WIP: Doctest ng #14
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| name: Linux Meson 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: Meson build | |
| 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/[email protected] | |
| 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@v3 | |
| 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: Mypy | |
| if: matrix.python-version == '3.10' | |
| run: | | |
| # Packages that are only needed for their annotations | |
| python -m pip install mypy==1.0.0 types-psutil typing_extensions | |
| python -m pip install pybind11 sphinx | |
| python -u dev.py mypy | |
| - name: doctest_ng | |
| run: | | |
| sudo apt-get install -y wamerican-small threadpoolctl | |
| python -m pip install git+https://github.com/ev-br/scpdt.git | |
| python -m pip install matplotlib | |
| python dev.py doctest | |
| - name: Test SciPy | |
| run: | | |
| export OMP_NUM_THREADS=2 | |
| export SCIPY_USE_PROPACK=1 | |
| python dev.py --no-build test -j2 -- --durations 10 --timeout=60 | |
| ################################################################################# | |
| test_venv_install: | |
| name: Pip install into venv | |
| 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/[email protected] | |
| 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 | |
| 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/[email protected] | |
| 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" | |
| ################################################################################# | |
| gcc8: | |
| # Purpose is to examine builds with oldest-supported gcc and test with pydata/sparse. | |
| name: Build with gcc-8 | |
| needs: get_commit_message | |
| if: > | |
| needs.get_commit_message.outputs.message == 1 | |
| && (github.repository == 'scipy/scipy' || github.repository == '') | |
| runs-on: ubuntu-20.04 # 22.04 doesn't support gcc-8 | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.9" | |
| - name: Setup OS | |
| run: | | |
| sudo apt-get -y update | |
| sudo apt install -y g++-8 gcc-8 gfortran-8 | |
| sudo apt install -y libatlas-base-dev liblapack-dev libgmp-dev \ | |
| libmpfr-dev libmpc-dev pkg-config libsuitesparse-dev liblapack-dev | |
| - name: Setup Python deps | |
| run: | | |
| pip install "numpy==1.22.4" && | |
| # build deps | |
| pip install build meson-python ninja pythran pybind11 cython | |
| # test deps | |
| pip install gmpy2 threadpoolctl mpmath pooch pythran pybind11 pytest pytest-xdist==2.5.0 pytest-timeout hypothesis | |
| pip install sparse | |
| - name: Build wheel and install | |
| run: | | |
| set -euo pipefail | |
| export PYTHONOPTIMIZE=2 | |
| # specify which compilers to use using environment variables | |
| CC=gcc-8 CXX=g++-8 FC=gfortran-8 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: 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 and 64-bit BLAS | |
| 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 2.0-dev at build time; 3.9 job then downgrades to | |
| # lowest supported NumPy version in order to test ABI compatibility. | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - uses: actions/[email protected] | |
| 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@v3 | |
| id: cache | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-prerelease | |
| - name: Install Python packages | |
| run: | | |
| python -m pip install cython pythran ninja meson-python pybind11 click rich_click pydevtool | |
| # Note: matplotlib not installed here to avoid issues around numpy 2.0 | |
| # (it can be put back after matplotlib has made a 2.0-compatible | |
| # release on PyPI. | |
| python -m pip install --pre --upgrade pytest pytest-cov pytest-xdist mpmath gmpy2 threadpoolctl pooch hypothesis | |
| # TODO: once the scipy_ symbol prefix issue is fixed, install | |
| # scipy-openblas32 from the pre-releases bucket again (see gh-19640) | |
| python -m pip install "scipy-openblas32<=0.3.23.293.2" | |
| # Install numpy last, to ensure we get 2.0.0-dev (avoid possible <2.0 constraints). | |
| python -m pip install --pre --upgrade --timeout=60 -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy | |
| - name: Prepare compiler cache | |
| id: prep-ccache | |
| shell: bash | |
| run: | | |
| mkdir -p "${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@v3 | |
| 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 == '3.9' | |
| run: | | |
| python -m pip install "numpy==1.22.4" | |
| - 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: Linux - 32 bit | |
| 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/[email protected] | |
| with: | |
| submodules: recursive | |
| - name: build + test | |
| run: | | |
| set -euo 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 && \ | |
| basedir=\$(python3.9 tools/openblas_support.py) && \ | |
| cp -r \$basedir/lib/* /usr/local/lib && \ | |
| cp \$basedir/include/* /usr/local/include && \ | |
| export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig && \ | |
| python3.9 -m venv test && \ | |
| source test/bin/activate && \ | |
| python -m pip install doit click rich_click pydevtool meson ninja && \ | |
| python -m pip install numpy==1.22.4 cython pybind11 pytest pytest-timeout pytest-xdist pytest-env 'Pillow<10.0.0' mpmath pythran pooch meson hypothesis && \ | |
| LD_LIBRARY_PATH=/usr/local/lib python dev.py build && \ | |
| LD_LIBRARY_PATH=/usr/local/lib python dev.py test" |