Improved filtering of restarted values in post processing and more ou… #1216
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 }} | |
| - 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: ${{ secrets.GITHUB_TOKEN }} | |
| user_cpu_tests_linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: ['3.7', '3.8', '3.9', '3.10'] | |
| env: ['base', 'fenics', 'mpi4py', 'petsc'] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: "etc/environment-${{ 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: | |
| - ${{ github.workspace }}:/pySDC | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install pySDC and pytest | |
| run: | | |
| source /pySDC/pySDC/projects/compression/Docker/install_pySDC.sh | |
| - name: Run pytest | |
| run: | | |
| source /opt/spack/share/spack/setup-env.sh | |
| spack load libpressio | |
| coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m libpressio | |
| - name: Make coverage report | |
| run: | | |
| source /opt/spack/share/spack/setup-env.sh | |
| spack load libpressio | |
| mv data data_libpressio | |
| coverage combine | |
| mv .coverage coverage_libpressio_3.10.dat | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cpu-test-artifacts | |
| path: | | |
| data_libpressio | |
| coverage_libpressio_3.10.dat | |
| user_cpu_tests_macos: | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| env: ['base', 'fenics', 'mpi4py', 'petsc'] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: "etc/environment-${{ 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 | |
| # - 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 | |
| # | |