cache pip dependencies in CI; pin setuptool[_scm] dependencies to fix build; codecov action bump #358
Workflow file for this run
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| name: tests+pypi | |
| defaults: | |
| run: | |
| shell: bash | |
| # arbitrarily selected runs | |
| env: | |
| animation_run: '3.10/ubuntu-latest/0/openmpi' | |
| codecov_run: '3.10/ubuntu-latest/1/openmpi' | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| schedule: | |
| - cron: '0 13 * * 4' | |
| release: | |
| types: [published] | |
| jobs: | |
| precommit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: '3.10' | |
| - name: Linting | |
| run: | | |
| pip install pre-commit | |
| pre-commit clean | |
| pre-commit autoupdate | |
| pre-commit run --all-files | |
| pdoc: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| persist-credentials: false | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - uses: mpi4py/setup-mpi@v1 | |
| - name: Build | |
| run: | | |
| pip install pdoc3 | |
| pip install -e . | |
| python -We -m pdoc --html PyMPDATA_MPI | |
| - name: Deploy | |
| if: github.ref == 'refs/heads/main' | |
| uses: JamesIves/[email protected] | |
| with: | |
| BRANCH: pdoc | |
| FOLDER: html/PyMPDATA_MPI | |
| CLEAN: true | |
| zenodo_json: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: notiz-dev/github-action-json-property@release | |
| with: | |
| path: '.zenodo.json' | |
| prop_path: 'creators' | |
| pylint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: mpi4py/setup-mpi@v1 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e .[tests] | |
| pip install pylint pytest matplotlib | |
| - name: Analysing the code with pylint | |
| run: | | |
| pylint --unsafe-load-any-extension=y --disable=fixme $(git ls-files '*.py') | |
| tests_setup: | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-latest, macos-latest] | |
| mpi: [ 'mpich', 'openmpi', 'intelmpi'] | |
| python-version: ["3.10"] | |
| exclude: | |
| # as of time of writing, mpi4py/setup-mpi does not support it | |
| - platform: macos-latest | |
| mpi: intelmpi | |
| # issues with: *** The MPI_Comm_rank() function was called before MPI_INIT was invoked. | |
| - platform: ubuntu-latest | |
| mpi: intelmpi | |
| # https://github.com/Homebrew/homebrew-core/issues/26974 | |
| - platform: macos-latest | |
| mpi: mpich | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: echo pip_user_site=$(python -c "import sysconfig; print(sysconfig.get_path('purelib'))") >> $GITHUB_ENV | |
| - id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pip_user_site }} | |
| key: ${{ matrix.platform }}-${{ matrix.mpi }}-${{ matrix.python-version }} | |
| - if: steps.cache.outputs.cache-hit != 'true' | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: ${{ matrix.mpi }} | |
| - if: steps.cache.outputs.cache-hit != 'true' && matrix.mpi == 'mpich' | |
| run: echo _ch="ch" >> $GITHUB_ENV | |
| - if: steps.cache.outputs.cache-hit != 'true' && startsWith(matrix.platform, 'ubuntu-') | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y libhdf5-mpi$_ch-dev pkg-config | |
| lscpu | |
| - if: steps.cache.outputs.cache-hit != 'true' && startsWith(matrix.platform, 'ubuntu-') && matrix.mpi == 'mpich' | |
| run: | | |
| echo HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich >> $GITHUB_ENV | |
| echo HDF5_INCLUDEDIR=/usr/include/hdf5/mpich >> $GITHUB_ENV | |
| - if: steps.cache.outputs.cache-hit != 'true' && startsWith(matrix.platform, 'macos-') | |
| run: | | |
| brew install hdf5-mpi && echo HDF5_DIR=/opt/homebrew >> $GITHUB_ENV | |
| sysctl -a | grep cpu | grep hw | |
| - if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| HDF5_MPI="ON" CC=mpicc pip install --no-binary=h5py h5py==3.10.0 | |
| pip install -e .[tests] | |
| - run: pip show numpy | |
| - id: cache-save | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{ env.pip_user_site }} | |
| key: ${{ matrix.platform }}-${{ matrix.mpi }}-${{ matrix.python-version }} | |
| tests: | |
| needs: [zenodo_json, pylint, pdoc, precommit, tests_setup] | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-latest, macos-latest] | |
| mpi: [ 'mpich', 'openmpi', 'intelmpi'] | |
| python-version: ["3.10"] | |
| disable-jit: [1, 0] | |
| mpi-np: [1, 2, 3] | |
| exclude: | |
| # as of time of writing, mpi4py/setup-mpi does not support it | |
| - platform: macos-latest | |
| mpi: intelmpi | |
| # issues with: *** The MPI_Comm_rank() function was called before MPI_INIT was invoked. | |
| - platform: ubuntu-latest | |
| mpi: intelmpi | |
| # https://github.com/Homebrew/homebrew-core/issues/26974 | |
| - platform: macos-latest | |
| mpi: mpich | |
| fail-fast: false | |
| runs-on: ${{ matrix.platform }} | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: echo pip_user_site=$(python -c "import sysconfig; print(sysconfig.get_path('purelib'))") >> $GITHUB_ENV | |
| - uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: ${{ matrix.mpi }} | |
| - if: matrix.mpi == 'mpich' | |
| run: echo _ch="ch" >> $GITHUB_ENV | |
| - if: startsWith(matrix.platform, 'ubuntu-') | |
| run: sudo apt-get update && sudo apt-get install -y libhdf5-mpi$_ch-dev pkg-config | |
| - if: startsWith(matrix.platform, 'macos-') | |
| run: brew install hdf5-mpi && echo HDF5_DIR=/opt/homebrew >> $GITHUB_ENV | |
| - if: startsWith(matrix.platform, 'ubuntu-') && matrix.mpi == 'mpich' | |
| run: | | |
| echo HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich >> $GITHUB_ENV | |
| echo HDF5_INCLUDEDIR=/usr/include/hdf5/mpich >> $GITHUB_ENV | |
| #- run: pip install -e .[tests] | |
| - id: cache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ${{ env.pip_user_site }} | |
| key: ${{ matrix.platform }}-${{ matrix.mpi }}-${{ matrix.python-version }} | |
| - run: PATH=$PATH:${{ env.pip_user_site }} | |
| - run: python -We -c "import PyMPDATA_MPI" | |
| - if: matrix.mpi == 'openmpi' | |
| run: echo _mpiexec_args="--oversubscribe" >> $GITHUB_ENV | |
| - name: "mpiexec pytest" | |
| env: | |
| NUMBA_DISABLE_JIT: ${{ matrix.disable-jit }} | |
| run: | | |
| echo $PATH | |
| pip show pytest | |
| if [ "$animation_run" == "${{ matrix.python-version }}/${{ matrix.platform }}/${{ matrix.disable-jit }}/${{ matrix.mpi }}" ]; then | |
| export CI_PLOTS_PATH=plots/$animation_run | |
| mkdir -p $CI_PLOTS_PATH | |
| fi | |
| if [ "${{ matrix.mpi-np }}" == "1" ] && [ "$codecov_run" == "${{ matrix.python-version }}/${{ matrix.platform }}/${{ matrix.disable-jit }}/${{ matrix.mpi }}" ]; then | |
| echo "CODECOV_RUN=1" >> $GITHUB_ENV | |
| export COV_ARGS="--cov=./ --cov-report=xml" | |
| pip install pytest-cov | |
| fi | |
| pytest -s -vv -We tests/local | |
| NUMBA_NUM_THREADS=3 mpiexec $_mpiexec_args -n ${{ matrix.mpi-np }} pytest $COV_ARGS --timeout=600 --timeout_method=thread -s -vv -We tests/local; | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: plots | |
| path: plots | |
| - if: env.CODECOV_RUN == '1' | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| verbose: true | |
| package: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480 | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.10" | |
| - run: pip install twine build | |
| - run: | | |
| unset CI | |
| python -m build 2>&1 | tee build.log | |
| exit `fgrep -i warning build.log | wc -l` | |
| - run: twine check --strict dist/* | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: dist | |
| path: dist | |
| dist: | |
| runs-on: ubuntu-latest | |
| needs: [package,tests] | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: dist | |
| path: dist | |
| - if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| uses: pypa/gh-action-pypi-publish@unstable/v1 | |
| with: | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| - if: startsWith(github.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@unstable/v1 | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| devops_tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480 | |
| - run: pip install -r tests/devops_tests/requirements.txt | |
| - env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: pytest --durations=10 -v -s -We -p no:unraisableexception tests/devops_tests | |
| tip-release-uploads: | |
| runs-on: ubuntu-latest | |
| needs: [tests, devops_tests] | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: plots | |
| path: plots | |
| - run: | | |
| sudo apt install -y librsvg2-bin | |
| for scenario in ./plots/${{ env.animation_run }}/*; do | |
| for test_plots in $scenario/*; do | |
| if [ ! $(find "$test_plots" -maxdepth 0 -empty | wc -l) -eq 1 ]; then | |
| for file in $test_plots/*.svg; do | |
| rsvg-convert $file -o tmp.png | |
| convert tmp.png -flatten -trim +repage -bordercolor white -border 10 $file.png | |
| done; | |
| rm tmp.png | |
| convert $test_plots/*.png plots/`basename $test_plots`-`basename $scenario`-anim.gif | |
| fi | |
| done; | |
| done; | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: anims | |
| path: plots/*-anim.gif | |
| - if: github.ref == 'refs/heads/main' | |
| uses: eine/tip@master | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| files: plots/*-anim.gif | |
| tag: 'latest-generated-plots' |