Ilp64 accelerate

.github/CODEOWNERS

@@ -57,7 +57,6 @@ benchmarks/asv.conf.json  @larsoner
 # CI config
 .circleci/  @larsoner
 .github/workflows/  @larsoner @andyfaff
-.cirrus.star  @larsoner @andyfaff
 
 # Doc
 requirements/doc.txt  @tupui

.github/label-globs.yml

@@ -156,7 +156,6 @@ CI:
     - .circleci/**
     - .github/workflows/**
     - ci/**
-    - .cirrus.star
 
 DX:
 - changed-files:

.github/workflows/linux.yml

@@ -285,7 +285,7 @@ jobs:
   #################################################################################
   prerelease_deps_coverage_64bit_blas:
     # TODO: re-enable ILP64 build.
-    name: Prerelease deps & coverage report, full, py3.11/npMin & py3.11/npPre, dev.py
+    name: Prerelease deps & coverage report, full, py3.11/npMin & py3.11/npPre, dev.py, SCIPY_ARRAY_API=1
     needs: get_commit_message
     if: >
       needs.get_commit_message.outputs.message == 1
@@ -362,6 +362,7 @@ jobs:
     - name: Test SciPy
       run: |
         export OPENBLAS_NUM_THREADS=1
+        export SCIPY_ARRAY_API=1
         python dev.py --no-build test --coverage -j2 --mode full -- --cov --cov-report term-missing
 
   #################################################################################
@@ -508,7 +509,6 @@ jobs:
       if: ${{ matrix.parallel == '1'}}
       env:
         # Excluded modules:
-        # - scipy.special and scipy.stats are waiting on special.errstate being made thread-safe
         # - scipy.spatial has multiple issues  in kdtree/qhull, and gh-20655 is pending.
         TEST_SUBMODULES: >-
           -t scipy.cluster
@@ -527,6 +527,8 @@ jobs:
           -t scipy.optimize
           -t scipy.signal
           -t scipy.sparse
+          -t scipy.special
+          -t scipy.stats
       run: |
         # Note: only fast tests; full test suite is unlikely to uncover anything more,
         #       and it'll be quite slow with pytest-run-parallel

.github/workflows/linux_blas_ilp64.yml

@@ -0,0 +1,129 @@
+name: BLAS tests (Linux)
+
+# This file is meant for testing different BLAS/LAPACK flavors and build
+# options on Linux. All other yml files for Linux will only test without BLAS
+# (mostly because that's easier and faster to build) or with the same 64-bit
+# OpenBLAS build that is used in the wheel jobs.
+#
+# Jobs and their purpose:
+#
+#   - mkl:
+#         Tests MKL installed from PyPI (because easiest/fastest, if broken) in
+#         3 ways: both LP64 and ILP64 via pkg-config, and then using the
+#         Single Dynamic Library (SDL, or `libmkl_rt`).
+#
+#    - scipy-openblas64:
+#         Test ILP64-enabled build with scipy-openblas32 and scipy-openblas64.
+#
+
+on:
+  pull_request:
+    branches:
+      - main
+      - maintenance/**
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+jobs:
+
+  mkl-lp64:
+    runs-on: ubuntu-latest
+    name: "MKL LP64"
+    steps:
+    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y gfortran
+        pip install cython numpy pybind11 pythran pytest hypothesis pytest-xdist pooch
+        pip install -r requirements/dev.txt
+        pip install git+https://github.com/numpy/meson.git@main-numpymeson
+        pip install mkl mkl-devel
+
+    - name: Build with defaults (LP64)
+      run: |
+        pkg-config --libs mkl-dynamic-lp64-seq  # check link flags
+        python dev.py build -C-Dblas=mkl
+
+    - name: Test
+      run: python dev.py test -j 2
+
+
+  mkl-ilp64:
+    runs-on: ubuntu-latest
+    name: "MKL ILP64"
+    steps:
+    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y gfortran
+        pip install cython numpy pybind11 pythran pytest hypothesis pytest-xdist pooch
+        pip install -r requirements/dev.txt
+        pip install git+https://github.com/numpy/meson.git@main-numpymeson
+        pip install mkl mkl-devel
+
+    - name: Build with ILP64
+      run: |
+        pkg-config --libs mkl-dynamic-ilp64-seq  # check link flags
+        python dev.py build -C-Dblas=mkl -C-Duse-ilp64=true
+
+    - name: Test
+      run: python dev.py test -j 2
+
+
+  scipy-openblas-ilp64:
+    runs-on: ubuntu-latest
+    name: "scipy-openblas ILP64"
+    steps:
+    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y gfortran
+        pip install cython numpy pybind11 pythran pytest hypothesis pytest-xdist pooch
+        pip install -r requirements/dev.txt
+        pip install git+https://github.com/numpy/meson.git@main-numpymeson
+        pip install scipy-openblas32 scipy-openblas64
+        # dev.py does this for scipy-openblas32
+        python -c'import scipy_openblas64 as so64; print(so64.get_pkg_config())' > scipy-openblas64.pc
+        export PKG_CONFIG_PATH=`pwd`
+
+    - name: Build with ILP64
+      run: |
+        python dev.py build --with-scipy-openblas -C-Duse-ilp64=true
+
+    - name: Test
+      run: python dev.py test -j 2
+
+

.github/workflows/macos.yml

@@ -217,3 +217,4 @@ jobs:
 
         pip install pooch pytest hypothesis
         python dev.py -n test
+

.github/workflows/macos_blas_ilp64.yml

@@ -0,0 +1,56 @@
+name: macOS BLAS ILP64 tests
+
+on:
+  push:
+    branches:
+      - maintenance/**
+  pull_request:
+    branches:
+      - main
+      - maintenance/**
+
+permissions:
+   contents: read  # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  accelerate:
+    name: Accelerate (ILP64)
+    if: "github.repository == 'ev-br/scipy'"
+    runs-on: macos-15
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      with:
+        submodules: recursive
+
+    - name: Setup Python
+      uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5.5.0
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Build and Install SciPy
+      run: |
+        sudo xcode-select -s /Applications/Xcode_16.app
+
+        git submodule update --init
+        GFORTRAN_LOC=$(which gfortran-13)
+        ln -s $GFORTRAN_LOC gfortran
+        export PATH=$PWD:$PATH
+
+        # Ensure we have gfortran dylib
+        GFORTRAN_LIB=$(dirname `gfortran --print-file-name libgfortran.dylib`)
+        export DYLD_LIBRARY_PATH=$GFORTRAN_LIB
+
+        pip install click doit pydevtool rich_click meson cython pythran pybind11 ninja numpy
+        python dev.py build -C-Dblas=accelerate -C-Duse-ilp64=true
+
+        pip install pooch pytest hypothesis
+        python dev.py -n test -v

.github/workflows/wheels.yml

@@ -216,8 +216,7 @@ jobs:
         env:
           CIBW_BUILD: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}*
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}
-          CIBW_PRERELEASE_PYTHONS: True
-          CIBW_FREE_THREADED_SUPPORT: True
+          CIBW_ENABLE: cpython-freethreading cpython-prerelease
 
       - name: Rename macOS wheels
         if: startsWith( matrix.buildplat[0], 'macos-' )

doc/source/building/blas_lapack.rst

@@ -96,6 +96,44 @@ user wants to override this autodetection mechanism for building against plain
     $ python -m build -C-Duse-g77-abi=true -Csetup-args=-Dblas=blas -Csetup-args=-Dlapack=lapack 
 
 
+64-bit integer (ILP64) BLAS/LAPACK
+----------------------------------
+
+Support for ILP64 BLAS and LAPACK is still experimental; at the time of writing
+(Apr 2025) it is only available for two BLAS/LAPACK configurations: MKL and
+``scipy-openblas``.
+
+SciPy always requires LP64 (32-bit integer size) BLAS/LAPACK. You can build SciPy
+with *additional* ILP64 support. This will result in SciPy requiring both BLAS and
+LAPACK variants, where some extensions link to the ILP64 variant, while other
+extensions link to the LP64 variant. From python, choosing the variant is done
+through the ``get_blas_funcs`` and ``get_lapack_funcs`` functions::
+
+    >>> from scipy.linalg.blas import get_blas_funcs
+    >>> daxpy = get_blas_funcs('axpy', (np.ones(3),), ilp64='preferred')
+    >>> daxpy.int_dtype
+    dtype('int64')
+
+Building with ILP64 support requires several NumPy additions to ``meson``, which have
+not been merged to upstream yet::
+
+    $ pip install git+https://github.com/numpy/meson.git@main-numpymeson
+
+For a development build with MKL, install the library and its development headers, and
+give use the ``ilp64=true`` command line argument
+
+    $ pip install mkl mkl-devel
+    $ python dev.py build -C-Dblas=mkl -C-Duse-ilp64=true
+
+For a development build with ``scipy-openblas64``, make sure you have installed both
+``scipy-openblas32`` and ``scipy-openblas64``, and generate the pkg-config file
+for the ILP64 variant::
+
+    >>> python -c'import scipy_openblas64 as so64; print(so64.get_pkg_config())' > scipy-openblas64.pc
+    >>> export PKG_CONFIG_PATH=`pwd`
+    >>> python dev.py build --with-scipy-openblas -C-Duse-ilp64=true
+
+
 Work-in-progress
 ----------------
 

doc/source/dev/contributor/continuous_integration.rst

@@ -56,12 +56,6 @@ CircleCI
 * ``run_benchmarks``: verify how the changes impact performance
 * ``refguide_check``: doctests from examples and benchmarks
 
-CirrusCI
---------
-* ``Tests``: test suite for specific architecture like
-  ``musllinux, arm, aarch``
-* ``Wheels``: build and upload some wheels
-
 .. _skip-ci:
 
 Skipping
@@ -79,7 +73,6 @@ Skipping CI can be achieved by adding a special text in the commit message:
 
 * ``[skip actions]``: will skip GitHub Actions
 * ``[skip circle]``: will skip CircleCI
-* ``[skip cirrus]``: will skip CirrusCI
 * ``[docs only]``: will skip *all but* the CircleCI checks and the linter
 * ``[lint only]``: will skip *all but* the linter
 * ``[skip ci]``: will skip *all* CI
@@ -88,7 +81,7 @@ Of course, you can combine these to skip multiple workflows.
 
 This skip information should be placed on a new line. In this example, we
 just updated a ``.rst`` file in the documentation and ask to skip all but the
-relevant docs checks (skip Cirrus and GitHub Actions' workflows)::
+relevant docs checks (skip GitHub Actions' workflows)::
 
     DOC: improve QMCEngine examples.
 

meson.options

@@ -2,6 +2,15 @@ option('blas', type: 'string', value: 'openblas',
         description: 'option for BLAS library switching')
 option('lapack', type: 'string', value: 'openblas',
         description: 'option for LAPACK library switching')
+
+# NB ILP64 build is experimental.
+# See https://scipy.github.io/devdocs/building/blas_lapack.html for details
+option('use-ilp64', type: 'boolean', value: false,
+       description: 'Use ILP64 (64-bit integer) BLAS and LAPACK interfaces')
+option('blas-symbol-suffix', type: 'string', value: 'auto',
+        description: 'BLAS and LAPACK symbol suffix to use, if any')
+option('mkl-threading', type: 'string', value: 'auto',
+        description: 'MKL threading method, one of: `seq`, `iomp`, `gomp`, `tbb`')
 option('use-g77-abi', type: 'boolean', value: false,
         description: 'If set to true, forces using g77 compatibility wrappers ' +
                      'for LAPACK functions. The default is to use gfortran ' +

mypy.ini

@@ -120,7 +120,7 @@ ignore_missing_imports = True
 [mypy-scipy.optimize._bglu_dense]
 ignore_missing_imports = True
 
-[mypy-scipy.optimize._slsqp]
+[mypy-scipy.optimize._slsqplib]
 ignore_missing_imports = True
 
 [mypy-scipy.interpolate._dfitpack]

pyproject.toml

@@ -82,7 +82,7 @@ test = [
     "scikit-umfpack",
     "pooch",
     "hypothesis>=6.30",
-    "array-api-strict>=2.3",
+    "array-api-strict>=2.3.1",
     "Cython",
     "meson",
     'ninja; sys_platform != "emscripten"',

requirements/test.txt

@@ -11,7 +11,7 @@ threadpoolctl
 # scikit-umfpack  # circular dependency issues
 pooch
 hypothesis>=6.30
-array-api-strict>=2.0,<2.1.1
+array-api-strict>=2.3.1
 Cython
 meson
 ninja; sys_platform != "emscripten"

scipy/_build_utils/int64.f2cmap.in

@@ -0,0 +1 @@
+{'integer': {'': '@int64_name@'}, 'logical': {'': '@int64_name@'}}