Merge branch 'main' into ig/parallel_kernels

Author: flying-sheep

.pre-commit-config.yaml

@@ -6,25 +6,21 @@ repos:
   - id: trailing-whitespace
   - id: no-commit-to-branch
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.14
+  rev: v0.15.4
   hooks:
   - id: ruff-check
     args: [--fix, --exit-non-zero-on-fix]
   - id: ruff-check
     args: [--preview, --select=CPY]
   - id: ruff-format
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: v2.12.1
+  rev: v2.16.2
   hooks:
   - id: pyproject-fmt
 - repo: https://github.com/biomejs/pre-commit
-  rev: v2.3.10
+  rev: v2.4.4
   hooks:
   - id: biome-format
-- repo: https://github.com/H4rryK4ne/update-mypy-hook
-  rev: v0.3.0
-  hooks:
-  - id: update-mypy-hook
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v1.19.1
   hooks:
@@ -33,77 +29,20 @@ repos:
     pass_filenames: false
     language_version: '3.13'
     additional_dependencies:
-    - alabaster==1.0.0
-    - anndata==0.12.7
-    - array-api-compat==1.13.0
-    - babel==2.17.0
-    - certifi==2026.1.4
-    - cffi==2.0.0
-    - charset-normalizer==3.4.4
-    - click==8.3.1
-    - cloudpickle==3.1.2
-    - colorama==0.4.6 ; sys_platform == 'win32'
-    - coverage==7.13.1
-    - dask==2026.1.1
-    - docutils==0.22.4
-    - donfig==0.8.1.post1
-    - execnet==2.1.2
-    - fsspec==2026.1.0
-    - google-crc32c==1.8.0
-    - h5py==3.15.1
-    - idna==3.11
-    - imagesize==1.4.1
-    - iniconfig==2.3.0
-    - jinja2==3.1.6
-    - joblib==1.5.3
-    - legacy-api-wrap==1.5
-    - llvmlite==0.46.0
-    - locket==1.0.0
-    - markdown-it-py==4.0.0
-    - markupsafe==3.0.3
-    - mdurl==0.1.2
-    - natsort==8.4.0
-    - numba==0.63.1
-    - numcodecs==0.16.5
-    - numpy==2.3.5
-    - numpy-typing-compat==20251206.2.3
-    - optype==0.15.0
-    - packaging==25.0
-    - pandas==2.3.3
-    - partd==1.4.2
-    - pluggy==1.6.0
-    - pycparser==2.23 ; implementation_name != 'PyPy'
-    - pygments==2.19.2
-    - pytest==9.0.2
-    - pytest-codspeed==4.2.0
-    - pytest-doctestplus==1.7.0
-    - pytest-xdist==3.8.0
-    - python-dateutil==2.9.0.post0
-    - pytz==2025.2
-    - pyyaml==6.0.3
-    - requests==2.32.5
-    - rich==14.2.0
-    - roman-numerals==4.1.0
-    - scikit-learn==1.8.0
-    - scipy==1.17.0
-    - scipy-stubs==1.17.0.1
-    - six==1.17.0
-    - snowballstemmer==3.0.1
-    - sphinx==9.1.0
-    - sphinxcontrib-applehelp==2.0.0
-    - sphinxcontrib-devhelp==2.0.0
-    - sphinxcontrib-htmlhelp==2.1.0
-    - sphinxcontrib-jsmath==1.0.1
-    - sphinxcontrib-qthelp==2.0.0
-    - sphinxcontrib-serializinghtml==2.0.0
-    - threadpoolctl==3.6.0
-    - toolz==1.1.0
-    - types-docutils==0.22.3.20251115
-    - tzdata==2025.3
-    - urllib3==2.6.3
-    - zarr==3.1.5
+    - anndata>=0.12
+    - array-api-compat>=1.13
+    - dask>=2026.1
+    - h5py>=3.15
+    - numba>=0.63
+    - packaging>=26
+    - pytest>=9
+    - pytest-codspeed>=4.3
+    - scikit-learn>=1.8
+    - scipy-stubs>=1.17
+    - sphinx>=9
+    - types-docutils>=0.22
+    - zarr>=3.1
 ci:
   autoupdate_commit_msg: 'ci: pre-commit autoupdate'
   skip:
   - mypy  # too big
-  - update-mypy-hook  # offline?

pyproject.toml

@@ -29,9 +29,9 @@ optional-dependencies.dask = [ "dask>=2023.6.1" ]
 optional-dependencies.full = [ "fast-array-utils[accel,dask,sparse]", "h5py", "zarr" ]
 optional-dependencies.sparse = [ "scipy>=1.13" ]
 optional-dependencies.testing = [ "packaging" ]
-urls.'Documentation' = "https://icb-fast-array-utils.readthedocs-hosted.com/"
-urls.'Issue Tracker' = "https://github.com/scverse/fast-array-utils/issues"
-urls.'Source Code' = "https://github.com/scverse/fast-array-utils"
+urls."Documentation" = "https://icb-fast-array-utils.readthedocs-hosted.com/"
+urls."Issue Tracker" = "https://github.com/scverse/fast-array-utils/issues"
+urls."Source Code" = "https://github.com/scverse/fast-array-utils"
 entry-points.pytest11.fast_array_utils = "testing.fast_array_utils.pytest"
 
 [dependency-groups]
@@ -42,6 +42,12 @@ test = [
   "zarr",
   { include-group = "test-min" },
 ]
+doc = [
+  "furo>=2024.8.6",
+  "pytest>=8.4",
+  "sphinx>=9.0.1",
+  "sphinx-autofixture>=0.4.1",
+]
 test-min = [
   "coverage[toml]",
   "fast-array-utils[sparse,testing]", # include sparse for testing numba-less to_dense
@@ -50,73 +56,40 @@ test-min = [
   "pytest-doctestplus",
   "pytest-xdist",
 ]
-doc = [
-  "furo>=2024.8.6",
-  "pytest>=8.4",
-  "sphinx>=9.0.1",
-  "sphinx-autofixture>=0.4.1",
-]
-# for update-mypy-hook
-mypy = [
-  "fast-array-utils[full]",
-  "scipy-stubs",
-  # TODO: replace sphinx with this: { include-group = "doc" },
-  "sphinx",
-  "types-docutils",
-  { include-group = "test" },
-]
 
-[tool.hatch.build.targets.wheel]
-packages = [ "src/testing", "src/fast_array_utils" ]
-
-[tool.hatch.envs.default]
-installer = "uv"
-
-[tool.hatch.envs.docs]
-dependency-groups = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build"
-scripts.clean = "git clean -fdX docs"
-scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
-
-[tool.hatch.envs.hatch-test]
-default-args = [  ]
-dependency-groups = [ "test-min" ]
+[tool.hatch]
+build.targets.wheel.packages = [ "src/testing", "src/fast_array_utils" ]
+envs.default.installer = "uv"
+envs.docs.dependency-groups = [ "doc" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build"
+envs.docs.scripts.clean = "git clean -fdX docs"
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.hatch-test.default-args = []
+envs.hatch-test.dependency-groups = [ "test-min" ]
 # TODO: remove scipy once https://github.com/pypa/hatch/pull/2127 is released
-extra-dependencies = [ "ipykernel", "ipycytoscape", "scipy" ]
-env-vars.CODSPEED_PROFILE_FOLDER = "test-data/codspeed"
-overrides.matrix.extras.features = [
+envs.hatch-test.extra-dependencies = [ "ipykernel", "ipycytoscape", "scipy" ]
+envs.hatch-test.env-vars.CODSPEED_PROFILE_FOLDER = "test-data/codspeed"
+envs.hatch-test.overrides.matrix.extras.features = [
   { if = [ "full" ], value = "full" },
 ]
-overrides.matrix.extras.dependency-groups = [
+envs.hatch-test.overrides.matrix.extras.dependency-groups = [
   { if = [ "full" ], value = "test" },
 ]
-overrides.matrix.resolution.dependencies = [
+envs.hatch-test.overrides.matrix.resolution.dependencies = [
   # TODO: move to `min-reqs` feature once this is fixed: https://github.com/tlambert03/hatch-min-requirements/issues/11
   { if = [ "lowest" ], value = "numpy==2" },
   { if = [ "lowest" ], value = "dask==2023.6.1" },
   { if = [ "lowest" ], value = "scipy==1.13.0" },
 ]
-
-[[tool.hatch.envs.hatch-test.matrix]]
-python = [ "3.13", "3.12" ]
-extras = [ "full", "min" ]
-
-[[tool.hatch.envs.hatch-test.matrix]]
-python = [ "3.12" ]
-extras = [ "full" ]
-resolution = [ "lowest" ]
-
-[tool.hatch.metadata.hooks.docstring-description]
-
-[tool.hatch.metadata.hooks.fancy-pypi-readme]
-content-type = "text/x-rst"
-[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
-path = "README.rst"
-start-after = ".. begin"
-
-[tool.hatch.version]
-source = "vcs"
-raw-options = { local_scheme = "no-local-version" } # be able to publish dev version
+envs.hatch-test.matrix = [
+  { python = [ "3.13", "3.12" ], extras = [ "full", "min" ] },
+  { python = [ "3.12" ], extras = [ "full" ], resolution = [ "lowest" ] },
+]
+metadata.hooks.docstring-description = {}
+metadata.hooks.fancy-pypi-readme.content-type = "text/x-rst"
+metadata.hooks.fancy-pypi-readme.fragments = [ { path = "README.rst", start-after = ".. begin" } ]
+version.source = "vcs"
+version.raw-options = { local_scheme = "no-local-version" }  # be able to publish dev version
 
 [tool.uv]
 override-dependencies = [ "sphinx>=9.0.1" ]
@@ -141,20 +114,23 @@ lint.ignore = [
   "S101",    # asserts are fine
   "TID252",  # relative imports are fine
 ]
-lint.per-file-ignores."docs/**/*.py" = [ "INP001" ] # No __init__.py in docs
-lint.per-file-ignores."src/**/stats/*.py" = [ "A001", "A004" ] # Shadows builtins like `sum`
+# No __init__.py in docs
+lint.per-file-ignores."docs/**/*.py" = [ "INP001" ]
+# Shadows builtins like `sum`
+lint.per-file-ignores."src/**/stats/*.py" = [ "A001", "A004" ]
 lint.per-file-ignores."tests/**/*.py" = [
   "D100",    # tests need no module docstrings
   "D103",    # tests need no function docstrings
   "INP001",  # tests should not have __init__.py
   "PLR2004", # tests use magic values
   "S101",    # tests use `assert`
 ]
-lint.per-file-ignores."typings/**/*.pyi" = [ "A002", "F403", "F405", "N801" ] # Stubs don’t follow name conventions
+# Stubs don’t follow name conventions
+lint.per-file-ignores."typings/**/*.pyi" = [ "A002", "F403", "F405", "N801" ]
 lint.allowed-confusables = [ "×", "’" ]
 lint.flake8-bugbear.extend-immutable-calls = [ "testing.fast_array_utils.Flags" ]
 lint.flake8-copyright.notice-rgx = "SPDX-License-Identifier: MPL-2\\.0"
-lint.flake8-type-checking.exempt-modules = [  ]
+lint.flake8-type-checking.exempt-modules = []
 lint.flake8-type-checking.strict = true
 lint.isort.known-first-party = [ "fast_array_utils" ]
 lint.isort.lines-after-imports = 2
@@ -183,10 +159,10 @@ markers = [
 
 [tool.coverage]
 run.data_file = "test-data/.coverage"
-xml.output = "test-data/coverage.xml"
-html.directory = "test-data/htmlcov"
 run.omit = [ "src/testing/*", "tests/*" ]
-report.exclude_also = [ "if TYPE_CHECKING:", "@numba[.]njit", "[.]{3}" ]
+report.exclude_also = [ "@numba[.]njit", "[.]{3}", "if TYPE_CHECKING:" ]
+html.directory = "test-data/htmlcov"
+xml.output = "test-data/coverage.xml"
 
 [tool.mypy]
 strict = true

src/testing/fast_array_utils/_array_type.py

@@ -317,7 +317,7 @@ def _to_scipy_sparse(
             x = to_dense(x, to_cpu_memory=True)
 
         cls = cast("type[types.CSBase]", cls or self.cls)
-        return cls(x, dtype=dtype)  # type: ignore[arg-type]
+        return cls(x, dtype=dtype)  # type: ignore[arg-type,misc]
 
     def _to_cupy_array(self, x: ArrayLike | Array, /, *, dtype: DTypeLike | None = None) -> types.CupyArray:
         import cupy as cu