main.yml

# NOTE:
# When we build kotekan on the Github VM we need to take into account a few
# limitations: first we can't lock very much memory so we need to disable
# mlock the buffers. Second, the VMs run across a range of CPU
# architectures (from Haswell to Skylake-AVX512 as of 2020/03). Because our
# use of ccache shares compiled objects we must target our build for the
# lowest architecture available or we will occasionally crash with SIGILL
# when a newer instruction is called than is available.  


name: kotekan-ci-tests
on:
  pull_request:
    branches:
    - chord
    - develop
    - master
  push:
    branches:
    - chord
    - develop
    - master

env:
  REGISTRY: ghcr.io
  IMG_IWYU: "ghcr.io/kotekan/kotekan/kotekan-iwyu"
  IMG_1804: "ghcr.io/${{ github.repository }}/kotekan-1804"
  IMG_2204: "ghcr.io/${{ github.repository }}/kotekan-2204"
  PYTEST_TIMEOUT: 60

jobs:

  # 2204 Tests

  # Ubuntu 22.04 docker image build and push
  build-docker-2204:
    runs-on: ubuntu-latest
    permissions: write-all

    steps:
    - name: Checkout repository
      uses: actions/checkout@v3

    - name: Check for file changes
      uses: tj-actions/changed-files@v37
      id: changed-files

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    # Rebuild (or build) for a push/pr from a local branch (separate workflow for PR merges)
    - name: Check to see if a docker rebuild is needed
      id: docker_img
      run: |
        echo "docker_build=" >> $GITHUB_OUTPUT; # Default to no rebuild

        if [[ ${{ contains(steps.changed-files.outputs.all_modified_files, 'tools/docker/22.04/Dockerfile') }} == "true" || ${DOCKER_BUILD} ]] ; then
          echo "Modified Dockerfile found (or re-build requested). Building on local branch."
          if [ "${GITHUB_EVENT_NAME}" = "push" ]; then
            IMAGE_NAME="${IMG_2204}:$(echo ${GITHUB_REF_NAME} | tr / .)"
          else
            IMAGE_NAME="${IMG_2204}:$(echo ${GITHUB_HEAD_REF} | tr / .)"
          fi
          echo "docker_build=1" >> $GITHUB_OUTPUT;
        else
          if [ "${GITHUB_EVENT_NAME}" = "pull_request" || "${GITHUB_EVENT_NAME}" = "pull_request_target" ]; then
            echo "Dockerfile was not modified. Using image from branch ${GITHUB_BASE_REF}."
            IMAGE_NAME="${IMG_2204}:$(echo ${GITHUB_BASE_REF} | tr / .)"
          else
            # This can happen when we're merging a chord branch back to chord, eg
            echo "Dockerfile was not modified. Using image from branch ${GITHUB_REF_NAME}."
            IMAGE_NAME="${IMG_2204}:$(echo ${GITHUB_REF_NAME} | tr / .)"
          fi
        fi

        if docker manifest inspect ${IMAGE_NAME} >/dev/null; then
          echo "Docker package found."
        else
          echo "Docker package NOT found. Setting docker_build=1."
          echo "docker_build=1" >> $GITHUB_OUTPUT;
        fi

        echo "img_name=${IMAGE_NAME}" >> $GITHUB_OUTPUT;
        echo "Image name: ${IMAGE_NAME}"

    - name: Output environment variable details
      run: |
        echo "The job_id is: $GITHUB_JOB"
        echo "The id of this action is: $GITHUB_ACTION"
        echo "The run id is: $GITHUB_RUN_ID"
        echo "The repository is: $GITHUB_REPOSITORY"
        echo "The GitHub Actor's username is: $GITHUB_ACTOR"
        echo "GitHub SHA: $GITHUB_SHA"
        echo "GitHub event name: $GITHUB_EVENT_NAME"
        echo "GitHub Ref: $GITHUB_REF"
        echo "GitHub Head Ref: $GITHUB_HEAD_REF"
        echo "GitHub Base Ref: $GITHUB_BASE_REF"
        echo "GitHub Ref Name: $GITHUB_REF_NAME"
        echo "Docker 1804 image: $IMG_1804"
        echo "Docker 2204 image: $IMG_2204"
        echo "Docker IWYU image: $IMG_IWYU"
        echo "Used docker image name: ${{ steps.docker_img.outputs.img_name }}"
        echo "docker_build: ${{ steps.docker_img.outputs.docker_build }}"
        echo "img_name: ${{ steps.docker_img.outputs.img_name }}"

    - name: Build and Push Docker Image
      if: steps.docker_img.outputs.docker_build
      run: |
        echo "Building and pushing ${{ steps.docker_img.outputs.img_name }}"
        docker build --cache-from=${IMG_2204} -t "${{ steps.docker_img.outputs.img_name }}" - < tools/docker/22.04/Dockerfile
        docker push "${{ steps.docker_img.outputs.img_name }}"

    outputs:
      docker_img_name: "${{ steps.docker_img.outputs.img_name }}"

  # Build kotekan documentation
  build-docs:
    runs-on: ubuntu-latest
    needs: build-docker-2204

    steps:
    - uses: actions/checkout@v3

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Build kotekan docs
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-docs/ "${{ needs.build-docker-2204.outputs.docker_img_name }}")
        docker run "${OPTS[@]}" \
          cmake \
            -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DDOXYGEN_EXECUTABLE=/usr/local/bin/doxygen \
            -DWERROR=ON \
            -DCOMPILE_DOCS=ON \
            ..
        docker run "${OPTS[@]}" make doc
        docker run "${OPTS[@]}" make sphinx

  # Linting
  lint:
    runs-on: ubuntu-latest
    needs: build-docker-2204

    steps:
    - uses: actions/checkout@v3

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Run cmakelint
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" tools/cmakelint.sh /code/kotekan

    - name: Run black
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" black --exclude docs --check .

    - name: Run clang-format
      run: |
        mkdir -p build-check-format
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-check-format/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated ..
        docker run "${OPTS[@]}" make clang-format
        git diff --exit-code

  # Build a basic version of kotekan
  build-base-2204:
    runs-on: ubuntu-latest
    needs: build-docker-2204

    steps:
    - uses: actions/checkout@v3

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Cache ccache files
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ccache-base-build-2204-${{ github.sha }}
        restore-keys: |
          ccache-base-build-2204
          ccache-full-build-2204

    - name: Build kotekan
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-2204/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_LINK_WHAT_YOU_USE=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DARCH=haswell \
            -DCCACHE=ON \
            -DWITH_TESTS=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" ccache -s

  # Build a full version of kotekan and run the unit tests
  build-full-tests-2204:
    runs-on: ubuntu-latest
    needs: build-docker-2204

    steps:
    - uses: actions/checkout@v3

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Cache ccache files
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ccache-full-build-2204-${{ github.sha }}
        restore-keys: |
          ccache-full-build-2204
          ccache-base-build-2204

    - name: Free disk space
      if: ${{ !env.ACT }} # Don't free up if running locally
      run: |
          df -h
          docker rmi $(docker image ls -aq)
          df -h
          sudo apt-get clean
          sudo apt-get autoclean
          df -h

    - name: Build kotekan
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-2204/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_LINK_WHAT_YOU_USE=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DUSE_ASDF=ON \
            -DUSE_HDF5=ON -DHIGHFIVE_PATH=/code/build/HighFive \
            -DUSE_LAPACK=ON -DBLAZE_PATH=/code/build/blaze \
            -DARCH=haswell \
            -DNO_MEMLOCK=ON \
            -DUSE_OMP=ON \
            -DWITH_BOOST_TESTS=ON \
            -DCCACHE=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" rm -r lib
        docker run "${OPTS[@]}" ccache -s
        df -h

    - name: Run direct Kotekan tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ./build-2204/kotekan/kotekan --bind-address 0:23000 --config config/tests/julia_hello_world.yaml

    - name: Run parallel python tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" pytest -v -n auto --dist=loadfile --timeout=${PYTEST_TIMEOUT} -x -m 'not serial'

    - name: Run serial python tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" bash -c "redis-server --daemonize yes; pytest -v -x --timeout=${PYTEST_TIMEOUT} -m serial"

    - name: Run boost tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-2204/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" pytest -v -x --timeout=${PYTEST_TIMEOUT}

  # Build an OpenCL version of kotekan and run the unit tests
  build-opencl-2204:
    runs-on: self-hosted
    container: 
      image: summerwind/actions-runner:ubuntu-22.04
      options: --user root
    needs: build-docker-2204

    steps:
    - uses: actions/checkout@v3

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Cache ccache files
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ccache-opencl-2204-${{ github.sha }}
        restore-keys: |
          ccache-opencl-2204
          ccache-base-build-2204

    - name: Build kotekan
      shell: bash
      run: |
        OPTS=(--pull=always --rm --mount type=bind,src=/home/lwlab/kotekan-runner/_work/kotekan/kotekan/,target=/code/kotekan -w /code/kotekan/build-2204/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DUSE_HDF5=ON -DHIGHFIVE_PATH=/code/build/HighFive \
            -DUSE_LAPACK=ON -DBLAZE_PATH=/code/build/blaze \
            -DNO_MEMLOCK=ON \
            -DUSE_OMP=ON \
            -DWITH_BOOST_TESTS=ON \
            -DUSE_CUDA=OFF \
            -DUSE_OPENCL=ON \
            -DCCACHE=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" rm -r lib
        docker run "${OPTS[@]}" ccache -s
        df -h

    - name: Run parallel python tests
      shell: bash
      run: |
        OPTS=(--rm --mount type=bind,src=/home/lwlab/kotekan-runner/_work/kotekan/kotekan/,target=/code/kotekan -w /code/kotekan/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" pytest -v -n auto --dist=loadfile --timeout=${PYTEST_TIMEOUT} -x -m 'not serial'

    - name: Run serial python tests
      shell: bash
      run: |
        OPTS=(--rm --mount type=bind,src=/home/lwlab/kotekan-runner/_work/kotekan/kotekan/,target=/code/kotekan -w /code/kotekan/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" bash -c "redis-server --daemonize yes; pytest -v -x --timeout=${PYTEST_TIMEOUT} -m serial"

    - name: Run boost tests
      shell: bash
      run: |
        OPTS=(--rm --mount type=bind,src=/home/lwlab/kotekan-runner/_work/kotekan/kotekan/,target=/code/kotekan -w /code/kotekan/build-2204/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" pytest -v -x --timeout=${PYTEST_TIMEOUT}

    - name: Clean up
      run: |
        rm -rf kotekan

  # Build a clang version of kotekan
  # Note that this build isn't working at the moment, so for now only run it upon request.
  build-clang-2204:
    runs-on: ubuntu-latest
    needs: build-docker-2204

    steps:
    - name: Checkout repository
      uses: actions/checkout@v3

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Cache ccache files
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ccache-clang-build-2204-${{ github.sha }}
        restore-keys: |
          ccache-clang-build-2204

    - name: Build kotekan
      env:
        CC: clang
        CXX: clang++
      if: env.RUN_2204_CLANG_TESTS
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-2204/ ${{ needs.build-docker-2204.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
        -DWERROR=ON \
        -DCMAKE_LINK_WHAT_YOU_USE=ON \
        -DUSE_OLD_DPDK=ON \
        -DCMAKE_BUILD_TYPE=Test \
        -DUSE_ASDF=ON \
        -DUSE_HDF5=ON \
        -DHIGHFIVE_PATH=/code/build/HighFive \
        -DUSE_LAPACK=ON \
        -DBLAZE_PATH=/code/build/blaze \
        -DARCH=haswell \
        -DNO_MEMLOCK=ON \
        -DUSE_OMP=ON \
        -DWITH_TESTS=ON \
        -DCCACHE=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" ccache -s



  # 1804 Tests

  # Build the docker image
  build-docker-1804:
    runs-on: ubuntu-latest
    permissions: write-all

    steps:
    - name: Checkout repository
      uses: actions/checkout@v3

    - name: Check for file changes
      uses: tj-actions/changed-files@v37
      id: changed-files

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    # Rebuild (or build) for a push/pr from a local branch (separate workflow for PR merges)
    - name: Check to see if a docker rebuild is needed
      id: docker_img
      run: |
        echo "docker_build=" >> $GITHUB_OUTPUT; # Default to no rebuild

        if [[ ${{ contains(steps.changed-files.outputs.all_modified_files, 'tools/docker/18.04/Dockerfile') }} == "true" || ${DOCKER_BUILD} ]] ; then
          echo "Modified Dockerfile found (or re-build requested). Building on local branch."
          if [ "${GITHUB_EVENT_NAME}" = "push" ]; then
            IMAGE_NAME="${IMG_1804}:$(echo ${GITHUB_REF_NAME} | tr / .)"
          else
            IMAGE_NAME="${IMG_1804}:$(echo ${GITHUB_HEAD_REF} | tr / .)"
          fi
          echo "docker_build=1" >> $GITHUB_OUTPUT;
        else
          echo "Dockerfile was not modified. Using develop branch image."
          IMAGE_NAME="${IMG_1804}:develop"
        fi

        if docker manifest inspect ${IMAGE_NAME} >/dev/null; then
          echo "Docker package found."
        else
          echo "Docker package NOT found. Setting docker_build=1."
          echo "docker_build=1" >> $GITHUB_OUTPUT;
        fi

        echo "img_name=${IMAGE_NAME}" >> $GITHUB_OUTPUT;
        echo "Image name: ${IMAGE_NAME}"

    - name: Output environment variable details
      run: |
        echo "The job_id is: $GITHUB_JOB"
        echo "The id of this action is: $GITHUB_ACTION"
        echo "The run id is: $GITHUB_RUN_ID"
        echo "The repository is: $GITHUB_REPOSITORY"
        echo "The GitHub Actor's username is: $GITHUB_ACTOR"
        echo "GitHub SHA: $GITHUB_SHA"
        echo "GitHub event name: $GITHUB_EVENT_NAME"
        echo "GitHub Ref: $GITHUB_REF"
        echo "GitHub Head Ref: $GITHUB_HEAD_REF"
        echo "GitHub Ref Name: $GITHUB_REF_NAME"
        echo "Docker 1804 image: $IMG_1804"
        echo "Docker 2204 image: $IMG_2204"
        echo "Docker IWYU image: $IMG_IWYU"
        echo "Used docker image name: ${{ steps.docker_img.outputs.img_name }}"
        echo "docker_build: ${{ steps.docker_img.outputs.docker_build }}"
        echo "img_name: ${{ steps.docker_img.outputs.img_name }}"

    - name: Build and Push Docker Image
      if: steps.docker_img.outputs.docker_build
      run: |
        echo "Building and pushing ${{ steps.docker_img.outputs.img_name }}"
        docker build --cache-from=${IMG_1804} -t "${{ steps.docker_img.outputs.img_name }}" - < tools/docker/18.04/Dockerfile
        docker push "${{ steps.docker_img.outputs.img_name }}"

    outputs:
      docker_img_name: "${{ steps.docker_img.outputs.img_name }}"

  # Build a basic version of kotekan
  build-base-1804:
    runs-on: ubuntu-latest
    needs: build-docker-1804

    steps:
    - uses: actions/checkout@v2

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Cache ccache files
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ccache-base-build-1804-${{ github.sha }}
        restore-keys: |
          ccache-base-build-1804
          ccache-full-build-1804

    - name: Build kotekan
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-1804/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_LINK_WHAT_YOU_USE=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DARCH=haswell \
            -DCCACHE=ON \
            -DWITH_TESTS=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" ccache -s

  # Build a full version of kotekan and run the unit tests
  build-full-tests-1804:
    runs-on: ubuntu-latest
    needs: build-docker-1804

    steps:
    - uses: actions/checkout@v2

    - name: Free disk space
      if: ${{ !env.ACT }} # Don't free up if running locally
      run: |
          df -h
          docker rmi $(docker image ls -aq)
          df -h
          sudo apt-get clean
          sudo apt-get autoclean
          df -h

    - name: Cache ccache files
      uses: actions/cache@v1
      with:
        path: .ccache
        key: ccache-full-build-1804-${{ github.sha }}
        restore-keys: |
          ccache-full-build-1804
          ccache-base-build-1804

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Build kotekan
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-1804/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_LINK_WHAT_YOU_USE=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DUSE_HDF5=ON -DHIGHFIVE_PATH=/code/build/HighFive \
            -DUSE_LAPACK=ON -DBLAZE_PATH=/code/build/blaze \
            -DARCH=haswell \
            -DNO_MEMLOCK=ON \
            -DUSE_OMP=ON \
            -DWITH_BOOST_TESTS=ON \
            -DCCACHE=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" rm -r lib
        docker run "${OPTS[@]}" ccache -s
        df -h

    - name: Run parallel python tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" pytest -v -n auto --dist=loadfile --timeout=${PYTEST_TIMEOUT} -x -m 'not serial'

    - name: Run serial python tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" bash -c "redis-server --daemonize yes; pytest -v -x --timeout=${PYTEST_TIMEOUT} -m serial"

    - name: Run boost tests
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-1804/tests/ -e PYTHONPATH=/code/kotekan/python/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" pytest -v -x --timeout=${PYTEST_TIMEOUT}

  # Build a full CHIME version of kotekan
  build-chime-1804:
    runs-on: ubuntu-latest
    needs: build-docker-1804

    steps:
    - uses: actions/checkout@v2

    - name: Cache ccache files
      uses: actions/cache@v1
      with:
        path: .ccache
        key: ccache-chime-build-1804-${{ github.sha }}
        restore-keys: |
          ccache-chime-build-1804
          ccache-full-build-1804

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Build kotekan
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-1804/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_LINK_WHAT_YOU_USE=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DUSE_OLD_DPDK=ON \
            -DUSE_HDF5=ON -DHIGHFIVE_PATH=/code/build/HighFive \
            -DUSE_LAPACK=ON -DBLAZE_PATH=/code/build/blaze \
            -DARCH=haswell \
            -DNO_MEMLOCK=ON \
            -DUSE_OMP=ON \
            -DUSE_HSA=ON \
            -DCCACHE=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" ccache -s

  # Build a full CHIME version with clang
  build-clang-1804:
    runs-on: ubuntu-latest
    needs: build-docker-1804

    steps:
    - uses: actions/checkout@v2

    - name: Cache ccache files
      uses: actions/cache@v1
      with:
        path: .ccache
        key: ccache-clang-build-1804-${{ github.sha }}
        restore-keys: |
          ccache-clang-build-1804

    - name: Login to GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ${{ env.REGISTRY }}
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Build kotekan
      env:
        CC: clang
        CXX: clang++
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-1804/ ${{ needs.build-docker-1804.outputs.docker_img_name }})
        docker run "${OPTS[@]}" ccache -s
        docker run "${OPTS[@]}" cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
        -DWERROR=ON \
        -DCMAKE_LINK_WHAT_YOU_USE=ON \
        -DUSE_OLD_DPDK=ON \
        -DCMAKE_BUILD_TYPE=Test \
        -DUSE_HDF5=ON \
        -DHIGHFIVE_PATH=/code/build/HighFive \
        -DUSE_LAPACK=ON \
        -DBLAZE_PATH=/code/build/blaze \
        -DARCH=haswell \
        -DNO_MEMLOCK=ON \
        -DUSE_OMP=ON \
        -DWITH_TESTS=ON \
        -DCCACHE=ON ..
        docker run "${OPTS[@]}" make -j 2
        docker run "${OPTS[@]}" ccache -s



  # IWYU tests

  # Build the iwyu docker image
  build-docker-iwyu:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Check if iwyu Dockerfile changed
      uses: technote-space/get-diff-action@v4
      id: git-diff-docker-iwyu
      with:
        PATTERNS: tools/iwyu/docker/18.04/Dockerfile

    - name: Extract branch name
      shell: bash
      # Get either branch name of a push or source branch of PR, replace all '/' with '.':
      run: >
        if [ "${GITHUB_EVENT_NAME}" = "push" ]; then
          echo "branch=$(echo ${GITHUB_REF_NAME} | tr / .)" >> $GITHUB_OUTPUT;
        else
          echo "branch=$(echo ${GITHUB_HEAD_REF} | tr / .)" >> $GITHUB_OUTPUT;
        fi
      id: extract_branch

    - name: Pull IWYU docker image
      run: |
        docker login ghcr.io -u ${GITHUB_REPOSITORY} -p "${{ secrets.GITHUB_TOKEN }}"
        docker pull --disable-content-trust ${IMG_IWYU}:${{ steps.extract_branch.outputs.branch }}
        echo ::set-output name=status::success
      if: steps.git-diff-docker-iwyu.outputs.diff
      continue-on-error: true
      id: pull-docker-iwyu
    - name: Pull docker image for develop branch
      run: |
        docker login ghcr.io -u ${GITHUB_REPOSITORY} -p "${{ secrets.GITHUB_TOKEN }}"
        docker pull --disable-content-trust ${IMG_IWYU}:develop
      if: steps.git-diff-docker-iwyu.outputs.diff != '' && steps.pull-docker-iwyu.outputs.status != 'success'
    - name: Build iwyu docker image
      run: >
        docker build --cache-from=rocm/dev-ubuntu-18.04,${IMG_1804},${IMG_IWYU} -t ${IMG_IWYU}:${{ steps.extract_branch.outputs.branch }} - < tools/iwyu/docker/18.04/Dockerfile
      if: steps.git-diff-docker-iwyu.outputs.diff
    - name: Push docker image
      run: |
        docker push ${IMG_IWYU}:${{ steps.extract_branch.outputs.branch }}
      if: steps.git-diff-docker-iwyu.outputs.diff

  iwyu:
    runs-on: ubuntu-latest
    needs: build-docker-iwyu

    steps:
    - uses: actions/checkout@v2

    - name: Check if IWYU Dockerfile changed
      uses: technote-space/get-diff-action@v4
      id: git-diff-docker-iwyu
      with:
        PATTERNS: tools/iwyu/docker/18.04/Dockerfile

    - name: Extract branch name for iwyu docker container
      shell: bash
      # Get either branch name of a push or source branch of PR, replace all '/' with '.'.
      # If Dockerfile didn't change, use 'develop'.
      run: >
        if [ -n "${{ steps.git-diff-docker-iwyu.outputs.diff }}" ]; then
          if [ "${GITHUB_EVENT_NAME}" = "push" ]; then
            echo "branch=$(echo ${GITHUB_REF_NAME} | tr / .)" >> $GITHUB_OUTPUT;
          else
            echo "branch=$(echo ${GITHUB_HEAD_REF} | tr / .)" >> $GITHUB_OUTPUT;
          fi
        else
          echo "branch=develop" >> $GITHUB_OUTPUT;
        fi
      id: extract_branch

    - name: Configure kotekan
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-1804/ ${IMG_IWYU}:${{ steps.extract_branch.outputs.branch }})
        docker login ghcr.io -u ${GITHUB_REPOSITORY} -p "${{ secrets.GITHUB_TOKEN }}"
        docker run "${OPTS[@]}" \
          cmake -Wdev -Werror=dev -Wdeprecated -Werror=deprecated \
            -DWERROR=ON \
            -DCMAKE_LINK_WHAT_YOU_USE=ON \
            -DCMAKE_BUILD_TYPE=Test \
            -DUSE_OLD_DPDK=ON \
            -DUSE_HDF5=ON -DHIGHFIVE_PATH=/code/build/HighFive \
            -DUSE_LAPACK=ON -DBLAZE_PATH=/code/build/blaze \
            -DARCH=haswell \
            -DNO_MEMLOCK=ON \
            -DUSE_OMP=ON \
            -DWITH_TESTS=ON \
            -DCMAKE_EXPORT_COMPILE_COMMANDS=ON \
            -DIWYU=ON \
            -DCCACHE=ON ..

    - name: Run iwyu
      run: |
        OPTS=(--rm --mount type=bind,src=$(pwd),target=/code/kotekan -w /code/kotekan/build-iwyu/ ${IMG_IWYU}:${{ steps.extract_branch.outputs.branch }})
        docker run "${OPTS[@]}" /code/kotekan/tools/iwyu/docker/iwyu.sh