Monodomain project #1575
Workflow file for this run
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| name: CI pipeline for pySDC | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '1 5 * * 1' | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| env: | |
| YML: 'etc/environment-lint.yml' | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v1 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ env.YML }} | |
| create-args: >- | |
| python=3.10 | |
| - name: Code reformatting with black | |
| run: | | |
| black pySDC --check --diff --color | |
| - name: Linting with flakeheaven | |
| run: | | |
| flakeheaven lint --benchmark pySDC | |
| # mirror_to_gitlab: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v1 | |
| # - name: Mirror | |
| # uses: jakob-fritz/github2lab_action@main | |
| # env: | |
| # MODE: 'mirror' # Either 'mirror', 'get_status', or 'both' | |
| # GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET_H }} | |
| # FORCE_PUSH: "true" | |
| # GITLAB_HOSTNAME: "codebase.helmholtz.cloud" | |
| # GITLAB_PROJECT_ID: "3525" | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| user_cpu_tests_linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: ['3.8', '3.9', '3.10'] | |
| env: ['base', 'fenics', 'mpi4py', 'petsc'] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: "etc/environment-${{ matrix.env }}.yml" | |
| create-args: >- | |
| python=${{ matrix.python }} | |
| - name: Run pytest for CPU stuff | |
| run: | | |
| echo "print('Loading sitecustomize.py...') | |
| import coverage | |
| coverage.process_startup() " > sitecustomize.py | |
| coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m ${{ matrix.env }} | |
| - name: Make coverage report | |
| run: | | |
| mv data data_${{ matrix.python }} | |
| coverage combine | |
| mv .coverage coverage_${{ matrix.env }}_${{ matrix.python }}.dat | |
| - name: Uploading artifacts | |
| uses: actions/upload-artifact@v3 | |
| if: matrix.python == '3.10' | |
| with: | |
| name: cpu-test-artifacts | |
| path: | | |
| data_3.10 | |
| coverage_${{ matrix.env }}_3.10.dat | |
| user_libpressio_tests: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: brownbaerchen/libpressio:amd64_2 | |
| volumes: | |
| - ${{ github.workspace }}:/pySDC | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install pySDC and pytest | |
| run: | | |
| source /pySDC/pySDC/projects/compression/Docker/install_pySDC.sh | |
| - name: Run pytest | |
| run: | | |
| source /opt/spack/share/spack/setup-env.sh | |
| spack load libpressio | |
| coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m libpressio | |
| - name: Make coverage report | |
| run: | | |
| source /opt/spack/share/spack/setup-env.sh | |
| spack load libpressio | |
| mv data data_libpressio | |
| coverage combine | |
| mv .coverage coverage_libpressio_3.10.dat | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cpu-test-artifacts | |
| path: | | |
| data_libpressio | |
| coverage_libpressio_3.10.dat | |
| user_monodomain_tests_linux: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: "pySDC/projects/Monodomain/etc/environment-monodomain.yml" | |
| create-args: >- | |
| python=3.10 | |
| - name: Compile C++ ionic models | |
| env: | |
| IONIC_MODELS_PATH: "pySDC/projects/Monodomain/problem_classes/ionicmodels/cpp" | |
| run: | | |
| c++ -O3 -Wall -shared -std=c++11 -fPIC -fvisibility=hidden $(python3 -m pybind11 --includes) ${IONIC_MODELS_PATH}/bindings_definitions.cpp -o ${IONIC_MODELS_PATH}/ionicmodels$(python3-config --extension-suffix) | |
| - name: Run pytest for CPU stuff | |
| run: | | |
| echo "print('Loading sitecustomize.py...') | |
| import coverage | |
| coverage.process_startup() " > sitecustomize.py | |
| coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m monodomain | |
| - name: Make coverage report | |
| run: | | |
| mv data data_monodomain | |
| coverage combine | |
| mv .coverage coverage_monodomain_3.10.dat | |
| - name: Uploading artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cpu-test-artifacts | |
| path: | | |
| data_monodomain | |
| coverage_monodomain_3.10.dat | |
| # user_cpu_tests_macos: | |
| # runs-on: macos-12 | |
| # | |
| # strategy: | |
| # matrix: | |
| # env: ['base', 'fenics', 'mpi4py', 'petsc'] | |
| # | |
| # defaults: | |
| # run: | |
| # shell: bash -l {0} | |
| # | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v3 | |
| # | |
| # - name: Install Conda environment with Micromamba | |
| # uses: mamba-org/setup-micromamba@v1 | |
| # with: | |
| # environment-file: "etc/environment-${{ matrix.env }}.yml" | |
| # | |
| # - name: Run pytest for CPU stuff | |
| # run: | | |
| # pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m ${{ matrix.env }} | |
| # wait_for_gitlab: | |
| # runs-on: ubuntu-latest | |
| # needs: | |
| # - mirror_to_gitlab | |
| # steps: | |
| # - name: Wait | |
| # uses: jakob-fritz/github2lab_action@main | |
| # env: | |
| # MODE: 'get_status' # Either 'mirror', 'get_status', or 'both' | |
| # GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET_H }} | |
| # FORCE_PUSH: "true" | |
| # GITLAB_HOSTNAME: "codebase.helmholtz.cloud" | |
| # GITLAB_PROJECT_ID: "3525" | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # # - name: Get and prepare artifacts | |
| # # run: | | |
| # # pipeline_id=$(curl --header "PRIVATE-TOKEN: ${{ secrets.GITLAB_SECRET_H }}" --silent "https://gitlab.hzdr.de/api/v4/projects/3525/repository/commits/${{ github.head_ref || github.ref_name }}" | jq '.last_pipeline.id') | |
| # # job_id=$(curl --header "PRIVATE-TOKEN: ${{ secrets.GITLAB_SECRET_H }}" --silent "https://gitlab.hzdr.de/api/v4/projects/3525/pipelines/$pipeline_id/jobs" | jq '.[] | select( .name == "bundle" ) | select( .status == "success" ) | .id') | |
| # # curl --output artifacts.zip "https://gitlab.hzdr.de/api/v4/projects/3525/jobs/$job_id/artifacts" | |
| # # rm -rf data | |
| # # unzip artifacts.zip | |
| # # ls -ratl | |
| post-processing: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.repository_owner == 'Parallel-in-Time'}} | |
| needs: | |
| - lint | |
| - user_cpu_tests_linux | |
| - user_libpressio_tests | |
| - user_monodomain_tests_linux | |
| # - wait_for_gitlab | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: "etc/environment-base.yml" | |
| - name: Downloading artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| path: . | |
| - name: Prepare artifacts | |
| run: | | |
| ls -artl cpu-test-artifacts | |
| cp cpu-test-artifacts/data_3.10/* data/. | |
| python -m coverage combine cpu-test-artifacts/coverage_*_3.10.dat | |
| python -m coverage xml | |
| python -m coverage html | |
| - name: Generate Coverage badge | |
| run: | | |
| pip install genbadge[all] | |
| genbadge coverage -i coverage.xml -o htmlcov/coverage-badge.svg | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| # - name: Generate benchmark report | |
| # uses: pancetta/github-action-benchmark@v1 | |
| # if: ${{ (!contains(github.event.head_commit.message, '[CI-no-benchmarks]')) && (github.event_name == 'push') }} | |
| # with: | |
| # name: pySDC Benchmark with pytest-benchmark | |
| # tool: 'pytest' | |
| # output-file-path: benchmarks/output.json | |
| # auto-push: false | |
| # skip-fetch-gh-pages: true | |
| # benchmark-data-dir-path: bench/${{ github.head_ref || github.ref_name }} | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # | |
| # - name: Push benchmark data | |
| # uses: dmnemec/copy_file_to_another_repo_action@main | |
| # if: "!contains(github.event.head_commit.message, '[CI-no-benchmarks]')" | |
| # env: | |
| # API_TOKEN_GITHUB: ${{ secrets.BENCHMARK_BOT }} | |
| # with: | |
| # source_file: 'bench/${{ github.head_ref || github.ref_name }}' | |
| # destination_repo: 'Parallel-in-Time/pySDC-benchmarks' | |
| # user_email: '[email protected]' | |
| # user_name: 'pancetta' | |
| - name: Build html I | |
| run: | | |
| chmod u+x ./docs/update_apidocs.sh | |
| ./docs/update_apidocs.sh | |
| sphinx-build -b html docs/source docs/build/html | |
| mkdir -p docs/build/html/coverage | |
| mv htmlcov/* docs/build/html/coverage/. | |
| # - name: Build html II | |
| # if: "!contains(github.event.head_commit.message, '[CI-no-benchmarks]')" | |
| # run: | | |
| # mkdir -p docs/build/html/benchmarks | |
| # cp -r bench/${{ github.head_ref || github.ref_name }}/* docs/build/html/benchmarks/. | |
| - name: Store docs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: docs | |
| path: docs/build/html | |
| - name: Deploy 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| if: ${{ github.event_name == 'push' && github.repository_owner == 'Parallel-in-Time' && github.ref == 'refs/heads/master' }} | |
| with: | |
| branch: gh-pages # The branch the action should deploy to. | |
| folder: docs/build/html # The folder the action should deploy. | |
| # spawn_gitlab_and_postprocess: | |
| # runs-on: ubuntu-latest | |
| # | |
| ## needs: | |
| ## - lint | |
| # | |
| # defaults: | |
| # run: | |
| # shell: bash -l {0} | |
| # | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v3 | |
| # with: | |
| # fetch-depth: 0 | |
| # ref: ${{ github.event.pull_request.head.sha }} | |
| # | |
| # - name: Checkout benchmark repository | |
| # uses: actions/checkout@v3 | |
| # if: ${{ github.event_name == 'push' }} | |
| # with: | |
| # repository: Parallel-in-Time/pySDC-benchmarks | |
| # token: ${{ secrets.BENCHMARK_BOT }} | |
| # path: bench | |
| # ref: main | |
| # | |
| # - name: Install Conda environment with Micromamba | |
| # uses: mamba-org/provision-with-micromamba@main | |
| # with: | |
| # environment-file: etc/environment-base.yml | |
| # | |
| # - name: Mirror + trigger CI | |
| # uses: SvanBoxel/gitlab-mirror-and-ci-action@master | |
| # with: | |
| # args: "https://gitlab.hzdr.de/r.speck/pysdc" | |
| # env: | |
| # FORCE_PUSH: "true" | |
| # GITLAB_HOSTNAME: "gitlab.hzdr.de" | |
| # GITLAB_USERNAME: ${{ secrets.GITLAB_SECRET_USER }} | |
| # GITLAB_PASSWORD: ${{ secrets.GITLAB_SECRET_PASS }} | |
| # GITLAB_PROJECT_ID: "3525" | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # | |
| # - name: Get and prepare artifacts | |
| # run: | | |
| # pipeline_id=$(curl --header "PRIVATE-TOKEN: ${{ secrets.GITLAB_SECRET_H }}" --silent "https://gitlab.hzdr.de/api/v4/projects/3525/repository/commits/${{ github.head_ref || github.ref_name }}" | jq '.last_pipeline.id') | |
| # job_id=$(curl --header "PRIVATE-TOKEN: ${{ secrets.GITLAB_SECRET_H }}" --silent "https://gitlab.hzdr.de/api/v4/projects/3525/pipelines/$pipeline_id/jobs" | jq '.[] | select( .name == "bundle" ) | select( .status == "success" ) | .id') | |
| # curl --output artifacts.zip "https://gitlab.hzdr.de/api/v4/projects/3525/jobs/$job_id/artifacts" | |
| # rm -rf data | |
| # unzip artifacts.zip | |
| # | |