Continuous integration #692
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}" | |
| ############################################# | |
| # If new tag, commit and push documentation | |
| ############################################# | |
| - id: commit-docs | |
| name: Commit the compiled documentation | |
| if: steps.check-new-release.outputs.needDeploy == 'true' | |
| run: | | |
| git config --local user.email "biosimulators.daemon@gmail.com" | |
| git config --local user.name "biosimulatorsdaemon" | |
| git config pull.rebase false | |
| # Need to check if we did the release on `dev` or not, very important! | |
| commitHash=$(git rev-parse ${{ steps.get-tagged-version.outputs.version }}^{commit}) | |
| onDev=$(git branch -a --contains $commitHash | grep remotes/origin/master) | |
| if [[ -z $onDev ]]; then | |
| git stash | |
| git checkout dev | |
| git pull origin dev | |
| set +e | |
| git stash pop | |
| git add docs | |
| git commit -m "Updating compiled documentation" | |
| git checkout . | |
| git clean -f -d | |
| if [[ $? = 0 ]]; then | |
| docsChanged=1 | |
| else | |
| docsChanged=0 | |
| fi | |
| else | |
| docsChanged=0 | |
| fi | |
| echo "docsChanged=$docsChanged" >> "$GITHUB_OUTPUT" | |
| - 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: dev | |
| ############################################# | |
| # 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 }} |