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adding PLA and stop condition to specifications, making model attribu…
…te changes more flexible, getting BioNetGen working and tested, upgrading CI action
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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 | ||
| simulatorVersionLatest: | ||
| description: Is this version the latest version of the underlying simulation tool ("true" or "false")? | ||
| required: false | ||
|
|
||
| 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: ${{ steps.commit-docs.outputs.docsChanged }} | ||
| steps: | ||
| - name: Clone repository | ||
| run: | | ||
| git clone https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} . | ||
| - id: get-main-branch | ||
| name: Determine main branch | ||
| run: | | ||
| mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD | cut -d '/' -f 4) | ||
| mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch}) | ||
| echo "::set-output name=mainBranch::$mainBranch" | ||
| echo "::set-output name=mainBranchRef::refs/heads/$mainBranch" | ||
| echo "::set-output name=mainBranchHeadRevision::$mainBranchHeadRevision" | ||
| - name: Checkout ref | ||
| run: | | ||
| if [[ "${{ github.ref }}" =~ ^refs/heads/ ]]; then | ||
| branch=$(echo "${{ github.ref }}" | cut -d'/' -f 3-) | ||
| git checkout ${branch} | ||
| else | ||
| git checkout ${{ github.ref }} | ||
| fi | ||
| ############################################# | ||
| ## Update the version of the simulator | ||
| ############################################# | ||
| - name: Update the version of the simulator | ||
| if: github.event.inputs.simulatorVersion | ||
| run: | | ||
| sudo apt-get update -y | ||
| sudo apt-get install -y --no-install-recommends jq moreutils | ||
| IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1) | ||
| jq ".version = \"${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json | sponge biosimulators.json | ||
| jq ".image.url = \"${IMAGE_BASE_URL}:${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json | sponge biosimulators.json | ||
| sed -i -E \ | ||
| "s/SIMULATOR_VERSION=([^ \n]+|\".*?\")/SIMULATOR_VERSION=\"${{ github.event.inputs.simulatorVersion }}\"/" \ | ||
| Dockerfile | ||
| ############################################# | ||
| ## Install package and its dependencies | ||
| ############################################# | ||
| - name: Install Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: '3.7' | ||
|
|
||
| - name: Setup pip cache | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: /opt/hostedtoolcache/Python | ||
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-pip- | ||
| - name: Install pip and setuptools | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| python -m pip install --upgrade setuptools | ||
| # install BioNetGen | ||
| - name: Install BioNetGen | ||
| run: | | ||
| sudo apt-get update -y | ||
| sudo apt-get install -y --no-install-recommends \ | ||
| jq \ | ||
| perl \ | ||
| tar \ | ||
| wget | ||
| SIMULATOR_VERSION=$(jq -r '.version' biosimulators.json) | ||
| wget https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-${SIMULATOR_VERSION}/BioNetGen-${SIMULATOR_VERSION}-linux.tgz | ||
| tar xvvf BioNetGen-${SIMULATOR_VERSION}-linux.tgz | ||
| sudo mv BioNetGen-${SIMULATOR_VERSION}/ /opt/ | ||
| export PATH=${PATH}:/opt/BioNetGen-${SIMULATOR_VERSION}/ | ||
| # install package | ||
| - name: Install the package | ||
| run: python -m pip install .[all] | ||
|
|
||
| ############################################# | ||
| ## Lint | ||
| ############################################# | ||
| - name: Install flake8 | ||
| run: python -m pip install flake8 | ||
|
|
||
| - name: Lint the package | ||
| run: python -m flake8 | ||
|
|
||
| ############################################# | ||
| ## Build Docker image | ||
| ############################################# | ||
| - id: get-version-number | ||
| name: Get version number | ||
| env: | ||
| TAG: ${{ github.ref }} | ||
| run: | | ||
| if [[ "${TAG}" =~ ^refs/tags/ ]]; then | ||
| version="${TAG/refs\/tags\//}" | ||
| else | ||
| versionFileDir=$(find -name _version.py | rev | cut -d / -f 2- | rev) | ||
| version=$(PYTHONPATH=$versionFileDir python -c "import _version; print(_version.__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 \ | ||
| . | ||
| ############################################# | ||
| ## Test and upload coverage report to Codecov | ||
| ############################################# | ||
| - name: Install pytest | ||
| run: python -m pip install pytest pytest-cov | ||
|
|
||
| - name: Install the requirements for the tests | ||
| run: python -m pip install .[tests] | ||
|
|
||
| - name: Run the tests | ||
| run: python -m pytest tests/ --cov=./ --cov-report=xml | ||
|
|
||
| - name: Upload the coverage report to Codecov | ||
| uses: codecov/codecov-action@v1.0.3 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| flags: unittests | ||
| file: ./coverage.xml | ||
|
|
||
| ############################################# | ||
| ## Compile documentation | ||
| ############################################# | ||
| - name: Install the requirements for compiling the documentation | ||
| run: python -m pip install -r docs-src/requirements.txt | ||
|
|
||
| - name: Compile the documentation | ||
| run: | | ||
| sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc | ||
| mkdir -p docs-src/_static | ||
| 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: github.event.inputs.simulatorVersion && github.event.inputs.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: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true' | ||
| uses: ad-m/github-push-action@master | ||
| with: | ||
| github_token: ${{ secrets.GITHUB_TOKEN }} | ||
| branch: ${{ github.ref }} | ||
|
|
||
| ############################################# | ||
| ## Release | ||
| ############################################# | ||
|
|
||
| - id: determine-if-release-needed | ||
| name: Determine if a release should be made | ||
| run: | | ||
| release="0" | ||
| if [ ! -z "${{ github.event.inputs.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: | ||
| TWINE_USERNAME: __token__ | ||
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | ||
| run: | | ||
| # Install pandoc | ||
| sudo apt-get update -y | ||
| sudo apt-get install -y --no-install-recommends wget | ||
| wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html | ||
| urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1` | ||
| wget "https://github.com/$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 | ||
| # Install twine | ||
| python -m pip install wheel twine | ||
| # Create packages to upload to PyPI | ||
| python setup.py sdist | ||
| python setup.py bdist_wheel | ||
| # Upload packages to PyPI | ||
| twine upload dist/* | ||
| # 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 [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ github.event.inputs.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) | ||
| 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 }}\nvalidateImage: true\ncommitSimulator: true\n\n---\"}" |
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