[pre-commit.ci] pre-commit autoupdate (#550)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.10
+    rev: v2.4.7
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.11.1
+    rev: v2.18.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.5
+    rev: v0.15.6
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

pyproject.toml

@@ -31,7 +31,6 @@ dependencies = [
   "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"
@@ -62,51 +61,29 @@ doc = [
   "sphinxext-opengraph",
 ]
 
-[tool.hatch.build.targets.wheel]
-packages = [ 'src/spatialdata_plot' ]
-
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.build.hooks.vcs]
-version-file = "_version.py"
-
-[tool.hatch.metadata]
-allow-direct-references = true
-
-[tool.hatch.envs.default]
-installer = "uv"
-dependency-groups = [ "dev" ]
-
-[tool.hatch.envs.docs]
-dependency-groups = [ "doc" ]
-
-[tool.hatch.envs.docs.scripts]
-build = "sphinx-build -M html docs docs/_build -W {args}"
-open = "python -m webbrowser -t docs/_build/html/index.html"
-clean = "git clean -fdX -- {args:docs}"
-
-[tool.hatch.envs.hatch-test]
-dependency-groups = [ "test" ]
-
-[tool.hatch.envs.hatch-test.scripts]
-run = "pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
-run-cov = "coverage run -m pytest{env:HATCH_TEST_ARGS:} -p no:cov {args}"
-cov-combine = "coverage combine"
-cov-report = [ "coverage report", "coverage xml -o coverage.xml" ]
-
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "stable" ]
-python = [ "3.11", "3.14" ]
-
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "pre" ]
-python = [ "3.14" ]
-
-[tool.hatch.envs.hatch-test.overrides]
-matrix.deps.env-vars = [
+[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
@@ -154,42 +131,35 @@ lint.ignore = [
   # 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" ]
-xfail_strict = true
-addopts = [
-  #    "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+[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
-filterwarnings = [
-  #     "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ini_options.filterwarnings = [
+  # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
-[tool.coverage.run]
-source = [ "spatialdata_plot" ]
-branch = true
-parallel = true
-omit = [
+[tool.coverage]
+run.branch = true
+run.omit = [
   "**/test_*.py",
 ]
-
-[tool.coverage.paths]
-source = [
+run.parallel = true
+run.source = [ "spatialdata_plot" ]
+paths.source = [
   "src/spatialdata_plot",
   "*/site-packages/spatialdata_plot",
 ]
@@ -209,39 +179,26 @@ skip = [
   "docs/notebooks/example.ipynb",
 ]
 
-[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]
+[tool.pixi]
+dependencies.python = ">=3.11"
 # 3.11 lane (for gh-actions)
-dev-py311 = { features = [ "dev", "test", "py311" ], solve-group = "py311" }
-docs-py311 = { features = [ "doc", "py311" ], solve-group = "py311" }
-
+environments.dev-py311 = { features = [ "dev", "test", "py311" ], solve-group = "py311" }
+environments.docs-py311 = { features = [ "doc", "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 = [ "doc", "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 \"sdata-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"
+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" ]