pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = [
  "hatch-docstring-description>=1.1.1",
  "hatch-fancy-pypi-readme",
  "hatch-min-requirements",
  "hatch-vcs",
  "hatchling",
]

[project]
name = "fast-array-utils"
license = "MPL-2.0"
authors = [
  { name = "Philipp A.", email = "flying-sheep@web.de" },
]
requires-python = ">=3.12"
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Intended Audience :: Developers",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
dynamic = [ "description", "readme", "version" ]
dependencies = [ "numpy>=2" ]
optional-dependencies.accel = [ "numba>=0.57" ]
optional-dependencies.dask = [ "dask>=2023.6.1" ]
optional-dependencies.doc = [
  "furo>=2024.8.6",
  "pytest>=8.4",
  "scanpydoc>=0.15.4",
  "sphinx>=8.2.3",
  "sphinx-autodoc-typehints>=3.2",
  "sphinx-autofixture>=0.4.1",
]
optional-dependencies.full = [ "fast-array-utils[accel,dask,sparse]", "h5py", "zarr" ]
optional-dependencies.sparse = [ "scipy>=1.13" ]
optional-dependencies.test = [
  "anndata",
  "fast-array-utils[accel,test-min]",
  "numcodecs<0.16",                   # zarr 2 needs this
  "zarr<3",                           # anndata needs this
]
optional-dependencies.test-min = [
  "coverage[toml]",
  "fast-array-utils[sparse,testing]", # include sparse for testing numba-less to_dense
  "pytest",
  "pytest-codspeed",
  "pytest-doctestplus",
  "pytest-xdist",
]
optional-dependencies.testing = [ "packaging" ]
urls.'Documentation' = "https://icb-fast-array-utils.readthedocs-hosted.com/"
urls.'Issue Tracker' = "https://github.com/scverse/fast-array-utils/issues"
urls.'Source Code' = "https://github.com/scverse/fast-array-utils"

entry-points.pytest11.fast_array_utils = "testing.fast_array_utils.pytest"

[tool.hatch.version]
source = "vcs"
raw-options = { local_scheme = "no-local-version" } # be able to publish dev version

[tool.hatch.metadata.hooks.fancy-pypi-readme]
content-type = "text/x-rst"
[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
path = "README.rst"
start-after = ".. begin"

[tool.hatch.metadata.hooks.docstring-description]
[tool.hatch.metadata.hooks.min_requirements]

[tool.hatch.build.targets.wheel]
packages = [ "src/testing", "src/fast_array_utils" ]

[tool.hatch.envs.default]
installer = "uv"

[tool.hatch.envs.docs]
features = [ "doc" ]
scripts.build = "sphinx-build -M html docs docs/_build"
scripts.clean = "git clean -fdX docs"
scripts.open = "python -m webbrowser -t docs/_build/html/index.html"

[tool.hatch.envs.hatch-test]
default-args = [  ]
features = [ "test-min" ]
extra-dependencies = [ "ipykernel", "ipycytoscape" ]
env-vars.CODSPEED_PROFILE_FOLDER = "test-data/codspeed"
overrides.matrix.extras.features = [
  { if = [ "full" ], value = "full" },
  { if = [ "full" ], value = "test" },
]
overrides.matrix.extras.dependencies = [
  { if = [ "full" ], value = "scipy-stubs" },
  { if = [ "full" ], value = "scikit-learn" },
]
overrides.matrix.resolution.features = [
  { if = [ "lowest" ], value = "min-reqs" }, # feature added by hatch-min-requirements
]
overrides.matrix.resolution.dependencies = [
  # TODO: move to min dep once this is fixed: https://github.com/tlambert03/hatch-min-requirements/issues/11
  { if = [ "lowest" ], value = "dask==2023.6.1" },
  { if = [ "lowest" ], value = "scipy==1.13.0" },
]

[[tool.hatch.envs.hatch-test.matrix]]
python = [ "3.13", "3.12" ]
extras = [ "full", "min" ]

[[tool.hatch.envs.hatch-test.matrix]]
python = [ "3.12" ]
extras = [ "full" ]
resolution = [ "lowest" ]

[tool.ruff]
line-length = 160
namespace-packages = [ "src/testing" ]
format.preview = true
format.docstring-code-format = true
lint.select = [ "ALL" ]
lint.ignore = [
  "A005",    # submodules never shadow builtins.
  "C408",    # dict() calls are nice
  "COM812",  # trailing commas handled by black
  "D203",    # prefer 0 to 1 blank line before class members
  "D213",    # prefer docstring summary on first line
  "FIX002",  # “TODO” comments
  "N812",    # lowercase imports are fine
  "PLC0415", # we rely heavily on non-top-level imports
  "PLR0913", # having many (kw)args is fine
  "Q",       # handled by formatter
  "S101",    # asserts are fine
  "TID252",  # relative imports are fine
]
lint.per-file-ignores."docs/**/*.py" = [ "INP001" ] # No __init__.py in docs
lint.per-file-ignores."src/**/stats/*.py" = [ "A001", "A004" ] # Shadows builtins like `sum`
lint.per-file-ignores."tests/**/*.py" = [
  "D100",    # tests need no module docstrings
  "D103",    # tests need no function docstrings
  "INP001",  # tests should not have __init__.py
  "PLR2004", # tests use magic values
  "S101",    # tests use `assert`
]
lint.per-file-ignores."typings/**/*.pyi" = [ "A002", "F403", "F405", "N801" ] # Stubs don’t follow name conventions
lint.allowed-confusables = [ "×", "’" ]
lint.flake8-bugbear.extend-immutable-calls = [ "testing.fast_array_utils.Flags" ]
lint.flake8-copyright.notice-rgx = "SPDX-License-Identifier: MPL-2\\.0"
lint.flake8-type-checking.exempt-modules = [  ]
lint.flake8-type-checking.strict = true
lint.isort.known-first-party = [ "fast_array_utils" ]
lint.isort.lines-after-imports = 2
lint.pydocstyle.convention = "numpy"
lint.future-annotations = true

[tool.pytest.ini_options]
addopts = [
  "--import-mode=importlib",
  "--strict-markers",
  "--doctest-modules",
  "--doctest-plus",
  "--pyargs",
]
testpaths = [ "./tests", "fast_array_utils" ]
doctest_subpackage_requires = [
  "src/fast_array_utils/conv/scipy/* = scipy",
  "src/fast_array_utils/conv/scipy/_to_dense.py = numba",
  "src/fast_array_utils/stats/* = numba",
  "src/fast_array_utils/_plugins/dask.py = dask",
  "src/fast_array_utils/_plugins/numba_sparse.py = numba;scipy",
]
filterwarnings = [
  "error",
  # codspeed seems to break this dtype added by h5py
  "ignore:.*numpy[.]longdouble:UserWarning",
  "ignore:FNV hashing is not implemented in Numba:UserWarning",
]
markers = [
  "benchmark: marks tests as benchmark (to run with `--codspeed`)",
]
xfail_strict = true

[tool.coverage]
run.data_file = "test-data/.coverage"
xml.output = "test-data/coverage.xml"
html.directory = "test-data/htmlcov"
run.omit = [ "src/testing/*", "tests/*" ]
report.exclude_also = [ "if TYPE_CHECKING:", "@numba[.]njit", "[.]{3}" ]

[tool.mypy]
strict = true
# https://github.com/dask/dask/issues/8853
implicit_reexport = true
explicit_package_bases = true
mypy_path = [ "$MYPY_CONFIG_FILE_DIR/typings", "$MYPY_CONFIG_FILE_DIR/src" ]

[tool.pyright]
stubPath = "./typings"
reportPrivateUsage = false