[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
   # Hooks that are run everywhere
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.0.0-beta.5
+    rev: v2.3.15
     hooks:
       - id: biome-format
   # Hooks that are run for scripts
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.6.0
+    rev: v2.16.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.11
+    rev: v0.15.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

pyproject.toml

@@ -8,26 +8,26 @@ description = "Modeling complex perturbations with flow matching at single-cell
 readme = "README.md"
 license = "PolyForm-Noncommercial-1.0.0"
 maintainers = [
-  { name = "Dominik Klein" },
-  { name = "Selman Oezleyen" },
-  { name = "Jonas Simon Fleck" },
   { name = "Daniil Bobrovskiy" },
+  { name = "Dominik Klein" },
   { name = "Guillaume Huguet" },
+  { name = "Jonas Simon Fleck" },
+  { name = "Selman Oezleyen" },
 ]
 authors = [
-  { name = "Dominik Klein" },
-  { name = "Jonas Simon Fleck" },
   { name = "Daniil Bobrovskiy" },
+  { name = "Dominik Klein" },
   { name = "Guillaume Huguet" },
+  { name = "Jonas Simon Fleck" },
 ]
 requires-python = ">=3.11"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
 ]
-
 dynamic = [ "version" ]
 dependencies = [
   "adjusttext",
@@ -45,7 +45,6 @@ dependencies = [
   "scipy<1.16",          # see https://github.com/statsmodels/statsmodels/issues/9584
   "session-info",
 ]
-
 optional-dependencies.dev = [
   "furo",
   "myst-nb",
@@ -66,7 +65,7 @@ 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",
@@ -97,23 +96,19 @@ optional-dependencies.test = [
   "pytest-mock>=3.5",
   "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
@@ -160,34 +155,32 @@ 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.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\"')",
 ]
 
-[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 = """
@@ -287,18 +280,14 @@ commands = biber --tool --output_file={tox_root}{/}docs{/}references.bib --nolog
 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
@@ -307,12 +296,10 @@ 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]