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timtreistimtreis
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switched install to pixi
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‎pyproject.toml‎

Lines changed: 168 additions & 80 deletions
Original file line numberDiff line numberDiff line change
@@ -1,83 +1,145 @@
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[build-system]
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build-backend = "hatchling.build"
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requires = ["hatchling", "hatch-vcs"]
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requires = ["hatchling", "hatch-vcs", "hatch-fancy-pypi-readme"]
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[project]
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name = "spatialdata-plot"
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dynamic = ["readme", "version"]
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description = "Static plotting for spatial data."
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requires-python = ">=3.11"
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license = "BSD-3-Clause"
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classifiers = [
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"Development Status :: 4 - Beta",
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"Intended Audience :: Science/Research",
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"Natural Language :: English",
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"Operating System :: POSIX :: Linux",
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"Operating System :: MacOS :: MacOS X",
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"Typing :: Typed",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Environment :: Console",
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"Framework :: Jupyter",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"Topic :: Scientific/Engineering :: Visualization",
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]
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keywords = [
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"spatial omics",
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"spatial data analysis",
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"visualization",
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"plotting",
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"bio-informatics",
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"single-cell",
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]
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authors = [
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{name = "scverse"},
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{name = "Tim Treis"},
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{name = "Wouter-Michiel Vierdag"},
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{name = "Sonja Stockhaus"},
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]
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maintainers = [
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{name = "scverse", email = "tim.treis@helmholtz-munich.de"},
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]
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urls.Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/index.html"
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urls.Source = "https://github.com/scverse/spatialdata-plot.git"
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urls.Home-page = "https://github.com/scverse/spatialdata-plot.git"
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requires-python = ">=3.10"
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dynamic= [
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"version" # allow version to be set by git tags
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{name = "Tim Treis", email = "tim.treis@helmholtz-munich.de"},
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]
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license = {file = "LICENSE"}
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readme = "README.md"
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dependencies = [
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"spatialdata>=0.3.0",
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"matplotlib",
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"scikit-learn",
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"scanpy",
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"matplotlib_scalebar",
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"matplotlib>=3.3",
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"matplotlib-scalebar>=0.8.0",
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"scikit-learn>=0.24.0",
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"scanpy>=1.9.3",
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"numpy>=1.23.0",
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"pandas>=2.1.0",
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]
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[project.optional-dependencies]
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dev = [
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"bump2version",
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"pre-commit>=3.0.0",
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"hatch>=1.9.0",
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"jupyterlab",
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"notebook",
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"ipykernel",
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"ipywidgets",
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"jupytext",
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"pytest",
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"pytest-cov",
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"ruff",
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]
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test = [
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"pytest>=7",
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"pytest-xdist>=3",
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"pytest-mock>=3.5.0",
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"pytest-cov>=4",
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"coverage[toml]>=7",
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"pytest-timeout>=2.1.0",
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"pooch", # for scipy.datasets module
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]
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docs = [
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"sphinx>=4.5",
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"ipython>=8.6.0",
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"ipywidgets>=8.0.0",
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"sphinx>=5.3",
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"sphinx-autodoc-annotation",
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"sphinx-autodoc-typehints>=1.10.3",
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"sphinx-book-theme>=1.0.0",
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"sphinx_rtd_theme",
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"myst-nb",
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"sphinxcontrib-bibtex>=1.0.0",
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"sphinx-autodoc-typehints",
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"sphinxcontrib-bibtex>=2.3.0",
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"myst-nb>=0.17.1",
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"sphinx-design",
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# For notebooks
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"ipython>=8.6.0",
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"sphinx-copybutton",
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]
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test = [
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"pytest",
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"pytest-cov",
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"pooch", # for scipy.datasets module
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"sphinx-copybutton>=0.5.0",
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]
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# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
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pre = [
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"spatialdata>=0.1.0-pre0"
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]
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[project.urls]
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Homepage = "https://github.com/scverse/spatialdata-plot"
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"Bug Tracker" = "https://github.com/scverse/spatialdata-plot/issues"
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Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/index.html"
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"Source Code" = "https://github.com/scverse/spatialdata-plot"
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57100
[tool.coverage.run]
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branch = true
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parallel = true
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source = ["spatialdata_plot"]
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omit = [
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"*/__init__.py",
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"*/_version.py",
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"**/test_*.py",
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]
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[tool.coverage.paths]
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source = [
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"spatialdata_plot",
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"*/site-packages/spatialdata_plot",
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]
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[tool.coverage.report]
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exclude_lines = [
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"\\#.*pragma:\\s*no.?cover",
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"^if __name__ == .__main__.:$",
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"^\\s*raise AssertionError\\b",
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"^\\s*raise NotImplementedError\\b",
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"^\\s*return NotImplemented\\b",
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]
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show_missing = true
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precision = 2
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skip_empty = true
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sort = "Miss"
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63129
[tool.pytest.ini_options]
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testpaths = ["tests"]
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xfail_strict = true
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addopts = [
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# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
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"--import-mode=importlib", # allow using test files with same name
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"-s" # print output from tests
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]
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# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
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filterwarnings = [
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# "ignore:.*U.*mode is deprecated:DeprecationWarning",
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"ignore::UserWarning",
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"ignore::DeprecationWarning",
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]
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[tool.jupytext]
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formats = "ipynb,md"
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[tool.hatch.build.targets.wheel]
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packages = ['src/spatialdata_plot']
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packages = ["src/spatialdata_plot"]
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[tool.hatch.version]
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source = "vcs"
@@ -88,6 +150,11 @@ version-file = "_version.py"
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[tool.hatch.metadata]
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allow-direct-references = true
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[tool.hatch.metadata.hooks.fancy-pypi-readme]
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content-type = "text/markdown"
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[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
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path = "README.md"
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[tool.ruff]
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line-length = 120
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exclude = [
@@ -97,76 +164,97 @@ exclude = [
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"build",
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"docs/_build",
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"dist",
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"setup.py",
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"setup.py"
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]
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[tool.ruff.format]
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docstring-code-format = true
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102173
[tool.ruff.lint]
103174
ignore = [
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# line too long -> we accept long comment lines; formatter gets rid of long code lines
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"E501",
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# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
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"E731",
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# allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
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"E741",
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# Missing docstring in public package
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"D104",
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# ... imported but unused
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"F401",
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# Missing docstring in public module
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"D100",
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# Missing docstring in __init__
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"D107",
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# Missing docstring in magic method
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"D105",
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# Do not perform function calls in argument defaults.
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"B008",
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# Missing docstring in magic method
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"D105",
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# Missing blank line before section
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"D411",
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# B024 Do not use `__class__` for string comparisons.
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"B024",
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]
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select = [
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"D", # flake8-docstrings
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"I", # isort
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"E", # pycodestyle
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"F", # pyflakes
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"W", # pycodestyle
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"Q", # flake8-quotes
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"SIM", # flake8-simplify
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"TID", # flake-8-tidy-imports
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"NPY", # NumPy-specific rules
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"PT", # flake8-pytest-style
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"B", # flake8-bugbear
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# below are not autofixed
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"UP", # pyupgrade
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"C4", # flake8-comprehensions
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"B", # flake8-bugbear
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"BLE", # flake8-blind-except
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"T20", # flake8-print
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"RET", # flake8-raise
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"PGH", # pygrep-hooks
139208
]
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unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
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unfixable = ["B", "C4", "BLE"]
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[tool.ruff.lint.isort]
212+
required-imports = ["from __future__ import annotations"]
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142214
[tool.ruff.lint.per-file-ignores]
143-
"tests/*" = ["D", "PT", "B024"]
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"*/__init__.py" = ["F401", "D104", "D107", "E402"]
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"docs/*" = ["D","B","E","A"]
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# "src/spatialdata/transformations/transformations.py" = ["D101","D102", "D106", "B024", "T201", "RET504"]
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"tests/conftest.py"= ["E402", "RET504"]
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"src/spatialdata_plot/pl/utils.py"= ["PGH003"]
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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[tool.bumpver]
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current_version = "0.0.2"
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version_pattern = "MAJOR.MINOR.PATCH"
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commit_message = "bump version {old_version} -> {new_version}"
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tag_message = "{new_version}"
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tag_scope = "default"
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pre_commit_hook = ""
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post_commit_hook = ""
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commit = true
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tag = true
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push = false
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[tool.bumpver.file_patterns]
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"pyproject.toml" = [
167-
'current_version = "{version}"',
168-
]
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"README.md" = [
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"{version}",
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"{pep440_version}",
172-
]
215+
"*/__init__.py" = ["D104", "F401"]
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"tests/*" = ["D"]
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"docs/*" = ["D", "B"]
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"src/spatialdata_plot/pl/utils.py" = ["PGH003"]
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[tool.ruff.lint.flake8-tidy-imports]
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# Disallow all relative imports.
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ban-relative-imports = "all"
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[tool.pixi.workspace]
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channels = ["conda-forge"]
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platforms = ["osx-arm64", "linux-64"]
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228+
[tool.pixi.dependencies]
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python = ">=3.11"
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231+
[tool.pixi.pypi-dependencies]
232+
spatialdata-plot = { path = ".", editable = true }
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# for gh-actions
235+
[tool.pixi.feature.py311.dependencies]
236+
python = "3.11.*"
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238+
[tool.pixi.feature.py313.dependencies]
239+
python = "3.13.*"
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241+
[tool.pixi.environments]
242+
# 3.11 lane
243+
dev-py311 = { features = ["dev", "test", "py311"], solve-group = "py311" }
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docs-py311 = { features = ["docs", "py311"], solve-group = "py311" }
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test-py311 = { features = ["test", "py311"], solve-group = "py311" }
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# 3.13 lane
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default = { features = ["py313"], solve-group = "py313" }
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dev-py313 = { features = ["dev", "test", "py313"], solve-group = "py313" }
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docs-py313 = { features = ["docs", "py313"], solve-group = "py313" }
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test-py313 = { features = ["test", "py313"], solve-group = "py313" }
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[tool.pixi.tasks]
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lab = "jupyter lab"
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kernel-install = "python -m ipykernel install --user --name pixi-dev --display-name \"spatialdata-plot (dev)\""
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test = "pytest -v --color=yes --tb=short --durations=10"
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lint = "ruff check ."
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format = "ruff format ."
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pre-commit-install = "pre-commit install"
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pre-commit-run = "pre-commit run --all-files"

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