pyproject.toml

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

[project]
name = "spatialdata-plot"
description = "Static plotting for spatial data."
readme = "README.md"
license = { file = "LICENSE" }
maintainers = [
  { name = "Tim Treis", email = "tim.treis@helmholtz-munich.de" },
]
authors = [
  { name = "scverse" },
]
requires-python = ">=3.11"
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
dynamic = [
  "version", # allow version to be set by git tags
]
dependencies = [
  "matplotlib",
  "matplotlib-scalebar",
  "scanpy",
  "scikit-learn",
  "spatialdata>=0.3",
]
urls.Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/index.html"
urls.Home-page = "https://github.com/scverse/spatialdata-plot.git"
urls.Source = "https://github.com/scverse/spatialdata-plot.git"

[dependency-groups]
dev = [
  "pre-commit",
  "twine>=4.0.2",
]
test = [
  "coverage[toml]>=7.4",
  "pooch",
  "pytest",
  "pytest-cov",
  "pytest-xdist[psutil]",
]
doc = [
  "ipykernel",
  "ipython>=8.6",
  "myst-nb>=1.1",
  "sphinx>=8.1",
  "sphinx-autodoc-typehints",
  "sphinx-book-theme>=1",
  "sphinx-copybutton",
  "sphinx-tabs",
  "sphinxcontrib-bibtex>=1",
  "sphinxcontrib-katex",
  "sphinxext-opengraph",
]

[tool.hatch]
build.hooks.vcs.version-file = "_version.py"
build.targets.wheel.packages = [ "src/spatialdata_plot" ]
envs.default.installer = "uv"
envs.default.dependency-groups = [ "dev" ]
envs.docs.dependency-groups = [ "doc" ]
envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
envs.hatch-test.dependency-groups = [ "test" ]
envs.hatch-test.matrix = [
  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
  { deps = [ "pre" ], python = [ "3.14" ] }
]
envs.hatch-test.overrides.matrix.deps.env-vars = [
  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
]
envs.hatch-test.scripts.run = "pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
envs.hatch-test.scripts.run-cov = "coverage run -m pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
envs.hatch-test.scripts.cov-combine = "coverage combine"
envs.hatch-test.scripts.cov-report = [ "coverage report", "coverage xml -o coverage.xml" ]
metadata.allow-direct-references = true
version.source = "vcs"

[tool.ruff]
line-length = 120
exclude = [
  ".git",
  ".tox",
  "__pycache__",
  "build",
  "dist",
  "docs/_build",
  "setup.py",
]
lint.select = [
  "B",   # flake8-bugbear
  "BLE", # flake8-blind-except
  "C4",  # flake8-comprehensions
  "D",   # flake8-docstrings
  "E",   # pycodestyle
  "F",   # pyflakes
  "I",   # isort
  "NPY", # NumPy-specific rules
  "PGH", # pygrep-hooks
  "PT",  # flake8-pytest-style
  "Q",   # flake8-quotes
  "RET", # flake8-raise
  "SIM", # flake8-simplify
  "T20", # flake8-print
  "TID", # flake-8-tidy-imports
  "UP",  # pyupgrade
  "W",   # pycodestyle
]
lint.ignore = [
  # Do not perform function calls in argument defaults.
  "B008",
  # Missing docstring in public module
  "D100",
  # Missing docstring in public package
  "D104",
  # Missing docstring in magic method
  "D105",
  # Missing docstring in __init__
  "D107",
  # 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",
]
lint.per-file-ignores."*/__init__.py" = [ "D104", "D107", "E402", "F401" ]
lint.per-file-ignores."docs/*" = [ "A", "B", "D", "E" ]
lint.per-file-ignores."src/spatialdata_plot/pl/utils.py" = [ "PGH003" ]
lint.per-file-ignores."tests/*" = [ "B024", "D", "PT" ]
lint.per-file-ignores."tests/conftest.py" = [ "E402", "RET504" ]
lint.unfixable = [ "B", "BLE", "C4", "RET", "T20", "UP" ]
lint.pydocstyle.convention = "numpy"

[tool.pytest]
ini_options.testpaths = [ "tests" ]
ini_options.xfail_strict = true
ini_options.addopts = [
  # "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
  "-s",                      # print output from tests
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
ini_options.filterwarnings = [
  # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.coverage]
run.branch = true
run.omit = [
  "**/test_*.py",
]
run.parallel = true
run.source = [ "spatialdata_plot" ]
paths.source = [
  "src/spatialdata_plot",
  "*/site-packages/spatialdata_plot",
]

[tool.jupytext]
formats = "ipynb,md"

[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",
]

[tool.pixi]
dependencies.python = ">=3.11"
# 3.11 lane (for gh-actions)
environments.dev-py311 = { features = [ "dev", "test", "py311" ], solve-group = "py311" }
environments.docs-py311 = { features = [ "doc", "py311" ], solve-group = "py311" }
# 3.13 lane
environments.default = { features = [ "py313" ], solve-group = "py313" }
environments.dev-py313 = { features = [ "dev", "test", "py313" ], solve-group = "py313" }
environments.docs-py313 = { features = [ "doc", "py313" ], solve-group = "py313" }
environments.test-py313 = { features = [ "test", "py313" ], solve-group = "py313" }
# for gh-actions
feature.py311.dependencies.python = "3.11.*"
feature.py313.dependencies.python = "3.13.*"
pypi-dependencies.spatialdata-plot = { path = ".", editable = true }
tasks.lab = "jupyter lab"
tasks.kernel-install = 'python -m ipykernel install --user --name pixi-dev --display-name "sdata-plot (dev)"'
tasks.test = "pytest -v --color=yes --tb=short --durations=10"
tasks.lint = "ruff check ."
tasks.format = "ruff format ."
tasks.pre-commit-install = "pre-commit install"
tasks.pre-commit-run = "pre-commit run --all-files"
workspace.channels = [ "conda-forge" ]
workspace.platforms = [ "osx-arm64", "linux-64" ]