[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

pyproject.toml

@@ -73,52 +73,37 @@ optional-dependencies.tutorials = [
   "sopa>=2",
   "squidpy>=1.6",
 ]
-
 # https://docs.pypi.org/project_metadata/#project-urls
 urls.Documentation = "https://cellmapper.readthedocs.io/"
 urls.Homepage = "https://github.com/quadbio/cellmapper"
 urls.Source = "https://github.com/quadbio/cellmapper"
 
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.envs.default]
-installer = "uv"
-features = [ "dev" ]
-
-[tool.hatch.envs.docs]
-features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build {args}"
-scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
-scripts.clean = "git clean -fdX -- {args:docs}"
-
-# Test the lowest and highest supported Python versions with normal deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "stable" ]
-python = [ "3.11", "3.14" ]
-
-# Test the newest supported Python version also with pre-release deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "pre" ]
-python = [ "3.14" ]
-
-[tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
-
-[tool.hatch.envs.hatch-test.overrides]
+[tool.hatch]
+envs.default.installer = "uv"
+envs.default.features = [ "dev" ]
+envs.docs.features = [ "doc" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build {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.features = [ "dev", "test" ]
+envs.hatch-test.matrix = [
+  # Test the lowest and highest supported Python versions with normal deps
+  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
+  # Test the newest supported Python version also with pre-release deps
+  { deps = [ "pre" ], python = [ "3.14" ] },
+]
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
-matrix.deps.env-vars = [
+envs.hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
+version.source = "vcs"
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -159,12 +144,12 @@ addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
 
-[tool.coverage.run]
-source = [ "cellmapper" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
+run.source = [ "cellmapper" ]
 
 [tool.cruft]
 skip = [