Continuous integration #671
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| 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: ${{ steps.commit-docs.outputs.docsChanged }} | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| #*******************************************# | |
| #* Validation *# | |
| #*******************************************# | |
| ############################################# | |
| ## Get Last Release's Info | |
| ############################################# | |
| - name: Gets latest created release info | |
| id: latest_release_info | |
| uses: fangqiuming/[email protected] | |
| ############################################# | |
| ## If Tagged, Set the `_version.py` File to Reflect it | |
| ############################################# | |
| - name: Align Version with tag | |
| id: get-tagged-version | |
| if: startsWith(github.ref, 'refs/tags/') | |
| run: | | |
| taggedVersion=$(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: ${{ secrets.CODECOV_TOKEN }} | |
| flags: unittests | |
| file: ./coverage.xml | |
| ############################################# | |
| ## Compile documentation | |
| ############################################# | |
| - name: Install the requirements for compiling the documentation | |
| run: poetry install --with docs | |
| - name: Compile the documentation | |
| run: | | |
| poetry run sphinx-apidoc . pyproject.toml --output-dir docs-src/source --force --module-first --no-toc | |
| mkdir -p docs-src/_static | |
| poetry run sphinx-build docs-src docs | |
| ############################################# | |
| ## Check for Deploy, Stop if not Deploying (disabled due to the fact it cancels, not passes) | |
| ############################################# | |
| # - name: Cancel build if not for release | |
| # uses: andymckay/[email protected] | |
| # if: steps.check-new-release.outputs.needDeploy != 'true' | |
| #*******************************************# | |
| #* Release *# | |
| #*******************************************# | |
| ############################################# | |
| # Give nice, clear heads up in GitHub Action that We are Deploying | |
| ############################################# | |
| - name: Start the Deploy Process | |
| if: steps.check-new-release.outputs.needDeploy == 'true' | |
| run: echo 'Beginning Deploy Steps' | |
| ############################################# | |
| ## Form-fill the versions to the container, `pyproject.toml`, and part of `biosimulators.json` | |
| ############################################# | |
| - name: Update versioning in "Dockerfile", "pyproject.toml", and part of "biosimulators.json" | |
| if: steps.check-new-release.outputs.needDeploy == 'true' | |
| run: | | |
| copasiVersion=${{ 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: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}" | |
| ############################################# | |
| # If new tag, commit and push documentation | |
| ############################################# | |
| - id: commit-docs | |
| name: Commit the compiled documentation | |
| if: steps.check-new-release.outputs.needDeploy == 'true' | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "biosimulatorsdaemon" | |
| git config pull.rebase false | |
| # Need to check if we did the release on `dev` or not, very important! | |
| commitHash=$(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 "[email protected]" | |
| # 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 }} |