add note about color vs colorby #271
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| name: tests | |
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| # only branches from forks which have the form 'user:branch-name' | |
| - '**:**' | |
| schedule: | |
| - cron: '42 0 * * 0' | |
| jobs: | |
| run_minimal_test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.13" | |
| - name: print conda environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: install package | |
| run: | | |
| pip install -v --no-deps . | |
| - name: check that package works | |
| run: | | |
| sugar -h | |
| python -c "from sugar import read; print(read())" | |
| run_tests: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python: ["3.11", "3.12", "3.13"] | |
| options: ["subset"] | |
| include: | |
| - os: ubuntu-latest | |
| python: "3.13" | |
| options: "" | |
| - os: ubuntu-latest | |
| python: "3.13" | |
| options: full | |
| - os: macos-latest | |
| python: "3.13" | |
| options: full | |
| - os: windows-latest | |
| python: "3.13" | |
| options: full | |
| - os: ubuntu-latest | |
| python: "3.13" | |
| options: full warnings | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: ${{ contains(matrix.options, 'warnings') }} | |
| env: | |
| # set additional runtest options (--web, -W error) | |
| test_options: ${{ contains(matrix.options, 'full') && '--web' || '' }} ${{ contains(matrix.options, 'warnings') && '-W error' || '' }} | |
| # set additional dependencies for full test | |
| deps: ${{ contains(matrix.options, 'full') && 'matplotlib pandas platformdirs seaborn requests biopython biotite tqdm' || contains(matrix.options, 'subset') && 'matplotlib' || '' }} | |
| depspip: ${{ contains(matrix.options, 'full') && 'dna_features_viewer binarysearchfile' || contains(matrix.options, 'subset') && 'binarysearchfile' || '' }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge,defaults | |
| - name: install dependencies | |
| run: | | |
| conda install -y pytest pytest-cov ${{ env.deps }} | |
| - name: install pip dependencies | |
| if: contains(matrix.options, 'full') || contains(matrix.options, 'subset') | |
| run: | |
| pip install ${{ env.depspip }} | |
| - name: print conda environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: install package | |
| run: | | |
| pip install -v --no-deps . | |
| - name: run test suite | |
| run: | | |
| sugar test -r a --durations=10 --cov sugar --cov=. --cov-report=xml:${{ github.workspace }}/coverage.xml --cov-append ${{ env.test_options }} | |
| - name: upload coverage | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| env_vars: OS,PYTHON |