updated git ingore #543
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: | |
| 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/[email protected] | |
| 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 sphinx-build 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 "[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.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: ${{ github.ref }} | |
| ############################################# | |
| ## Release | |
| ############################################# | |
| - id: determine-if-release-needed | |
| name: Determine if a release should be made | |
| run: | | |
| release="0" | |
| echo "Simulator Version: `${{ github.event.inputs.simulatorVersion }}`" | |
| echo "Input Version: `${{ steps.update-simulator-version.outputs.simulatorVersion }}`" | |
| echo "Simulator Version: `${{ github.event.inputs.simulatorVersion }}`"3 | |
| if [ "true" == "${{ github.event.inputs.simulatorVersion }}" ]; then | |
| release="1" | |
| fi | |
| if [ ! -z "${{ steps.update-simulator-version.outputs.simulatorVersion }}" ]; then | |
| if [ "${{ github.ref }}" == "dev" ]; then | |
| release="1" | |
| fi | |
| fi | |
| if [[ "${{ 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 "[email protected]" | |
| 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---\"}" |