Fix for some biosimulators test suite tests. #168
Workflow file for this run
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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/${mainBranch}) | |
| echo "mainBranch=$mainBranch" >> $GITHUB_OUTPUT | |
| echo "mainBranchRef=refs/heads/$mainBranch" >> $GITHUB_OUTPUT | |
| echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT | |
| - name: Checkout ref | |
| run: | | |
| if [[ "${{ 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@v3 | |
| with: | |
| python-version: '3.11' | |
| - name: Setup pip cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/hostedtoolcache/Python | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install libXML2, libncurses5 | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends libxml2 libncurses5 | |
| - name: Install pip | |
| run: | | |
| python -m pip install pip==23.0.0 | |
| python -m pip install pip==23.0.0 | |
| python -m pip --version | |
| #python -m pip install --upgrade setuptools | |
| #python -m setuptools --version | |
| - name: Install 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="${TAG/refs\/tags\//}" | |
| else | |
| version=$(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 "version=$version" >> $GITHUB_OUTPUT | |
| - id: get-docker-image-tag | |
| name: Determine Docker image tag | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends jq | |
| SIMULATOR_ID=$(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 $IMAGE_BASE_URL | cut -d / -f 1) | |
| echo "simulatorId=${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}" >> $GITHUB_OUTPUT | |
| - name: Build Docker image | |
| run: | | |
| REVISION=$(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=biosimulators_tellurium --cov-report=xml | |
| - name: Upload the coverage report to Codecov | |
| uses: codecov/codecov-action@v3 | |
| 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" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then | |
| release="1" | |
| fi | |
| fi | |
| echo "release=$release" >> $GITHUB_OUTPUT | |
| echo "release=$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 [[ $? = 0 ]]; then | |
| docsChanged=1 | |
| else | |
| docsChanged=0 | |
| fi | |
| echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT | |
| - 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/download/3.1.3/pandoc-3.1.3-1-amd64.deb" -O /tmp/pandoc.deb | |
| sudo dpkg -i /tmp/pandoc.deb | |
| 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) | |
| 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---\"}" |