ci_pipeline.yml

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: 'sig.pancetta+github@email.com'
#          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
#