
lint.per-file-ignores.".scripts/ci/download_data.py" = [ "B", "D" ]
# Sphinx calls event handlers with a fixed positional signature
lint.per-file-ignores."docs/*" = [ "B", "D", "PLR0917" ]
lint.per-file-ignores."src/squidpy/_constants/_constants.py" = [ "D101" ]
lint.per-file-ignores."src/squidpy/_constants/_pkg_constants.py" = [ "D101", "D102", "D106" ]
# ImageContainer is left as it is until it is deprecated, positional arguments included
lint.per-file-ignores."src/squidpy/im/_container.py" = [ "PLR0917" ]
lint.per-file-ignores."src/squidpy/im/_feature_mixin.py" = [ "PLR0917" ]
lint.per-file-ignores."src/squidpy/im/_segment.py" = [ "PLR0917" ]
lint.per-file-ignores."src/squidpy/pl/_ligrec.py" = [ "B", "D" ]
lint.per-file-ignores."tests/*" = [ "D", "PLR0917" ]
lint.unfixable = [
  "B",
  "BLE",
  "C4",
  "F401", # ... imported but unused
]
# Disallow all relative imports.
lint.flake8-tidy-imports.ban-relative-imports = "all"
lint.isort.required-imports = [ "from __future__ import annotations" ]
lint.preview = true
# "squidpy/*.py" = [ "RST303" ]

[tool.pytest]
addopts = [
  "--ignore=docs",
]
filterwarnings = [
  "error::numba.NumbaPerformanceWarning",
  "ignore::UserWarning",
  "ignore::anndata.OldFormatWarning",
  "ignore:.*pkg_resources:DeprecationWarning",
]
markers = [
  "internet: tests that require internet",
  # the below markers are just there because we import from anndata.tests.helpers,
  # which means pytest sees them despite us not using them.
  "gpu: tests that require GPU",
  "array_api: tests that require array-api-compat",
]
python_files = [ "test_*.py" ]
strict = true
testpaths = [ "tests/" ]

[tool.coverage]
run.source = [ "squidpy" ]
run.omit = [
  "*/__init__.py",
  "*/_version.py",
  "tox/*",
]
run.branch = true
run.parallel = true
paths.source = [
  "squidpy",
  "*/site-packages/squidpy",
]
report.precision = 2
report.exclude_lines = [
  "\\#.*pragma:\\s*no.?cover",
  "^\\s*raise AssertionError\\b",
  "^\\s*raise NotImplementedError\\b",
  "^\\s*return NotImplemented\\b",
  "^if __name__ == .__main__.:$",
]
report.skip_empty = true
report.show_missing = true
report.sort = "Miss"

[tool.cruft]
skip = [
  "tests",
  "src/**/__init__.py",
  "src/**/basic.py",
  "docs/api.md",
  "docs/changelog.md",
  "docs/references.bib",
  "docs/references.md",
  "docs/notebooks/example.ipynb",
]