[CI/CD](env.yaml): Update biobb_common version. #39
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| name: tests | |
| on: | |
| # workflow_dispatch | |
| push: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '.gitignore' | |
| - '.readthedocs.yaml' | |
| - 'LICENSE' | |
| - 'setup.py' | |
| - 'README.md' | |
| - 'CITATION.cff' | |
| - 'references.jsonld' | |
| - '**/docs/**' | |
| - '**/json_schemas/**' | |
| jobs: | |
| # Name of the Job | |
| lint_and_test: | |
| strategy: | |
| matrix: | |
| os: [self-hosted] | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - run: echo "Repository -> ${{ github.repository }}" | |
| - run: echo "Branch -> ${{ github.ref }}" | |
| - run: echo "Trigger event -> ${{ github.event_name }}" | |
| - run: echo "Runner OS -> ${{ runner.os }}" | |
| - name: List files in the repository | |
| run: | | |
| ls ${{ github.workspace }} | |
| - name: Remove all micromamba installations | |
| run: | | |
| rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null | |
| touch /home/user/.bash_profile | |
| - name: setup-micromamba | |
| uses: mamba-org/setup-micromamba@v2.0.0 | |
| with: | |
| generate-run-shell: true | |
| micromamba-version: '2.0.2-2' | |
| post-cleanup: 'all' | |
| init-shell: bash | |
| environment-file: .github/env.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| pytest | |
| pytest-cov | |
| pytest-html | |
| flake8 | |
| pip | |
| - name: Install genbadge from pip | |
| shell: bash -l {0} | |
| run: pip install genbadge[all] | |
| - name: List installed package versions | |
| shell: bash -l {0} | |
| run: micromamba list | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html | |
| # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes | |
| # Workflow fails: Stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # Create directory for flake8 reports | |
| mkdir -p ./reports/flake8 | |
| # Exit-zero treats all errors as warnings, workflow will not fail: | |
| flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=9999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt | |
| - name: Generate Flake8 badge | |
| shell: bash -l {0} | |
| run: | | |
| genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt --output-file ./reports/flake8/flake8badge.svg | |
| - name: Checkout biobb_common | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: bioexcel/biobb_common | |
| path: './biobb_common' | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| # Ignoring docker and singularity tests | |
| export PYTHONPATH=.:./biobb_common:$PYTHONPATH | |
| # Create directory for tests reports | |
| mkdir -p ./reports/junit | |
| # Producction one | |
| pytest biobb_structure_utils/test/unitests/ --cov=biobb_structure_utils/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html | |
| - name: Generate Tests badge | |
| shell: bash -l {0} | |
| run: | | |
| genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml --output-file ./reports/junit/testsbadge.svg | |
| - name: Generate Coverage badge | |
| shell: bash -l {0} | |
| run: | | |
| # Create directory for flake8 reports | |
| mkdir -p ./reports/coverage | |
| coverage xml -o ./reports/coverage/coverage.xml | |
| coverage html -d ./reports/coverage/ | |
| genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml --output-file ./reports/coverage/coveragebadge.svg | |
| - name: Publish coverage report to GitHub Pages | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| folder: ./reports | |
| # - name: Restore .bash_profile | |
| # run: cp ~/.bash_profile_orig ~/.bash_profile | |