Merge branch 'main' into newHighs

Author: rgommers

.github/workflows/array_api.yml

@@ -27,8 +27,10 @@ env:
     -t scipy.integrate.tests.test_tanhsinh
     -t scipy.integrate.tests.test_cubature
     -t scipy.optimize.tests.test_chandrupatla
+    -t scipy.optimize.tests.test_optimize
     -t scipy.stats
     -t scipy.ndimage
+    -t scipy.integrate.tests.test_quadrature
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
@@ -72,7 +74,7 @@ jobs:
 
     - name: Install Python packages
       run: |
-        python -m pip install numpy cython pytest pytest-xdist pytest-timeout pybind11 mpmath gmpy2 pythran ninja meson click rich-click doit pydevtool pooch hypothesis array-api-strict
+        python -m pip install numpy cython pytest pytest-xdist pytest-timeout pybind11 mpmath gmpy2 pythran ninja meson click rich-click doit pydevtool pooch hypothesis array-api-strict==2.1.0
 
     - name: Install PyTorch CPU
       run: |

.github/workflows/free_threaded_wheels.yml

@@ -460,10 +460,10 @@ jobs:
         submodules: recursive
         fetch-tags: true
     # TODO: replace with setup-python when there is support
-    - uses: deadsnakes/action@e640ac8743173a67cca4d7d77cd837e514bf98e8 # v3.2.0
+    - uses: Quansight-Labs/setup-python@b9ab292c751a42bcd2bb465b7fa202ea2c3f5796  # v5.3.1
       with:
-          python-version: '3.13-dev'
-          nogil: true
+        python-version: '3.13t'
+
     - name: Install Ubuntu dependencies
       run: |
         sudo apt-get update

.github/workflows/linux.yml

@@ -53,7 +53,7 @@ jobs:
           COMMIT_MSG=$(git log --no-merges -1)
           RUN="0"
           if [[ "$COMMIT_MSG" == *"[wheel build]"* ]]; then
-              RUN="1" 
+              RUN="1"
           fi
           echo "message=$RUN" >> $GITHUB_OUTPUT
           echo github.ref ${{ github.ref }}
@@ -86,7 +86,7 @@ jobs:
         - [macos-14, macosx, arm64, openblas, "12.3"]
         - [macos-14, macosx, arm64, accelerate, "14.0"]
         - [windows-2019, win, AMD64, "", ""]
-        python: [["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"], ["cp313", "3.13"]]
+        python: [["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"], ["cp313", "3.13"], ["cp313t", "3.13"]]
         # python[0] is used to specify the python versions made by cibuildwheel
 
     env:
@@ -150,7 +150,7 @@ jobs:
           echo "CIBW_ENVIRONMENT=$CIBW" >> "$GITHUB_ENV"
 
           echo "REPAIR_PATH=$LIB_PATH" >> "$GITHUB_ENV"
-          
+
           PREFIX=DYLD_LIBRARY_PATH="\$(dirname \$(gfortran --print-file-name libgfortran.dylib))"
           # remove libgfortran from location used for linking (if any), to
           # check wheel has bundled things correctly and all tests pass without
@@ -162,13 +162,13 @@ jobs:
             {delocate_archs} -w {dest_dir} {wheel} && echo "-----------" &&\
             delocate-listdeps -d {dest_dir}/*.whl && echo "-----------" &&\
             $POSTFIX"
-          
+
           # Rename x86 Accelerate wheel to test on macOS 13 runner
           if [[ ${{ matrix.buildplat[0] }} == 'macos-13' && ${{ matrix.buildplat[4] }} == '14.0' ]]; then
             CIBW+=" && mv {dest_dir}/\$(basename {wheel}) \
               {dest_dir}/\$(echo \$(basename {wheel}) | sed 's/14_0/13_0/')"
           fi
-          
+
           # macos-arm64-openblas wheels that target macos-12 need a
           # MACOS_DEPLOYMENT_TARGET of 12.3 otherwise delocate complains.
           # Unclear of cause, possibly build tool related.
@@ -178,39 +178,44 @@ jobs:
           if [[ ${{ matrix.buildplat[0] }} == 'macos-14' && ${{ matrix.buildplat[4] }} == '12.3' ]]; then
             CIBW+=" && echo \$(ls {dest_dir}) && \
             mv {dest_dir}/*.whl \$(find {dest_dir} -type f -name '*.whl' | sed 's/12_3/12_0/')"
-          fi          
+          fi
           echo "CIBW_REPAIR_WHEEL_COMMAND_MACOS=$CIBW" >> "$GITHUB_ENV"
 
-      - name: Inject environment variable for python dev version
-        if: matrix.python[1] == '3.13'
+      # - name: Inject environment variable for python dev version
+      #   if: ${{ matrix.python[1] == '3.14-dev'
+      #   shell: bash
+      #   run: |
+      #     # For dev versions of python need to use wheels from scientific-python-nightly-wheels
+      #     # When the python version is released please comment out this section, but do not remove
+      #     # (there will soon be another dev version to target).
+      #     DEPS0="pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy"
+      #     DEPS1="pip install ninja meson-python pybind11 pythran cython"
+
+      #     CIBW="$DEPS0;$DEPS1;bash {project}/tools/wheels/cibw_before_build_linux.sh {project}"
+      #     echo "CIBW_BEFORE_BUILD_LINUX=$CIBW" >> "$GITHUB_ENV"
+
+      #     CIBW="$DEPS0 && $DEPS1 && bash {project}/tools/wheels/cibw_before_build_win.sh {project}"
+      #     echo "CIBW_BEFORE_BUILD_WINDOWS=$CIBW" >> "$GITHUB_ENV"
+
+      #     CIBW="$DEPS0;$DEPS1;bash {project}/tools/wheels/cibw_before_build_macos.sh {project}"
+      #     echo "CIBW_BEFORE_BUILD_MACOS=$CIBW" >> "$GITHUB_ENV"
+
+      #     echo "CIBW_BEFORE_TEST=$DEPS0" >> "$GITHUB_ENV"
+
+      - name: Disable build isolation for python free-threaded version
+        if: endsWith(matrix.python[0], 't')
         shell: bash
         run: |
-          # For dev versions of python need to use wheels from scientific-python-nightly-wheels
-          # When the python version is released please comment out this section, but do not remove
-          # (there will soon be another dev version to target).
-          DEPS0="pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy"
-          DEPS1="pip install ninja meson-python pybind11 pythran cython"
-          
-          CIBW="$DEPS0;$DEPS1;bash {project}/tools/wheels/cibw_before_build_linux.sh {project}"
-          echo "CIBW_BEFORE_BUILD_LINUX=$CIBW" >> "$GITHUB_ENV"
-          
-          CIBW="$DEPS0 && $DEPS1 && bash {project}/tools/wheels/cibw_before_build_win.sh {project}"
-          echo "CIBW_BEFORE_BUILD_WINDOWS=$CIBW" >> "$GITHUB_ENV"
-          
-          CIBW="$DEPS0;$DEPS1;bash {project}/tools/wheels/cibw_before_build_macos.sh {project}"
-          echo "CIBW_BEFORE_BUILD_MACOS=$CIBW" >> "$GITHUB_ENV"
-
-          echo "CIBW_BEFORE_TEST=$DEPS0" >> "$GITHUB_ENV"
-          
           CIBW="pip; args: --no-build-isolation"
-          echo "CIBW_BUILD_FRONTEND=$CIBW" >> "$GITHUB_ENV" 
+          echo "CIBW_BUILD_FRONTEND=$CIBW" >> "$GITHUB_ENV"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@d4a2945fcc8d13f20a1b99d461b8e844d5fc6e23 # v2.21.1
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
         env:
           CIBW_BUILD: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}*
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}
           CIBW_PRERELEASE_PYTHONS: True
+          CIBW_FREE_THREADED_SUPPORT: True
 
       - name: Rename macOS wheels
         if: startsWith( matrix.buildplat[0], 'macos-' )
@@ -255,7 +260,7 @@ jobs:
           # an upload to:
           #
           # https://anaconda.org/scientific-python-nightly-wheels/scipy
-          # 
+          #
           # Pushes to a maintenance branch that contain '[wheel build]' will
           # cause wheels to be built and uploaded to:
           #

.github/workflows/wheels.yml

@@ -107,7 +107,7 @@ doc/source/.jupyterlite.doit.db
 .cache/
 .pytest_cache/
 
-# github cache #
+# GitHub cache #
 ################
 gh_cache.json
 

.gitignore

@@ -22,6 +22,9 @@
 [submodule "scipy/_lib/cobyqa"]
 	path = scipy/_lib/cobyqa
 	url = https://github.com/cobyqa/cobyqa.git
+[submodule "scipy/_lib/array_api_extra"]
+	path = scipy/_lib/array_api_extra
+	url = https://github.com/lucascolley/array-api-extra.git
 # All submodules used as a Meson `subproject` are required to be under the
 # subprojects/ directory - see:
 # https://mesonbuild.com/Subprojects.html#why-must-all-subprojects-be-inside-a-single-directory