Use pixi for CI/CD

.github/workflows/test.yaml

@@ -49,6 +49,7 @@ jobs:
           pip install pytest-cov
       - name: Install dependencies
         run: |
+          pip install numpy
           pip install --pre -e ".[dev,test,pre]"
       - name: Test
         env:

pyproject.toml

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