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

  user_cpu_tests_linux:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        env: ['base', 'fenics', 'mpi4py', 'petsc', 'pytorch']
        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - 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: Install additional packages as needed
        run: |
          micromamba install -y --file etc/environment-tests.yml --freeze-installed
      - 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@v4
        if: matrix.python == '3.10'
        with:
          name: test-artifacts-cpu-${{ matrix.env }}
          path: |
            data_3.10
            coverage_${{ matrix.env }}_3.10.dat

  project_cpu_tests_linux:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        env: 
          - AllenCahn_Bayreuth
          - AsympConv
          - DAE
          - FastWaveSlowWave
          - Hamiltonian
          - matrixPFASST
          - parallelSDC
          - parallelSDC_reloaded
          - PinTSimE
          - RDC
          - Resilience
          - SDC_showdown
          - Second_orderSDC
          - soft_failure
          - TOMS
        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
        exclude:
          - env: parallelSDC
            python: '3.11'
          - env: parallelSDC
            python: '3.12'
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Install Conda environment with Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: "pySDC/projects/${{ matrix.env }}/environment.yml"
          create-args: >-
              python=${{ matrix.python }}
      - name: Install additional packages as needed
        run: |
          micromamba install -y --file etc/environment-tests.yml --freeze-installed
      - 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/projects/${{ matrix.env }}/tests
      - name: Make coverage report
        run: |
          mv data data_${{ matrix.python }}
          coverage combine
          mv .coverage coverage_${{ matrix.env }}_${{ matrix.python }}.dat
      - name: Uploading artifacts
        uses: actions/upload-artifact@v4
        if: matrix.python == '3.10'
        with:
          name: test-artifacts-project-${{ matrix.env }}
          path: |
            data_3.10
            coverage_${{ 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@v4
      - 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/projects/compression/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@v4
        with:
          name: test-artifacts-libpressio
          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@v4
      - 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/projects/Monodomain/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@v4
        with:
          name: test-artifacts-monodomain
          path: |
            data_monodomain
            coverage_monodomain_3.10.dat

  post-processing:
    runs-on: ubuntu-latest
    if: ${{ github.repository_owner == 'Parallel-in-Time'}}
    needs:
      - lint
      - user_cpu_tests_linux
      - project_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@v4
      - name: Install Conda environment with Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: "etc/environment-postprocess.yml"
      - name: Downloading artifacts
        uses: actions/download-artifact@v4
        with:
          path: .
          merge-multiple: true
      - name: Prepare artifacts
        run: |
          cp data_3.10/* data/.
          python -m coverage combine coverage_*_3.10.dat
          python -m coverage xml
          python -m coverage html
      - name: Generate Coverage badge
        run: |
          genbadge coverage -i coverage.xml -o htmlcov/coverage-badge.svg
      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV }}
        
#      - 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: Store docs
        uses: actions/upload-artifact@v4
        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.