Added tests and fixed incorrect exception type #1296
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| name: Continuous integration | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| getVersionNumber: | |
| name: Get version number | |
| if: "startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'" | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| version: ${{ steps.get-version-number.outputs.version }} | |
| steps: | |
| - id: get-version-number | |
| name: Get version number | |
| env: | |
| TAG: ${{ github.ref }} | |
| run: | | |
| version="${TAG/refs\/tags\//}" | |
| echo "version=$version" >> $GITHUB_OUTPUT | |
| build: | |
| name: Lint, test, and compile docs (python ${{ matrix.python-version }}) | |
| if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'" | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: [ "3.10", "3.11" ] | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Install Java # for pyNeuroML | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - name: Install Perl # for BioNetGen | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends perl | |
| - name: Install XPP | |
| run: | | |
| sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev xppaut | |
| - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| # install package | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-poetry-env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Lint the package | |
| run: poetry run python -m flake8 | |
| - name: Run the tests | |
| uses: coactions/setup-xvfb@v1 | |
| env: | |
| MPLBACKEND: PDF | |
| # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to execute tests with the dev deployment | |
| with: | |
| run: poetry run python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml | |
| - name: Upload the coverage report to Codecov | |
| uses: codecov/codecov-action@v4 | |
| 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 . setup.py --output-dir docs-src/source --force --module-first --no-toc | |
| mkdir -p docs-src/_static | |
| poetry run sphinx-build docs-src docs | |
| release: | |
| name: Release a new version | |
| needs: [getVersionNumber, build] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| ref: dev | |
| - name: Configure Git | |
| run: | | |
| git config --local user.email "biosimulators.daemon@gmail.com" | |
| git config --local user.name "biosimulatorsdaemon" | |
| git config pull.rebase false | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-poetry-env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # update Identifiers.org namespaces | |
| - name: Update Identifiers.org namespaces | |
| run: poetry run python -c "from biosimulators_utils.utils.identifiers_org import get_identifiers_org_namespaces; get_identifiers_org_namespaces(reload=True);" | |
| - name: Test the updated Identifiers.org namespaces | |
| uses: GabrielBB/xvfb-action@v1 | |
| env: | |
| MPLBACKEND: PDF | |
| with: | |
| run: poetry run python -m pytest tests/utils/test_identifiers_org_utils.py | |
| - id: commit-identifiers-namespaces | |
| name: Commit the Identifiers.org namespaces | |
| run: | | |
| git stash | |
| git pull | |
| set +e | |
| git stash pop | |
| git add biosimulators_utils/utils/identifiers_org.json | |
| git commit -m "chore: Updated Identifiers.org namespaces [skip ci]" | |
| if [[ $? = 0 ]]; then | |
| changed=1 | |
| else | |
| changed=0 | |
| fi | |
| echo "changed=$changed" >> $GITHUB_OUTPUT | |
| # compile and push documentation | |
| - name: Install the requirements for compiling the documentation | |
| run: poetry install --with docs | |
| - name: Compile the documentation | |
| run: | | |
| poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc | |
| mkdir -p docs-src/_static | |
| poetry run sphinx-build docs-src docs | |
| - id: commit-docs | |
| name: Commit the compiled documentation | |
| run: | | |
| git stash | |
| git pull | |
| set +e | |
| git stash pop | |
| git add docs | |
| git commit -m "chore: Updated compiled documentation [skip ci]" | |
| if [[ $? = 0 ]]; then | |
| changed=1 | |
| else | |
| changed=0 | |
| fi | |
| echo "changed=$changed" >> $GITHUB_OUTPUT | |
| - name: Push the compiled documentation | |
| if: steps.commit-identifiers-namespaces.outputs.changed == '1' || steps.commit-docs.outputs.changed == '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 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ needs.getVersionNumber.outputs.version }} | |
| release_name: Release ${{ needs.getVersionNumber.outputs.version }} | |
| # Create PyPI release | |
| - name: Create packages to upload to PyPI | |
| run: | | |
| poetry build | |
| - name: Upload packages to PyPI | |
| env: | |
| POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }} | |
| run: | | |
| poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI |