Update logics of loading metabolomics data #392
Workflow file for this run
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| name: Build and test Python package | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| paths: | |
| - bin/** | |
| - src/** | |
| - tests/** | |
| - setup.py | |
| - .github/workflows/build.yml | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| paths: | |
| - bin/** | |
| - src/** | |
| - tests/** | |
| - setup.py | |
| - .github/workflows/build.yml | |
| types: | |
| - opened | |
| - reopened | |
| - synchronize | |
| - ready_for_review | |
| jobs: | |
| smoke_test: | |
| name: Smoke test on ubuntu for python 3.10 | |
| runs-on: ubuntu-latest | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Python info | |
| shell: bash -l {0} | |
| run: | | |
| which python3 | |
| python3 --version | |
| - name: Upgrade pip and install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip setuptools | |
| pip install build pytest wheel | |
| - name: Build the package | |
| run: python -m build | |
| - name: Install nplinker | |
| run: | | |
| pip install $(ls dist/nplinker*.whl) | |
| install-nplinker-deps --run-on-github | |
| - name: Run unit tests | |
| run: pytest -v | |
| build: | |
| needs: smoke_test | |
| name: Build for (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest'] | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Python info | |
| shell: bash -l {0} | |
| run: | | |
| which python3 | |
| python3 --version | |
| - name: Upgrade pip and install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip setuptools | |
| pip install build pytest wheel | |
| - name: Build the package | |
| run: python -m build | |
| - name: Install nplinker | |
| run: | | |
| pip install $(ls dist/nplinker*.whl) | |
| install-nplinker-deps --run-on-github | |
| - name: Run unit tests | |
| run: pytest -v | |
| sonarcloud: | |
| name: SonarCloud | |
| needs: smoke_test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Python info | |
| shell: bash -l {0} | |
| run: | | |
| which python3 | |
| python3 --version | |
| - name: Upgrade pip and setuptools | |
| run: | | |
| python3 -m pip install --upgrade pip setuptools wheel | |
| - name: Install nplinker and its dependencies | |
| run: | | |
| python3 -m pip install .[dev] | |
| install-nplinker-deps --run-on-github | |
| - name: Check style against standards using ruff | |
| run: ruff . | |
| - name: Run unit tests with coverage | |
| run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/ | |
| - name: Correct coverage paths | |
| run: sed -i "s+$PWD/++g" coverage.xml | |
| - name: SonarCloud Scan | |
| uses: SonarSource/sonarcloud-github-action@master | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{secrets.SONAR_TOKEN }} |