[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

@@ -26,8 +26,8 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
 ]
-
 dynamic = [ "version" ]
 dependencies = [
   "adjusttext",
@@ -46,7 +46,6 @@ dependencies = [
   "scipy<1.16",           # see https://github.com/statsmodels/statsmodels/issues/9584
   "session-info",
 ]
-
 optional-dependencies.dev = [
   "furo",
   "myst-nb",
@@ -67,7 +66,7 @@ optional-dependencies.docs = [
   "myst-nb>=1.1",
   "pandas",
   "scvi-tools>=1.3.1",
-  "setuptools",               # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+  "setuptools",                      # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
   "sphinx>=8",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
@@ -99,23 +98,19 @@ optional-dependencies.test = [
   "pytest-split",
   "pytest-xdist>=3",
 ]
-
 urls.Documentation = "https://cellflow.readthedocs.io/"
 urls.Home-page = "https://github.com/theislab/cellflow"
 urls.Source = "https://github.com/theislab/cellflow"
 
-[tool.hatch.build.targets.wheel]
-packages = [ 'src/cellflow' ]
-
-[tool.hatch.version]
-source = "vcs"
-fallback-version = "0.1.0"
+[tool.hatch]
+build.targets.wheel.packages = [ "src/cellflow" ]
+version.source = "vcs"
+version.fallback-version = "0.1.0"
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
 lint.select = [
   "B",      # flake8-bugbear
@@ -162,35 +157,59 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
-testpaths = [ "tests" ]
-xfail_strict = true
-addopts = [
+[tool.mypy]
+mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
+python_version = "3.11"
+plugins = "numpy.typing.mypy_plugin"
+ignore_errors = false
+warn_redundant_casts = true
+warn_unused_configs = true
+warn_unused_ignores = true
+disallow_untyped_calls = false
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+disallow_any_generics = true
+strict_optional = true
+strict_equality = true
+warn_return_any = false
+warn_unreachable = false
+check_untyped_defs = true
+no_implicit_optional = true
+no_implicit_reexport = true
+no_warn_no_return = true
+show_error_codes = true
+show_column_numbers = true
+error_summary = true
+ignore_missing_imports = true
+disable_error_code = [ "assignment", "comparison-overlap", "no-untyped-def", "override" ]
+
+[tool.pytest]
+ini_options.testpaths = [ "tests" ]
+ini_options.xfail_strict = true
+ini_options.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
-markers = [
+ini_options.markers = [
   "slow: marks tests as slow (deselect with '-m \"not slow\"')",
   "internet: marks tests that require internet access (deselect with '-m \"not internet\"')",
 ]
 
-[tool.coverage.run]
-branch = true
-source = [ "src/" ]
-concurrency = [ "multiprocessing" ]
-parallel = "true"
-
-[tool.coverage.report]
-exclude_lines = [
-  '\#.*pragma:\s*no.?cover',
+[tool.coverage]
+run.branch = true
+run.concurrency = [ "multiprocessing" ]
+run.parallel = "true"
+run.source = [ "src/" ]
+report.exclude_lines = [
+  "\\#.*pragma:\\s*no.?cover",
+  "^\\s*raise AssertionError\\b",
+  "^\\s*raise NotImplementedError\\b",
+  "^\\s*return NotImplemented\\b",
   "^if __name__ == .__main__.:$",
-  '^\s*raise AssertionError\b',
-  '^\s*raise NotImplementedError\b',
-  '^\s*return NotImplemented\b',
 ]
-precision = 2
-show_missing = true
-skip_empty = true
-sort = "Miss"
+report.precision = 2
+report.show_missing = true
+report.skip_empty = true
+report.sort = "Miss"
 
 [tool.tox]
 legacy_tox_ini = """
@@ -286,38 +305,6 @@ commands = biber --tool --output_file={tox_root}{/}docs{/}references.bib --nolog
     {tox_root}{/}docs{/}references.bib
 """
 
-[tool.mypy]
-mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
-python_version = "3.11"
-plugins = "numpy.typing.mypy_plugin"
-
-ignore_errors = false
-
-warn_redundant_casts = true
-warn_unused_configs = true
-warn_unused_ignores = true
-
-disallow_untyped_calls = false
-disallow_untyped_defs = true
-disallow_incomplete_defs = true
-disallow_any_generics = true
-
-strict_optional = true
-strict_equality = true
-warn_return_any = false
-warn_unreachable = false
-check_untyped_defs = true
-no_implicit_optional = true
-no_implicit_reexport = true
-no_warn_no_return = true
-
-show_error_codes = true
-show_column_numbers = true
-error_summary = true
-ignore_missing_imports = true
-
-disable_error_code = [ "assignment", "comparison-overlap", "no-untyped-def", "override" ]
-
 [tool.cruft]
 skip = [
   "tests",