More dask fixes

.github/workflows/array_api.yml

@@ -15,24 +15,8 @@ permissions:
 env:
   CCACHE_DIR: "${{ github.workspace }}/.ccache"
   INSTALLDIR: "build-install"
-  XP_TESTS: >-
-    -t scipy.cluster
-    -t scipy.constants
-    -t scipy.fft
-    -t scipy.special.tests.test_logsumexp
-    -t scipy.special.tests.test_support_alternative_backends
-    -t scipy._lib.tests.test_array_api
-    -t scipy._lib.tests.test__util
-    -t scipy.differentiate.tests.test_differentiate
-    -t scipy.integrate.tests.test_tanhsinh
-    -t scipy.integrate.tests.test_cubature
-    -t scipy.optimize.tests.test_bracket
-    -t scipy.optimize.tests.test_chandrupatla
-    -t scipy.optimize.tests.test_optimize
-    -t scipy.stats
-    -t scipy.ndimage
-    -t scipy.integrate.tests.test_quadrature
-    -t scipy.signal.tests.test_signaltools
+  # Only run tests that use the `xp` fixture
+  XP_TESTS: -m array_api_backends
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
@@ -43,8 +27,8 @@ jobs:
     name: Get commit message
     uses: ./.github/workflows/commit_message.yml
 
-  pytorch_cpu:
-    name: Linux PyTorch/JAX/xp-strict CPU
+  xp_cpu:
+    name: Linux PyTorch/JAX/Dask/xp-strict CPU
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
@@ -86,6 +70,10 @@ jobs:
       run: |
         python -m pip install "jax[cpu]"
 
+    - name: Install Dask
+      run: |
+        python -m pip install git+https://github.com/dask/dask.git
+
     - name:  Prepare compiler cache
       id:    prep-ccache
       shell: bash
@@ -111,6 +99,4 @@ jobs:
     - name: Test SciPy
       run: |
         export OMP_NUM_THREADS=2
-        # expand as more modules are supported by adding to `XP_TESTS` above
         python dev.py --no-build test -b all $XP_TESTS -- --durations 3 --timeout=60
-

.github/workflows/commit_message.yml

@@ -18,6 +18,7 @@ jobs:
       message: ${{ steps.skip_check.outputs.message }}
     steps:
       - name: Checkout scipy
+        if: ${{ !contains(github.actor, 'nektos/act') }}
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         # Gets the correct commit message for pull request
         with:
@@ -29,10 +30,14 @@ jobs:
         # and changing the output here based on the combination of tags (if desired).
         run: |
           set -xe
-          COMMIT_MSG=$(git log --no-merges -1)
           RUN="1"
-          if [[ "$COMMIT_MSG" == *"[lint only]"* || "$COMMIT_MSG" == *"[docs only]"* ]]; then
-              RUN="0"
+          # For running a job locally with Act (https://github.com/nektos/act),
+          # always run the job rather than skip based on commit message
+          if [[ $ACT != true ]]; then
+            COMMIT_MSG=$(git log --no-merges -1)
+            if [[ "$COMMIT_MSG" == *"[lint only]"* || "$COMMIT_MSG" == *"[docs only]"* ]]; then
+                RUN="0"
+            fi
           fi
           echo "message=$RUN" >> $GITHUB_OUTPUT
           echo github.ref ${{ github.ref }}

.gitignore

@@ -247,7 +247,7 @@ scipy/signal/_bspline_util.c
 scipy/sparse/_csparsetools.c
 scipy/sparse/_csparsetools.pyx
 scipy/sparse/csgraph/_min_spanning_tree.c
-scipy/sparse/csgraph/_shortest_path.c
+scipy/sparse/csgraph/_shortest_path.cxx
 scipy/sparse/csgraph/_tools.c
 scipy/sparse/csgraph/_traversal.c
 scipy/sparse/csgraph/_flow.c

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2001-2002 Enthought, Inc. 2003-2024, SciPy Developers.
+Copyright (c) 2001-2002 Enthought, Inc. 2003-2025, SciPy Developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

benchmarks/benchmarks/sparse_csgraph_dijkstra.py

@@ -20,7 +20,7 @@ def setup(self, n, min_only, format):
         rng = np.random.default_rng(1234)
         if format == 'random':
             # make a random connectivity matrix
-            data = scipy.sparse.rand(n, n, density=0.2, format='csc',
+            data = scipy.sparse.rand(n, n, density=0.2, format='lil',
                                      random_state=42, dtype=np.bool_)
             data.setdiag(np.zeros(n, dtype=np.bool_))
             self.data = data

dev.py

@@ -710,7 +710,8 @@ class Test(Task):
         multiple=True,
         help=(
             "Array API backend "
-            "('all', 'numpy', 'torch', 'cupy', 'array_api_strict', 'jax.numpy')."
+            "('all', 'numpy', 'torch', 'cupy', 'array_api_strict',"
+            " 'jax.numpy', 'dask.array')."
         )
     )
     # Argument can't have `help=`; used to consume all of `-- arg1 arg2 arg3`

doc/Makefile

@@ -109,14 +109,11 @@ upload:
 # Basic Sphinx generation rules for different formats
 #------------------------------------------------------------------------------
 
-html: version-check convert-notebooks html-build
+html: version-check html-build
 html-build:
 	mkdir -p build/html build/doctrees
 	$(SPHINXBUILD) -WT --keep-going $(VERSIONWARNING) -b html $(ALLSPHINXOPTS) build/html $(FILES)
 
-convert-notebooks:
-	$(PYTHON) convert_notebooks.py
-
 coverage: build version-check
 	mkdir -p build/coverage build/doctrees
 	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) build/coverage $(FILES)

doc/source/_static/version_switcher.json

@@ -5,9 +5,14 @@
         "url": "https://scipy.github.io/devdocs/"
     },
     {
-        "name": "1.14.1 (stable)",
-        "version":"1.14.1",
+        "name": "1.15.0 (stable)",
+        "version":"1.15.0",
         "preferred": true,
+        "url": "https://docs.scipy.org/doc/scipy-1.15.0/"
+    },
+    {
+        "name": "1.14.1",
+        "version":"1.14.1",
         "url": "https://docs.scipy.org/doc/scipy-1.14.1/"
     },
     {

doc/source/building/index.rst

@@ -419,6 +419,16 @@ interface is self-documenting, so please see ``python dev.py --help`` and
     on how things work under the hood.
 
 
+Installing static type stubs
+----------------------------
+
+If you would like to install static type stubs to aid your development of SciPy,
+you can include the ``scipy-stubs`` package in your development environment.
+It is available on PyPI and conda-forge - see the scipy-stubs_ installation guide.
+
+.. _scipy-stubs: https://github.com/jorenham/scipy-stubs?tab=readme-ov-file#installation
+
+
 Customizing builds
 ------------------
 

doc/source/conf.py

@@ -411,6 +411,9 @@
 # interactive renditions of the notebooks
 strip_tagged_cells = True
 
+# Enable overrides for JupyterLite settings at runtime
+jupyterlite_overrides = "overrides.json"
+
 #------------------------------------------------------------------------------
 # Interactive examples with jupyterlite-sphinx
 #------------------------------------------------------------------------------

doc/source/dev/api-dev/array_api.rst

@@ -236,10 +236,11 @@ large and hard-to-detect performance bottleneck.
 Adding tests
 ------------
 
+To run a test on multiple array backends, you should add the ``xp`` fixture to it,
+which is valued to the currently tested array namespace. 
+
 The following pytest markers are available:
 
-* ``array_api_compatible -> xp``: use a parametrisation to run a test on
-  multiple array backends.
 * ``skip_xp_backends(backend=None, reason=None, np_only=False, cpu_only=False, exceptions=None)``:
   skip certain backends or categories of backends.
   ``@pytest.mark.usefixtures("skip_xp_backends")`` must be used alongside this
@@ -262,18 +263,33 @@ The following pytest markers are available:
   causing the test to fail. When ``SCIPY_ARRAY_API=1`` behavior becomes the
   default and only behavior, these tests (and the decorator itself) will be
   removed.
+* ``array_api_backends``: this marker is automatically added by the ``xp`` fixture to
+  all tests that use it. This is useful e.g. to select all and only such tests::
+
+    python dev.py test -b all -- -m array_api_backends
+
+  Note that this includes tests that use the ``xp`` fixture indirectly through another
+  array API fixture, such as ``@pytest.mark.usefixtures("skip_xp_backends")``, even if
+  they don't explicitly consume ``xp`` themselves.
+
+* OBSOLETE: ``array_api_compatible`` (does nothing; pending removal)
 
 ``scipy._lib._array_api`` contains array-agnostic assertions such as ``xp_assert_close``
 which can be used to replace assertions from `numpy.testing`.
 
+When these assertions are executed within a test that uses the ``xp`` fixture, they
+enforce that the namespaces of both the actual and desired arrays match the namespace
+which was set by the fixture. Tests without the ``xp`` fixture infer the namespace from
+the desired array. This machinery can be overridden by explicitly passing the ``xp=``
+parameter to the assertion functions.
+
 The following examples demonstrate how to use the markers::
 
-  from scipy.conftest import array_api_compatible, skip_xp_invalid_arg
+  from scipy.conftest import skip_xp_invalid_arg
   from scipy._lib._array_api import xp_assert_close
   ...
   @pytest.mark.skip_xp_backends(np_only=True, reason='skip reason')
   @pytest.mark.usefixtures("skip_xp_backends")
-  @array_api_compatible
   def test_toto1(self, xp):
       a = xp.asarray([1, 2, 3])
       b = xp.asarray([0, 2, 5])
@@ -284,7 +300,6 @@ The following examples demonstrate how to use the markers::
   @pytest.mark.skip_xp_backends('cupy',
                                 reason='skip reason 2')
   @pytest.mark.usefixtures("skip_xp_backends")
-  @array_api_compatible
   def test_toto2(self, xp):
       ...
   ...
@@ -310,17 +325,14 @@ for compiled code::
   @pytest.mark.skip_xp_backends('array_api_strict', reason='skip reason 1')
   @pytest.mark.skip_xp_backends('cupy', reason='skip reason 2')
   @pytest.mark.usefixtures("skip_xp_backends")
-  @array_api_compatible
   def test_toto(self, xp):
       ...
 
 When every test function in a file has been updated for array API
 compatibility, one can reduce verbosity by telling ``pytest`` to apply the
 markers to every test function using ``pytestmark``::
 
-    from scipy.conftest import array_api_compatible
-
-    pytestmark = [array_api_compatible, pytest.mark.usefixtures("skip_xp_backends")]
+    pytestmark = [pytest.mark.usefixtures("skip_xp_backends")]
     skip_xp_backends = pytest.mark.skip_xp_backends
     ...
     @skip_xp_backends(np_only=True, reason='skip reason')