chore(deps): autoupdate uv.lock

pyproject.toml

@@ -62,7 +62,7 @@ benchmark = [
 # Run unit tests with coverage assessment
 test = [
     "coreax[benchmark]",
-    "beartype>=0.19, !=0.20.1, !=0.20.2",
+    "beartype>=0.19",
     "pytest>=8",
     "pytest-cov>=6",
     "pytest-rerunfailures>=15",

requirements-doc.txt

@@ -1,7 +1,7 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --format requirements-txt --no-hashes --no-dev --no-editable --extra doc --output-file requirements-doc.txt
 .
-absl-py==2.2.2
+absl-py==2.3.0
     # via
     #   chex
     #   optax
@@ -29,7 +29,7 @@ beautifulsoup4==4.13.4
     #   sphinx-toolbox
 cachecontrol==0.14.3
     # via sphinx-toolbox
-certifi==2025.4.26
+certifi==2025.6.15
     # via
     #   requests
     #   sphinx-prompt
@@ -62,16 +62,14 @@ domdf-python-tools==3.10.0
     #   sphinx-toolbox
 equinox==0.11.10 ; python_full_version < '3.10'
     # via coreax
-equinox==0.12.1 ; python_full_version >= '3.10'
+equinox==0.12.2 ; python_full_version >= '3.10'
     # via coreax
 etils==1.5.2 ; python_full_version < '3.10'
     # via
     #   optax
     #   orbax-checkpoint
 etils==1.12.2 ; python_full_version >= '3.10'
-    # via
-    #   optax
-    #   orbax-checkpoint
+    # via orbax-checkpoint
 filelock==3.18.0
     # via
     #   cachecontrol
@@ -80,7 +78,7 @@ flax==0.8.5 ; python_full_version < '3.10'
     # via coreax
 flax==0.10.6 ; python_full_version >= '3.10'
     # via coreax
-fsspec==2025.3.2
+fsspec==2025.5.1
     # via etils
 furo==2024.8.6
     # via coreax
@@ -111,7 +109,7 @@ jax==0.4.30 ; python_full_version < '3.10'
     #   jaxopt
     #   optax
     #   orbax-checkpoint
-jax==0.6.0 ; python_full_version >= '3.10'
+jax==0.6.1 ; python_full_version >= '3.10'
     # via
     #   chex
     #   coreax
@@ -127,7 +125,7 @@ jaxlib==0.4.30 ; python_full_version < '3.10'
     #   jaxopt
     #   optax
     #   orbax-checkpoint
-jaxlib==0.6.0 ; python_full_version >= '3.10'
+jaxlib==0.6.1 ; python_full_version >= '3.10'
     # via
     #   chex
     #   jax
@@ -147,9 +145,9 @@ jinja2==3.1.6
     # via
     #   sphinx
     #   sphinx-jinja2-compat
-joblib==1.5.0
+joblib==1.5.1
     # via scikit-learn
-jsonschema==4.23.0
+jsonschema==4.24.0
     # via sphobjinv
 jsonschema-specifications==2025.4.1
     # via jsonschema
@@ -170,7 +168,7 @@ ml-dtypes==0.5.1
     #   tensorstore
 more-itertools==10.7.0
     # via cssutils
-msgpack==1.1.0
+msgpack==1.1.1
     # via
     #   cachecontrol
     #   flax
@@ -192,7 +190,7 @@ numpy==2.0.2 ; python_full_version < '3.10'
     #   scikit-learn
     #   scipy
     #   tensorstore
-numpy==2.2.5 ; python_full_version >= '3.10'
+numpy==2.2.6 ; python_full_version >= '3.10'
     # via
     #   chex
     #   flax
@@ -208,19 +206,23 @@ numpy==2.2.5 ; python_full_version >= '3.10'
     #   treescope
 opt-einsum==3.4.0
     # via jax
-optax==0.2.4
+optax==0.2.4 ; python_full_version < '3.10'
+    # via
+    #   coreax
+    #   flax
+optax==0.2.5 ; python_full_version >= '3.10'
     # via
     #   coreax
     #   flax
 orbax-checkpoint==0.6.4 ; python_full_version < '3.10'
     # via flax
-orbax-checkpoint==0.11.13 ; python_full_version >= '3.10'
+orbax-checkpoint==0.11.15 ; python_full_version >= '3.10'
     # via flax
 packaging==25.0
     # via sphinx
 platformdirs==4.3.8
     # via apeye
-protobuf==6.30.2
+protobuf==6.31.1
     # via orbax-checkpoint
 pybtex==0.24.0
     # via
@@ -244,7 +246,7 @@ referencing==0.36.2
     # via
     #   jsonschema
     #   jsonschema-specifications
-requests==2.32.3
+requests==2.32.4
     # via
     #   apeye
     #   cachecontrol
@@ -253,15 +255,17 @@ rich==14.0.0
     # via flax
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
     # via sphinx
-rpds-py==0.24.0
+rpds-py==0.25.1
     # via
     #   jsonschema
     #   referencing
-ruamel-yaml==0.18.10
+ruamel-yaml==0.18.14
     # via sphinx-toolbox
-ruamel-yaml-clib==0.2.12 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
+ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
     # via ruamel-yaml
-scikit-learn==1.6.1
+scikit-learn==1.6.1 ; python_full_version < '3.10'
+    # via coreax
+scikit-learn==1.7.0 ; python_full_version >= '3.10'
     # via coreax
 scipy==1.13.1 ; python_full_version < '3.10'
     # via
@@ -275,7 +279,7 @@ scipy==1.15.3 ; python_full_version >= '3.10'
     #   jaxlib
     #   jaxopt
     #   scikit-learn
-setuptools==80.4.0 ; python_full_version >= '3.12'
+setuptools==80.9.0
     # via
     #   chex
     #   sphinxcontrib-bibtex
@@ -344,11 +348,11 @@ sphinx-prompt==1.9.0 ; python_full_version >= '3.10'
     # via sphinx-toolbox
 sphinx-tabs==3.4.5
     # via sphinx-toolbox
-sphinx-toolbox==3.10.0
+sphinx-toolbox==4.0.0
     # via coreax
 sphinxcontrib-applehelp==2.0.0
     # via sphinx
-sphinxcontrib-bibtex==2.6.3
+sphinxcontrib-bibtex==2.6.4
     # via coreax
 sphinxcontrib-devhelp==2.0.0
     # via sphinx
@@ -360,7 +364,7 @@ sphinxcontrib-qthelp==2.0.0
     # via sphinx
 sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
-sphobjinv==2.3.1.2
+sphobjinv==2.3.1.3
     # via coreax
 standard-imghdr==3.10.14 ; python_full_version >= '3.13'
     # via sphinx-jinja2-compat
@@ -370,7 +374,7 @@ tensorstore==0.1.69 ; python_full_version < '3.10'
     # via
     #   flax
     #   orbax-checkpoint
-tensorstore==0.1.74 ; python_full_version >= '3.10'
+tensorstore==0.1.75 ; python_full_version >= '3.10'
     # via
     #   flax
     #   orbax-checkpoint
@@ -384,7 +388,7 @@ tqdm==4.67.1
     # via coreax
 treescope==0.1.9 ; python_full_version >= '3.10'
     # via flax
-typing-extensions==4.13.2
+typing-extensions==4.14.0
     # via
     #   beautifulsoup4
     #   chex
@@ -402,13 +406,13 @@ urllib3==2.4.0
     # via
     #   requests
     #   sphinx-prompt
-wadler-lindig==0.1.5 ; python_full_version >= '3.10'
+wadler-lindig==0.1.6 ; python_full_version >= '3.10'
     # via
     #   equinox
     #   jaxtyping
 webencodings==0.5.1
     # via html5lib
-zipp==3.21.0
+zipp==3.23.0
     # via
     #   etils
     #   importlib-metadata

tests/unit/test_data.py

@@ -207,13 +207,13 @@ def test_jaxtyping_compatibility(
         valid_shape = " ".join(str(dim) for dim in data.shape)
         invalid_shape = " ".join(str(dim + 1) for dim in data.shape)
 
-        assert is_bearable(data, Shaped[coreax.data.Data, valid_shape])
+        assert is_bearable(data, Shaped[coreax.data.Data, valid_shape])  # pyright: ignore reportArgumentType see #1007
         assert is_bearable(data, valid_jax_type[coreax.data.Data, valid_shape])
         assert not is_bearable(data, invalid_jax_type[coreax.data.Data, invalid_shape])
-        assert not is_bearable(data, Shaped[coreax.data.Data, invalid_shape])
+        assert not is_bearable(data, Shaped[coreax.data.Data, invalid_shape])  # pyright: ignore reportArgumentType see #1007
         if not isinstance(data, coreax.data.SupervisedData):
             incorrect_instance_type = Shaped[coreax.data.SupervisedData, "..."]
-            assert not is_bearable(data, incorrect_instance_type)
+            assert not is_bearable(data, incorrect_instance_type)  # pyright: ignore reportArgumentType see #1007
 
 
 class TestSupervisedData:

tests/unit/test_kernels.py

@@ -69,10 +69,12 @@ class _Problem(NamedTuple):
 class BaseKernelTest(ABC, Generic[_ScalarValuedKernel]):
     """Test the ``compute`` methods of a ``coreax.kernels.ScalarValuedKernel``."""
 
+    @pytest.fixture
     @abstractmethod
     def kernel(self) -> _ScalarValuedKernel:
         """Abstract pytest fixture which initialises a kernel with parameters fixed."""
 
+    @pytest.fixture
     @abstractmethod
     def problem(
         self, request: pytest.FixtureRequest, kernel: _ScalarValuedKernel

tests/unit/test_least_squares.py

@@ -58,10 +58,12 @@ class _InverseProblem(NamedTuple):
 class InverseApproximationTest(ABC, Generic[_RegularisedLeastSquaresSolver]):
     """Tests related to inverting kernel gramians via methods in least_squares.py."""
 
+    @pytest.fixture
     @abstractmethod
     def approximator(self) -> _RegularisedLeastSquaresSolver:
         """Abstract pytest fixture which initialises a least-squares approximator."""
 
+    @pytest.fixture
     @abstractmethod
     def problem(self) -> _InverseProblem:
         """Abstract fixture which returns a problem for least-squares approximation."""

tests/unit/test_solvers.py

@@ -123,6 +123,7 @@ class SolverTest:
     random_key: KeyArrayLike = jr.key(2024)
     shape: tuple[int, int] = (128, 10)
 
+    @pytest.fixture
     @abstractmethod
     def solver_factory(self, request: pytest.FixtureRequest) -> jtu.Partial:
         """

tests/unit/test_weights.py

@@ -58,6 +58,7 @@ class BaseWeightsOptimiserTest(ABC, Generic[_Data]):
     data_shape: tuple = (100, 2)
     coreset_size: int = data_shape[0] // 10
 
+    @pytest.fixture
     @abstractmethod
     def problem(self) -> _Problem:
         """Abstract pytest fixture which returns a weight optimisation problem."""