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
            forceRelease:
                description: Type "true" (case sensitive) to ensure a release will happen (use carefully!)
                required: true
    schedule:
        -   cron: "0 0 * * *"

jobs:
    continuousIntegration:
        name: Update simulator version, lint, test, compile documentation, and release
        runs-on: ubuntu-latest
        outputs:
            version: ${{ steps.get-tagged-version.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 }}
            docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
        defaults:
            run:
                shell: bash
        steps:
            -   name: Checkout repository
                uses: actions/checkout@v4
                with:
                    fetch-depth: 1

            #*******************************************#
            #*                Validation               *#
            #*******************************************#

            #############################################
            ## Get Last Release's Info
            #############################################
            - name: Gets latest created release info
              id: latest_release_info
              uses: fangqiuming/latest-release-version@v1.1.1

            #############################################
            ## If Tagged, Set the `_version.py` File to Reflect it
            #############################################
            -   name: Align Version with tag
                id: get-tagged-version
                if: startsWith(github.ref, 'refs/tags/')
                run: |
                    taggedVersion=$(echo $(echo ${{ github.ref }} | cut -d '/' -f 3))
                    echo "processing `$taggedVersion`"
                    echo "__version__ = '${taggedVersion}'" > biosimulators_copasi/_version.py
                    echo "version=${taggedVersion}" >> "$GITHUB_OUTPUT"
                    echo $(cat biosimulators_copasi/_version.py)
    

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

            #############################################
            ## Check if we need to perform a release
            #############################################
            -   id: check-new-release
                name: Check if we need to perform a release
                run: |
                    # We version the containers with the `biosimulators_copasi` version, but list the version 
                    # online as the COPASI version within the container.
                    taggedVersion="'${{ steps.get-tagged-version.outputs.version }}'"
                    
                    copasiVersion=$(poetry -q run python -c "import COPASI; print(COPASI.__version__)")
                    echo "copasiVersion=$copasiVersion" >> "$GITHUB_OUTPUT"
                    echo "copasiVersion=$copasiVersion"
                    
                    bioSimVersion=$(poetry -q run python -c "import biosimulators_copasi as bsc; print(bsc.__version__)")
                    echo "bioSimVersion=$bioSimVersion" >> "$GITHUB_OUTPUT"
                    echo "bioSimVersion=$bioSimVersion"
                    
                    oldBioSimVersion=${{ steps.latest_release_info.outputs.tag_name }}
                    echo "oldBioSimVersion=$oldBioSimVersion"
                    
                    if [[ $oldBioSimVersion < $bioSimVersion ]] && ! [[ -z $taggedVersion ]]; then
                        echo "needDeploy=true" >> "$GITHUB_OUTPUT"
                        echo "Deploy will be performed!"
                    else
                        echo "needDeploy=false" >> "$GITHUB_OUTPUT"
                        echo "Deploy will NOT be performed:"
                        # Get an idea of why we will not deploy
                        if [[ $oldBioSimVersion > $bioSimVersion ]]; then
                            echo "Version is not newer than existing version"
                        fi
                        if [[ $oldBioSimVersion == $bioSimVersion ]]; then
                            echo "Old and new versions are the same"
                        fi
                        if [[ -z $taggedVersion ]]; then
                            echo "This is not a tagged action; push a new tag to release."
                        fi
                    fi

            #############################################
            ## 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

            #############################################
            ## 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 sphinx-build docs-src docs

            #############################################
            ## Check for Deploy, Stop if not Deploying (disabled due to the fact it cancels, not passes)
            #############################################
#            -   name: Cancel build if not for release
#                uses: andymckay/cancel-action@0.2
#                if: steps.check-new-release.outputs.needDeploy != 'true'

            #*******************************************#
            #*                Release                  *#
            #*******************************************#

            #############################################
            # Give nice, clear heads up in GitHub Action that We are Deploying
            #############################################
            -   name: Start the Deploy Process
                if: steps.check-new-release.outputs.needDeploy == 'true'
                run: echo 'Beginning Deploy Steps'

            #############################################
            ## Form-fill the versions to the container, `pyproject.toml`, and part of `biosimulators.json`
            #############################################
            - name: Update versioning in "Dockerfile", "pyproject.toml", and part of "biosimulators.json"
              if: steps.check-new-release.outputs.needDeploy == 'true'
              run: |
                  copasiVersion=${{ steps.check-new-release.outputs.copasiVersion }}
                  bioSimVersion=${{ steps.check-new-release.outputs.bioSimVersion }}

                  sed -i -E "s/ARG SIMULATOR_VERSION=([^ \n]+|\".*?\")/ARG SIMULATOR_VERSION=\"${copasiVersion}\"/" Dockerfile
                  sed -i -E "s/ARG VERSION=([^ \n]+|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" Dockerfile

                  sed -i -E "s/^version\s+=\s+(\".*?\")/version = \"${bioSimVersion}\"/mg" pyproject.toml
                  
                  sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json
                  poetry update

            #############################################
            # Create PyPI release
            #############################################
            -   name: Create PyPI release
                if: steps.check-new-release.outputs.needDeploy == 'true'
                env:
                    POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
                run: |
                    echo''
                    # 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 and Push Docker image
            #############################################
            - id: get-docker-image-tag
              name: Determine Docker image tag
              if: steps.check-new-release.outputs.needDeploy == 'true'
              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 "simulatorId=${SIMULATOR_ID}" >> "$GITHUB_OUTPUT"
                  echo "simulatorVersion=${SIMULATOR_VERSION}" >> "$GITHUB_OUTPUT"
                  echo "simulatorName=${SIMULATOR_NAME}" >> "$GITHUB_OUTPUT"
                  echo "dockerImageBaseUrl=${IMAGE_BASE_URL}" >> "$GITHUB_OUTPUT"
                  echo "dockerRegistry=${DOCKER_REGISTRY}" >> "$GITHUB_OUTPUT"
                  
                  echo "simulatorId=${SIMULATOR_ID}"
                  echo "simulatorVersion=${SIMULATOR_VERSION}"
                  echo "simulatorName=${SIMULATOR_NAME}"
                  echo "dockerImageBaseUrl=${IMAGE_BASE_URL}"
                  echo "dockerRegistry=${DOCKER_REGISTRY}"

            - name: Build Docker image
              if: steps.check-new-release.outputs.needDeploy == 'true'
              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-tagged-version.outputs.version }} \
                    --build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
                    --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.check-new-release.outputs.copasiVersion }} \
                    --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \
                    .

            -   name: Push Docker image
                if: steps.check-new-release.outputs.needDeploy == 'true'
                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.check-new-release.outputs.simulatorVersionLatest }}" == "true" ]; then
                      docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
                    fi

            #############################################
            ## Form-fill the digest portion of "biosimulators.json"
            #############################################
            - name: Update versioning in "biosimulators.json"
              if: steps.check-new-release.outputs.needDeploy == 'true'
              run: |
                  containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
                  docker pull $containerLabel
                  imageId=docker image ls | grep ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }} \
                    grep ${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | awk '{ print $3; ]'
                  
                  dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId | cut -d '@' -f 2
                  
                  sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json

            #############################################
            # Submit to BioSimulators registry
            #############################################
            -   name: Submit to BioSimulators registry
                if: steps.check-new-release.outputs.needDeploy == 'true'
                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---\"}"

            #############################################
            # If new tag, commit and push documentation
            #############################################
            - id: commit-docs
              name: Commit the compiled documentation
              if: steps.check-new-release.outputs.needDeploy == 'true'
              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: 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
              uses: actions/create-release@v1
              if: steps.check-new-release.outputs.needDeploy == 'true'
              env:
                  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
              with:
                  tag_name: ${{ steps.get-tagged-version.outputs.version }}
                  release_name: Release ${{ steps.get-tagged-version.outputs.version }}

            #############################################
            ## 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.check-new-release.outputs.needDeploy == '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.check-new-release.outputs.simulatorVersion && steps.check-new-release.outputs.simulatorVersionLatest == 'true'
#                uses: ad-m/github-push-action@master
#                with:
#                    github_token: ${{ secrets.GITHUB_TOKEN }}
#                    branch: ${{ github.ref }}