Merge branch 'main' into array-api-implementation

Author: amalia-k510

.github/workflows/ci.yml

@@ -46,8 +46,8 @@ jobs:
         os: [ubuntu-latest]
         include:
           - env:
-              name: hatch-test.py3.13-full
-              python: "3.13"
+              name: hatch-test.py3.14-full
+              python: "3.14"
             os: macos-latest
     steps:
       - uses: actions/checkout@v6
@@ -77,7 +77,7 @@ jobs:
         with: { fetch-depth: 0, filter: "blob:none" }
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: '3.14'
       - uses: astral-sh/setup-uv@v7
       - run: uv pip install --system --group=test -e .[full]
       - uses: CodSpeedHQ/action@v3
@@ -92,7 +92,7 @@ jobs:
         with: { fetch-depth: 0, filter: "blob:none" }
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: '3.14'
       - uses: astral-sh/setup-uv@v7
       - run: uv pip install --system -e .
       - run: python -c 'import fast_array_utils as fau; print(fau.__all__)'

.pre-commit-config.yaml

@@ -6,28 +6,27 @@ repos:
   - id: trailing-whitespace
   - id: no-commit-to-branch
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.6
+  rev: v0.15.11
   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: v2.18.1
+  rev: v2.21.1
   hooks:
   - id: pyproject-fmt
 - repo: https://github.com/biomejs/pre-commit
-  rev: v2.4.7
+  rev: v2.4.12
   hooks:
   - id: biome-format
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.19.1
+  rev: v1.20.1
   hooks:
   - id: mypy
     args: [--config-file=pyproject.toml, .]
     pass_filenames: false
-    language_version: '3.13'
     additional_dependencies:
     - anndata>=0.12
     - array-api-compat>=1.13

.readthedocs.yml

@@ -2,7 +2,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.13"
+    python: "3.14"
   jobs:
     create_environment:
       - asdf plugin add uv

.vscode/settings.json

@@ -17,4 +17,6 @@
     },
     "python.testing.pytestArgs": ["-vv", "--color=yes", "-m", "not benchmark"],
     "python.testing.pytestEnabled": true,
+    "python-envs.defaultEnvManager": "flying-sheep.hatch:hatch",
+    "python-envs.defaultPackageManager": "flying-sheep.hatch:hatch",
 }

docs/conf.py

@@ -71,6 +71,8 @@
     zarr=("https://zarr.readthedocs.io/en/stable/", None),
 )
 nitpick_ignore = [
+    ("py:class", "P"),
+    ("py:class", "R"),
     ("py:class", "Arr"),
     ("py:class", "Array"),
     ("py:class", "ToDType"),

docs/index.rst

@@ -7,6 +7,7 @@
    fast-array-utils <self>
    conv
    stats
+   numba
    typing
    testing
 

docs/numba.rst

@@ -0,0 +1,5 @@
+``fast_array_utils.numba``
+==========================
+
+.. automodule:: fast_array_utils.numba
+   :members:

pyproject.toml

@@ -84,7 +84,7 @@ envs.hatch-test.overrides.matrix.resolution.dependencies = [
   { if = [ "lowest" ], value = "scipy==1.13.0" },
 ]
 envs.hatch-test.matrix = [
-  { python = [ "3.13", "3.12" ], extras = [ "full", "min" ] },
+  { python = [ "3.14", "3.12" ], extras = [ "full", "min" ] },
   { python = [ "3.12" ], extras = [ "full" ], resolution = [ "lowest" ] },
 ]
 metadata.hooks.docstring-description = {}
@@ -139,6 +139,20 @@ lint.isort.lines-after-imports = 2
 lint.pydocstyle.convention = "numpy"
 lint.future-annotations = true
 
+[tool.mypy]
+strict = true
+# https://github.com/dask/dask/issues/8853
+implicit_reexport = true
+explicit_package_bases = true
+mypy_path = [ "$MYPY_CONFIG_FILE_DIR/typings", "$MYPY_CONFIG_FILE_DIR/src" ]
+
+[tool.pyright]
+stubPath = "./typings"
+reportPrivateUsage = false
+
+[tool.ty]
+environment.extra-paths = [ "./typings" ]
+
 [tool.pytest]
 strict = true
 addopts = [
@@ -151,38 +165,18 @@ testpaths = [ "./tests", "fast_array_utils" ]
 doctest_subpackage_requires = [
   "src/fast_array_utils/conv/scipy/* = scipy",
   "src/fast_array_utils/conv/scipy/_to_dense.py = numba",
+  "src/fast_array_utils/numba/* = numba",
   "src/fast_array_utils/stats/* = numba",
   "src/fast_array_utils/_plugins/dask.py = dask",
   "src/fast_array_utils/_plugins/numba_sparse.py = numba;scipy",
 ]
-filterwarnings = [
-  "error",
-  # codspeed seems to break this dtype added by h5py
-  "ignore:.*numpy[.]longdouble:UserWarning",
-  "ignore:FNV hashing is not implemented in Numba:UserWarning",
-]
 markers = [
   "benchmark: marks tests as benchmark (to run with `--codspeed`)",
 ]
 
 [tool.coverage]
 run.data_file = "test-data/.coverage"
 run.omit = [ "src/testing/*", "tests/*" ]
-report.exclude_also = [ "@numba[.]njit", "[.]{3}", "if TYPE_CHECKING:" ]
+report.exclude_also = [ "@(numba[.])?njit", "[.]{3}", "if TYPE_CHECKING:" ]
 html.directory = "test-data/htmlcov"
 xml.output = "test-data/coverage.xml"
-
-[tool.mypy]
-strict = true
-# https://github.com/dask/dask/issues/8853
-implicit_reexport = true
-explicit_package_bases = true
-mypy_path = [ "$MYPY_CONFIG_FILE_DIR/typings", "$MYPY_CONFIG_FILE_DIR/src" ]
-
-[[tool.mypy.overrides]]
-module = [ "jax", "jax.*" ]
-ignore_missing_imports = true
-
-[tool.pyright]
-stubPath = "./typings"
-reportPrivateUsage = false

src/fast_array_utils/__init__.py

@@ -8,17 +8,20 @@
     This submodule requires :doc:`numba <numba:index>` to be installed
     and contains statistics utilities.
 
+:mod:`fast_array_utils.numba`
+    This submodule contains numba utilities.
+
 :mod:`fast_array_utils.typing` and :mod:`fast_array_utils.types`
     These submodules contain types for annotations and checks, respectively.
     Stubs for these types are available even if the respective packages are not installed.
 """
 
 from __future__ import annotations
 
-from . import _plugins, conv, stats, types
+from . import _plugins, conv, numba, stats, types
 
 
-__all__ = ["conv", "stats", "types"]
+__all__ = ["conv", "numba", "stats", "types"]
 
 _plugins.patch_dask()
 _plugins.register_numba_sparse()

src/fast_array_utils/conv/scipy/_to_dense.py

@@ -5,6 +5,8 @@
 
 import numba
 
+from ...numba import njit
+
 
 if TYPE_CHECKING:
     from typing import Any
@@ -18,14 +20,14 @@
 __all__ = ["_to_dense_csc_numba", "_to_dense_csr_numba"]
 
 
-@numba.njit(cache=True)
+@njit
 def _to_dense_csc_numba(x: CSBase, out: NDArray[np.number[Any]]) -> None:
     for c in numba.prange(out.shape[1]):
         for i in range(x.indptr[c], x.indptr[c + 1]):
             out[x.indices[i], c] = x.data[i]
 
 
-@numba.njit(cache=True)
+@njit
 def _to_dense_csr_numba(x: CSBase, out: NDArray[np.number[Any]]) -> None:
     for r in numba.prange(out.shape[0]):
         for i in range(x.indptr[r], x.indptr[r + 1]):