linux.yml

name: Linux tests

on:
  push:
    branches:
      - maintenance/**
  pull_request:
    branches:
      - main
      - maintenance/**

permissions:
   contents: read  # to fetch code (actions/checkout)

env:
  CCACHE_DIR: "${{ github.workspace }}/.ccache"
  INSTALLDIR: "build-install"

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
  cancel-in-progress: true

jobs:
  get_commit_message:
    name: Get commit message
    uses: ./.github/workflows/commit_message.yml

  test_meson:
    name: mypy (py3.10) & dev deps (py3.12), fast, dev.py
    needs: get_commit_message
    # If using act to run CI locally the github object does not exist and
    # the usual skipping should not be enforced
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-22.04
    strategy:
      matrix:
        python-version: ['3.10', '3.12'] # this run will use python dev versions when available
        maintenance-branch:
          - ${{ contains(github.ref, 'maintenance/') || contains(github.base_ref, 'maintenance/') }}
        exclude:
          - maintenance-branch: true
            python-version: '3.12'

    steps:
    - uses: actions/checkout@v4.1.1
      with:
        submodules: recursive

    - name: Setup Python
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        cache: 'pip'
        cache-dependency-path: 'environment.yml'

    - name: Install Ubuntu dependencies
      run: |
        # NOTE: not the same OpenBLAS version as in upstream CI (I'm being lazy here)
        sudo apt-get update
        sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev

    - name: Install Python packages
      if: matrix.python-version == '3.10'
      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

    - name: Install Python packages from repositories
      if: matrix.python-version == '3.12' # this run will use python dev versions when available
      run: |
        python -m pip install git+https://github.com/numpy/numpy.git
        python -m pip install ninja cython pytest pybind11 pytest-xdist pytest-timeout click rich-click doit pydevtool pooch hypothesis "setuptools<67.3"
        python -m pip install git+https://github.com/serge-sans-paille/pythran.git
        python -m pip install git+https://github.com/mesonbuild/meson.git

    - name:  Prepare compiler cache
      id:    prep-ccache
      shell: bash
      run: |
        mkdir -p "${CCACHE_DIR}"
        echo "dir=$CCACHE_DIR" >> $GITHUB_OUTPUT
        NOW=$(date -u +"%F-%T")
        echo "timestamp=${NOW}" >> $GITHUB_OUTPUT

    - name: Setup compiler cache
      uses:  actions/cache@v4
      id:    cache-ccache
      # Reference: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key
      # NOTE: The caching strategy is modeled in a way that it will always have a unique cache key for each workflow run
      # (even if the same workflow is run multiple times). The restore keys are not unique and for a partial match, they will
      # return the most recently created cache entry, according to the GitHub Action Docs.
      with:
        path: ${{ steps.prep-ccache.outputs.dir }}
        # Restores ccache from either a previous build on this branch or on main
        key:  ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-${{ steps.prep-ccache.outputs.timestamp }}
        # This evaluates to `Linux Tests-3.10-ccache-linux-` which is not unique. As the CI matrix is expanded, this will
        # need to be updated to be unique so that the cache is not restored from a different job altogether.
        restore-keys: |
          ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-

    - name: Setup build and install scipy
      run: |
        python dev.py build --werror

    - name: Ccache performance
      shell: bash -l {0}
      run: ccache -s

    - name: Check installation
      run: |
        pushd tools
        python check_installation.py ${{ env.INSTALLDIR }}
        ./check_pyext_symbol_hiding.sh ../build
        popd

    - name: Check usage of install tags
      run: |
        rm -r ${{ env.INSTALLDIR }}
        python dev.py build --tags=runtime,python-runtime,devel
        python tools/check_installation.py ${{ env.INSTALLDIR }} --no-tests
        rm -r ${{ env.INSTALLDIR }}
        python dev.py build --tags=runtime,python-runtime,devel,tests
        python tools/check_installation.py ${{ env.INSTALLDIR }}

    - name: Mypy
      if: matrix.python-version == '3.10'
      run: |
        # Packages that are only needed for their annotations
        python -m pip install mypy==1.10.0 types-psutil typing_extensions
        python -m pip install pybind11 sphinx

        python -u dev.py mypy

    - name: Test SciPy
      run: |
        export OMP_NUM_THREADS=2
        python dev.py --no-build test -j2 -- --durations 10 --timeout=60

  #################################################################################
  test_venv_install:
    name: Install into venv, cluster only, pyAny/npAny, pip+cluster.test()
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4.1.1
      with:
        submodules: recursive

    - name: Install Ubuntu dependencies
      run: |
        # We're not running the full test suite here, only testing the install
        # into a venv is working, so leave out optional dependencies. That's
        # also why we can get away with an old version of OpenBLAS from Ubuntu
        sudo apt-get update
        sudo apt-get install -y python3-dev libopenblas-dev pkg-config gfortran

    - name: Create venv, install SciPy
      run: |
        python -m venv ../venvs/scipy-venv
        source ../venvs/scipy-venv/bin/activate
        # Note that this uses build isolation. That's why we don't need build
        # dependencies to be installed in the venv itself.
        python -m pip install . -vv

    - name: Basic imports and tests
      run: |
        source ../venvs/scipy-venv/bin/activate
        cd ..
        python -c "import scipy"
        python -c "import scipy.linalg"
        python -m pip install pytest hypothesis
        python -c "from scipy import cluster; cluster.test()"

    - name: Create venv inside source tree
      # This is a regression test for gh-16312
      run: |
        python -m venv .venv
        source .venv/bin/activate
        # Install build dependencies. Use meson-python from its main branch,
        # most convenient to test in this job because we're using pip without
        # build isolation here.
        python -m pip install numpy pybind11 pythran cython pytest ninja hypothesis
        python -m pip install git+https://github.com/mesonbuild/meson-python.git
        # Non-isolated build, so we use dependencies installed inside the source tree
        python -m pip install -U pip  # need pip >=23 for `--config-settings`
        python -m pip install . --no-build-isolation --config-settings=compile-args=-j2

        # Basic tests
        cd ..
        python -c "import scipy"
        python -c "import scipy.linalg"
        python -c "from scipy import cluster; cluster.test()"

  #################################################################################
  python_debug:
    # also uses the vcs->sdist->wheel route.
    name: Python-debug & ATLAS & sdist+wheel, fast, py3.10/npMin, pip+pytest
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-22.04  # provides python3.10-dbg
    steps:
      - uses: actions/checkout@v4.1.1
        with:
          submodules: recursive
      - name: Configuring Test Environment
        run: |
          sudo apt-get update
          sudo apt install python3-dbg python3-dev libatlas-base-dev liblapack-dev gfortran ccache libgmp-dev libmpfr-dev libmpc-dev
          python3-dbg --version # just to check
          python3-dbg -c 'import sys; print("Python debug build:", hasattr(sys, "gettotalrefcount"))'
      - name: Build SciPy
        run: |
          python3-dbg -m pip install build
          python3-dbg -m build -Csetup-args=-Dbuildtype=debugoptimized -Csetup-args=-Dblas=blas-atlas -Csetup-args=-Dlapack=lapack-atlas -Ccompile-args=-j2
          python3-dbg -m pip install dist/scipy*.whl
      - name: Testing SciPy
        run: |
          cd doc
          python3-dbg -m pip install pytest pytest-xdist pytest-timeout mpmath gmpy2 threadpoolctl pooch hypothesis
          python3-dbg -m pytest --pyargs scipy -n2 --durations=10 -m "not slow"

  #################################################################################
  gcc9:
    # Purpose is to examine builds with oldest-supported gcc and test with pydata/sparse.
    name: Oldest GCC & pydata/sparse, fast, py3.10/npMin, pip+pytest
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4.1.1
        with:
          submodules: recursive

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"

      - name: Setup system dependencies
        run: |
          sudo apt-get -y update
          sudo apt install -y g++-9 gcc-9 gfortran-9
          sudo apt install -y libatlas-base-dev liblapack-dev libgmp-dev \
            libmpfr-dev libmpc-dev pkg-config libsuitesparse-dev liblapack-dev

      - name: Setup Python build deps
        run: |
          pip install build meson-python ninja pythran pybind11 cython "numpy>=2.0.0b1"

      - name: Build wheel and install
        run: |
          set -euo pipefail
          export PYTHONOPTIMIZE=2

          # specify which compilers to use using environment variables
          CC=gcc-9 CXX=g++-9 FC=gfortran-9 python -m build --wheel --no-isolation -Csetup-args=-Dblas=blas-atlas -Csetup-args=-Dlapack=lapack-atlas -Ccompile-args=-j2
          python -m pip install dist/scipy*.whl

      - name: Install test dependencies
        run: |
          # Downgrade numpy to oldest supported version
          pip install gmpy2 threadpoolctl mpmath pooch pytest pytest-xdist==2.5.0 pytest-timeout hypothesis sparse "numpy==1.23.5"

      - name: Run tests
        run: |
          # can't be in source directory
          pushd $RUNNER_TEMP
          export PYTHONOPTIMIZE=2
          python -m pytest --pyargs scipy -n2 --durations=10
          popd

  #################################################################################
  prerelease_deps_coverage_64bit_blas:
    # TODO: re-enable ILP64 build.
    name: Prerelease deps & coverage report, full, py3.10/npMin & py3.11/npPre, dev.py
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # Both use numpy 2.x-dev at build time; 3.10 job then downgrades to
        # lowest supported NumPy version in order to test ABI compatibility.
        python-version: ['3.10', '3.11']

    steps:
    - uses: actions/checkout@v4.1.1
      with:
        submodules: recursive

    - name: Setup Python
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install Ubuntu dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y libgmp-dev libmpfr-dev libmpc-dev ccache gfortran

    - name: Caching Python dependencies
      uses: actions/cache@v4
      id: cache
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-prerelease

    - name: Install Python packages
      run: |
        python -m pip install cython pythran ninja meson-python pybind11 click rich_click pydevtool
        # Note: matplotlib not installed here to avoid issues around numpy 2.0
        # (it can be put back after matplotlib has made a 2.0-compatible
        # release on PyPI.
        python -m pip install --pre --upgrade pytest pytest-cov pytest-xdist mpmath gmpy2 threadpoolctl pooch hypothesis
        python -m pip install -r requirements/openblas.txt
        # Install numpy last, to ensure we get nightly (avoid possible <2.0 constraints).
        python -m pip install --pre --upgrade --timeout=60 -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy

    - name:  Prepare compiler cache
      id:    prep-ccache
      shell: bash
      run: |
        mkdir -p "${CCACHE_DIR}"
        echo "dir=$CCACHE_DIR" >> $GITHUB_OUTPUT
        NOW=$(date -u +"%F-%T")
        echo "timestamp=${NOW}" >> $GITHUB_OUTPUT

    - name: Setup compiler cache
      uses:  actions/cache@v4
      id:    cache-ccache
      with:
        path: ${{ steps.prep-ccache.outputs.dir }}
        # Restores ccache from either a previous build on this branch or on main
        key:  ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-prerelease-${{ steps.prep-ccache.outputs.timestamp }}
        restore-keys: |
          ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-prerelease-

    - name: Build and install SciPy
      run: |
        python dev.py build --gcov --with-scipy-openblas

    - name: Ccache performance
      shell: bash -l {0}
      run: ccache -s

    - name: Downgrade NumPy from 2.0-dev to lowest supported
      if: matrix.python-version == '3.10'
      run: |
        python -m pip install "numpy==1.23.5"

    - name: Test SciPy
      run: |
        export OPENBLAS_NUM_THREADS=1
        python dev.py --no-build test -j2 --mode full -- --cov --cov-report term-missing

  #################################################################################
  linux_32bit:
    name: 32-bit, fast, py3.10/npMin, dev.py
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-latest
    # I tried running directly in a container:, using the image: and options:
    # entries. Unfortunately at this time options: does not seem to listen to
    # --platform linux/i386.
    steps:
    - uses: actions/checkout@v4.1.1
      with:
        submodules: recursive

    - name: build + test
      run: |
        set -exuo pipefail
        docker pull quay.io/pypa/manylinux2014_i686
        docker run -v $(pwd):/scipy --platform=linux/i386 quay.io/pypa/manylinux2014_i686 /bin/bash -c "cd /scipy && \
        uname -a && \
        python3.10 -m venv test && \
        source test/bin/activate && \
        python -m pip install doit click rich_click pydevtool meson ninja && \
        python -m pip install -r requirements/openblas.txt && \
        # Ensure that scipy-openblas is picked up by the numpy<1.26 build
        cat > \$HOME/.numpy-site.cfg <<EOL
        [openblas]
        libraries = \$(python -c 'import scipy_openblas32; print(scipy_openblas32.get_library())')
        library_dirs = \$(python -c 'import scipy_openblas32; print(scipy_openblas32.get_lib_dir())')
        include_dirs = \$(python -c 'import scipy_openblas32; print(scipy_openblas32.get_include_dir())')
        runtime_library_dirs = \$(python -c 'import scipy_openblas32; print(scipy_openblas32.get_lib_dir())')
        symbol_prefix = scipy_
        EOL
        python -m pip install numpy==1.23.5 cython pybind11 pytest pytest-timeout pytest-xdist pytest-env 'Pillow<10.0.0' mpmath pythran pooch meson hypothesis && \
        python -c 'import numpy as np; np.show_config()' && \
        python dev.py build --with-scipy-openblas && \
        python dev.py --no-build test"

  #################################################################################
  distro_multiple_pythons:
    # Purpose is to build for a non-default Python interpreter in a Linux distro
    # For such a build config, `python`/`python3` executables may not have
    # build dependencies like Cython or NumPy installed.
    name: non-default Python interpreter, fast, py3.10/npMin, pip+pytest
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4.1.1
        with:
          submodules: recursive

      - name: Setup system dependencies
        run: |
          sudo apt-get -y update
          # `python3-dev` yields Python 3.10 on Ubuntu 22.04
          sudo apt install -y python3-dev python3.11-dev ninja-build pkg-config libatlas-base-dev liblapack-dev

      - name: Setup Python build deps
        run: |
          python3.11 -m pip install build pythran pybind11 cython numpy meson-python

      - name: Build wheel and install
        run: |
          python3.11 -m build -wnx -Csetup-args=-Dblas=blas-atlas -Csetup-args=-Dlapack=lapack-atlas -Ccompile-args=-j2
          python3.11 -m pip install dist/*.whl

      - name: Install test dependencies
        run: |
          python3.11 -m pip install pytest hypothesis
          python3.10 -m pip install meson  # ensure compile test work with this

      - name: Run tests
        run: |
          # Just a small subset of tests; this will be fine if the build
          # succeeds (that's the real purpose of this job)
          pushd $RUNNER_TEMP
          python3.11 -m pytest --pyargs scipy.cluster
          python3.11 -m pytest --pyargs scipy.linalg
          popd

  free-threaded:
    needs: get_commit_message
    runs-on: ubuntu-latest
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    steps:
    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
      with:
        submodules: recursive
        fetch-tags: true
    # TODO: replace with setup-python when there is support
    - uses: deadsnakes/action@6c8b9b82fe0b4344f4b98f2775fcc395df45e494 # v3.1.0
      with:
          python-version: '3.13-dev'
          nogil: true
    - name: Install Ubuntu dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y libgmp-dev libmpfr-dev libmpc-dev ccache gfortran
    # TODO: remove pip pre-release install after Python 3.13 release
    - name: Install pre-release pip
      run: |
        pip install -U --pre pip
    # TODO: remove cython nightly install when cython does a release
    - name: Install nightly Cython
      run: |
        pip install git+https://github.com/cython/cython
    - name: Install nightly NumPy
      run: |
        pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
    - name: Install Python dependencies
      run: |
        pip install git+https://github.com/serge-sans-paille/pythran
        pip install ninja meson-python pybind11 click rich_click pydevtool
        pip install --pre --upgrade pytest pytest-xdist gmpy2 threadpoolctl pooch hypothesis
        pip install -r requirements/openblas.txt
    - name: Build and run tests
      env:
        PYTHON_GIL: 0
      # TODO: For some reason the Meson installation path points to
      # python3/site-packages as opposed to python3.13/site-packages,
      # then the dev.py scripts do not work as expected.
      run: |
        # python dev.py build --with-scipy-openblas
        # python dev.py --no-build test -j2 --mode full
        python -c "import scipy_openblas32; print(scipy_openblas32.get_pkg_config())" > scipy-openblas.pc
        PKG_CONFIG_PATH="$PWD" pip install . -vv --no-build-isolation
        pushd $RUNNER_TEMP
        PYTHON_GIL=0 python -m pytest --pyargs scipy -n2 --durations=10
  #################################################################################
  clang-17-build-only:
    # Purpose is to check for warnings in builds with latest clang.
    # We do not run the test suite here.
    name: Clang-17 build-only (-Werror)
    needs: get_commit_message
    if: >
      needs.get_commit_message.outputs.message == 1
      && (github.repository == 'scipy/scipy' || github.repository == '')
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4.1.1
        with:
          submodules: recursive

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"

      - name: Setup system dependencies
        run: |
          sudo apt-get -y update
          wget https://apt.llvm.org/llvm.sh
          chmod u+x llvm.sh
          sudo ./llvm.sh 17
          sudo apt install -y libopenblas-dev liblapack-dev

      - name: Setup Python build deps
        run: |
          pip install -r requirements/build.txt
          pip install build

      - name: Build wheel, check for compiler warnings
        run: |
          # specify which compilers to use using environment variables
          CC=clang-17 CXX=clang++-17 FC=gfortran python -m build -wnx -Csetup-args=--werror