ci.yml

name: Continuous integration

on:
    push:
    workflow_dispatch:
        inputs:
            simulatorVersion:
                description: New version of the underlying simulation tool (e.g., '1.5.6')
                required: true
    schedule:
        -   cron: "0 0 * * *"

jobs:
    continuousIntegration:
        name: Update simulator version, lint, test, compile documentation, and release
        runs-on: ubuntu-latest
        outputs:
            mainBranch: ${{ steps.get-main-branch.outputs.mainBranch }}
            mainBranchRef: ${{ steps.get-main-branch.outputs.mainBranchRef }}
            mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}
            version: ${{ steps.get-version-number.outputs.version }}
            simulatorId: ${{ steps.get-docker-image-tag.outputs.simulatorId }}
            simulatorVersion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
            simulatorName: ${{ steps.get-docker-image-tag.outputs.simulatorName }}
            dockerImageBaseUrl: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}
            dockerRegistry: ${{ steps.get-docker-image-tag.outputs.dockerRegistry }}
            release: ${{ steps.determine-if-release-needed.outputs.release }}
            docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
        defaults:
            run:
                shell: bash
        steps:
            -   name: Checkout repository
                uses: actions/checkout@v4
                with:
                    fetch-depth: 1

            #############################################
            ## Install package and its dependencies
            #############################################
            # install package
            -   name: Set up the environment
                uses: ./.github/actions/setup-poetry-env
                with:
                    python-version: "3.10"

            #############################################
            ## Update the version of the simulator
            #############################################
            -   id: update-simulator-version
                name: Update the version of the simulator
                if: github.event_name == 'workflow_dispatch' || github.event_name == 'schedule'
                run: |
                    if [ "${{ github.event_name }}" == "workflow_dispatch" ]; then
                      simulatorVersion="${{ github.event.inputs.simulatorVersion }}"
                    else
                      simulatorVersion=$(poetry -q run python -c "import COPASI; print(COPASI.__version__)")
                    fi
                    
                    simulatorSpecVersion=$(jq -r '.version' biosimulators.json)
                    set +e
                    dpkg --compare-versions "$simulatorVersion" ge "$simulatorSpecVersion"
                    if [[ $? = 0 ]]; then
                      simulatorVersionLatest="true"
                    else
                      simulatorVersionLatest="false"
                    fi
                    dpkg --compare-versions "$simulatorVersion" gt "$simulatorSpecVersion"
                    if [[ $? = 0 ]]; then
                      simulatorVersionNewer="true"
                    else
                      simulatorVersionNewer="false"
                    fi
                    set -e
                    
                    sudo apt-get update -y
                    sudo apt-get install -y --no-install-recommends jq moreutils
                    
                    IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
                    jq ".version = \"${simulatorVersion}\"" biosimulators.json | sponge biosimulators.json
                    jq ".image.url = \"${IMAGE_BASE_URL}:${simulatorVersion}\"" biosimulators.json | sponge biosimulators.json
                    
                    sed -i -E \
                      "s/SIMULATOR_VERSION=([^ \n]+|\".*?\")/SIMULATOR_VERSION=\"${simulatorVersion}\"/" \
                      Dockerfile
                    
                    echo "::set-output name=simulatorVersion::$simulatorVersion"
                    echo "::set-output name=simulatorVersionLatest::$simulatorVersionLatest"
                    echo "::set-output name=simulatorVersionNewer::$simulatorVersionNewer"

            -   name: Cancel build if the specifications already have the latest version of COPASI
                uses: andymckay/cancel-action@0.2
                if: github.event_name == 'schedule' && steps.update-simulator-version.outputs.simulatorVersionNewer != 'true'

            #############################################
            ## Lint and Test
            #############################################
            -   name: Lint the package
                run: poetry run python -m flake8

            -   name: Run the tests
                run: poetry run python -m pytest tests/ --cov=./biosimulators_copasi/ --cov-report=xml

            -   name: Upload the coverage report to Codecov
                uses: codecov/codecov-action@v2
                with:
                    token: ${{ secrets.CODECOV_TOKEN }}
                    flags: unittests
                    file: ./coverage.xml

            #############################################
            ## Build Docker image
            #############################################
            -   id: get-version-number
                name: Get version number
                env:
                    TAG: ${{ github.ref }}
                run: |
                    if [[ "${TAG}" =~ ^refs/tags/ ]]; then
                      version="${TAG/refs\/tags\//}"
                    else
                      version=$(poetry run python -c "import glob; import importlib.util; version_filename = glob.glob('**/_version.py', recursive=True)[0]; spec = importlib.util.spec_from_file_location('module.name', version_filename); module = importlib.util.module_from_spec(spec); spec.loader.exec_module(module); print(module.__version__)")
                    fi
                    
                    echo "::set-output name=version::$version"

            -   id: get-docker-image-tag
                name: Determine Docker image tag
                run: |
                    sudo apt-get update -y
                    sudo apt-get install -y --no-install-recommends jq
                    
                    SIMULATOR_ID=$(jq -r '.id' biosimulators.json)
                    SIMULATOR_VERSION=$(jq -r '.version' biosimulators.json)
                    SIMULATOR_NAME=$(jq -r '.name' biosimulators.json)
                    IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
                    DOCKER_REGISTRY=$(echo $IMAGE_BASE_URL | cut -d / -f 1)
                    
                    echo "::set-output name=simulatorId::${SIMULATOR_ID}"
                    echo "::set-output name=simulatorVersion::${SIMULATOR_VERSION}"
                    echo "::set-output name=simulatorName::${SIMULATOR_NAME}"
                    echo "::set-output name=dockerImageBaseUrl::${IMAGE_BASE_URL}"
                    echo "::set-output name=dockerRegistry::${DOCKER_REGISTRY}"

            -   name: Build Docker image
                run: |
                    REVISION=$(git rev-parse HEAD)
                    CREATED=$(date --rfc-3339=seconds | sed 's/ /T/')
                    docker build \
                      --label org.opencontainers.image.source=https://github.com/${{ github.repository }} \
                      --label org.opencontainers.image.revision=${REVISION} \
                      --label org.opencontainers.image.created=${CREATED} \
                      --build-arg VERSION=${{ steps.get-version-number.outputs.version }} \
                      --build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
                      --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
                      --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \
                      .


            #############################################
            ## Compile documentation
            #############################################
            -   name: Install the requirements for compiling the documentation
                run: poetry install --with docs

            -   name: Compile the documentation
                run: |
                    poetry run sphinx-apidoc . pyproject.toml --output-dir docs-src/source --force --module-first --no-toc
                    mkdir -p docs-src/_static
                    poetry run docs-src docs

            #############################################
            ## Commit and push new version of simulator
            #############################################
            # If new version of simulator, commit and push the new version
            -   name: Commit the revised version of the simulator
                if: steps.update-simulator-version.outputs.simulatorVersion && steps.update-simulator-version.outputs.simulatorVersionLatest == 'true'
                run: |
                    git config --local user.email "biosimulators.daemon@gmail.com"
                    git config --local user.name "biosimulatorsdaemon"
                    git config pull.rebase false
                    git stash -- biosimulators.json Dockerfile
                    git clean -f -d
                    git checkout .
                    git pull
                    git stash pop
                    git add biosimulators.json Dockerfile
                    git commit -m "Updating version of simulator"

            -   name: Push the revised version of the simulator
                if: steps.update-simulator-version.outputs.simulatorVersion && steps.update-simulator-version.outputs.simulatorVersionLatest == 'true'
                uses: ad-m/github-push-action@master
                with:
                    github_token: ${{ secrets.GITHUB_TOKEN }}
                    branch: ${{ github.ref }}

            #############################################
            ## Release
            #############################################

            -   id: determine-if-release-needed
                name: Determine if a release should be made
                run: |
                    release="0"
                    
                    if [ ! -z "${{ steps.update-simulator-version.outputs.simulatorVersion }}" ]; then
                      if [ "${{ github.ref }}" == "${{ steps.get-main-branch.outputs.mainBranchRef }}" ]; then
                        release="1"
                      fi
                    fi
                    
                    if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
                      tag_hash=$(git rev-parse "${{ github.ref }}")
                      if [ "$tag_hash" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then
                        release="1"
                      fi
                    fi
                    
                    echo "::set-output name=release::$release"

            # If new tag, commit and push documentation
            -   id: commit-docs
                name: Commit the compiled documentation
                if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
                run: |
                    git config --local user.email "biosimulators.daemon@gmail.com"
                    git config --local user.name "biosimulatorsdaemon"
                    git config pull.rebase false
                    git stash
                    git checkout ${{ steps.get-main-branch.outputs.mainBranch }}
                    git pull
                    set +e
                    git stash pop
                    git add docs
                    git commit -m "Updating compiled documentation"
                    git checkout .
                    git clean -f -d
                    if [[ $? = 0 ]]; then
                      docsChanged=1
                    else
                      docsChanged=0
                    fi
                    echo "::set-output name=docsChanged::$docsChanged"

            -   name: Push the compiled documentation
                if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1' && steps.commit-docs.outputs.docsChanged == '1'
                uses: ad-m/github-push-action@master
                with:
                    github_token: ${{ secrets.GITHUB_TOKEN }}
                    branch: ${{ steps.get-main-branch.outputs.mainBranch }}

            # Create GitHub release
            -   name: Create GitHub release
                if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
                uses: actions/create-release@v1
                env:
                    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
                with:
                    tag_name: ${{ steps.get-version-number.outputs.version }}
                    release_name: Release ${{ steps.get-version-number.outputs.version }}

            # Create PyPI release
            -   name: Create PyPI release
                if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
                env:
                    POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
                run: |
                    # Install pandoc
                    sudo apt-get update -y
                    sudo apt-get install -y --no-install-recommends wget
                    
                    wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
                    urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1`
                    wget "https://github.com/$urlPart" -O /tmp/pandoc.deb
                    sudo dpkg -i /tmp/pandoc.deb
                    rm /tmp/pandocVersions.html
                    rm /tmp/pandoc.deb
                    
                    # Convert README to .rst format
                    pandoc --from=gfm --output=README.rst --to=rst README.md
                    
                    # Build and Publish
                    poetry build
                    poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI
            # build Docker image and push to GitHub Container Registry
            -   name: Push Docker image
                if: steps.determine-if-release-needed.outputs.release == '1'
                run: |
                    docker login ${{ steps.get-docker-image-tag.outputs.dockerRegistry }} \
                      --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
                      --password ${{ secrets.DOCKER_REGISTRY_TOKEN }}
                    docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
                    
                    if [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ steps.update-simulator-version.outputs.simulatorVersionLatest }}" == "true" ]; then
                      docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
                    fi

            # Submit to BioSimulators registry
            -   name: Submit to BioSimulators registry
                if: steps.determine-if-release-needed.outputs.release == '1'
                run: |
                    REVISION=$(git rev-parse HEAD)
                    IMAGE_DIGEST=$(docker image inspect ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-)
                    curl \
                      -X POST \
                      -u ${{ secrets.GH_ISSUE_USERNAME }}:${{ secrets.GH_ISSUE_TOKEN }} \
                      -H "Accept: application/vnd.github.v3+json" \
                      https://api.github.com/repos/biosimulators/Biosimulators/issues \
                      -d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit ${{ steps.get-docker-image-tag.outputs.simulatorName }} ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\", \"body\": \"---\nid: ${{ steps.get-docker-image-tag.outputs.simulatorId }}\nversion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\nspecificationsUrl: https://raw.githubusercontent.com/${{ github.repository }}/${REVISION}/biosimulators.json\nspecificationsPatch:\n  version: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\n  image:\n    url: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\n    digest: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}"