feat(docs): update README.md #203
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| name: Main Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: psf/black@stable | |
| - uses: actions/setup-python@v4 | |
| - name: Flake8 Install | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 | |
| - name: Flake8 Run | |
| run: | | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. black will have made line length 88 | |
| # also disable E203 (space before :) since that's how black likes it | |
| flake8 . --count --exit-zero --max-complexity=15 --ignore=E203 \ | |
| --max-line-length=88 --statistics | |
| unit_test: | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ ubuntu-latest ] | |
| python-version: ['3.10'] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| runs-on: ${{ matrix.os }} | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: virprof | |
| environment-file: environment_pytest.yaml | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| - name: Pytest Run | |
| run: | | |
| pytest | |
| run: | |
| needs: [lint, unit_test] | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| # - macos-latest | |
| target: | |
| # - test.ref_hg38gtest.rnaseq_salmon | |
| - test.ref_hg38gtest.rnaseq_star_salmon | |
| # - test.ref_hg38gtest.rnaseq_star_rsem | |
| - test.ref_hg38gtest.rnaseq_salmon.pathogen | |
| fail-fast: false | |
| runs-on: | |
| - ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: virprof | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: virprof | |
| environment-file: virprof/environment.yml | |
| mamba-version: "*" | |
| python-version: "3.10" | |
| - name: Install YMP | |
| run: | | |
| mamba update conda | |
| mamba env update --file virprof/environment.yml --name base | |
| mamba clean --all | |
| - name: Install Test Data | |
| run: | | |
| echo "Current directory: $PWD" | |
| ./virprof/test_data/install_testdata.sh | |
| - name: Dry-Run | |
| run: | | |
| echo "Current directory: $PWD" | |
| echo "test_data/:" | |
| ls test_data -l | |
| echo "test.csv:" | |
| cat test_data/test.csv | |
| ymp make -n ${{matrix.target}} | |
| - name: Install deps | |
| run: | | |
| echo "Current directory: $PWD" | |
| echo "Disk usage:" | |
| df -h | |
| ymp env prepare ${{matrix.target}} | |
| echo "Disk usage:" | |
| df -h | |
| mamba clean --all | |
| mamba info | |
| echo "Disk usage:" | |
| df -h | |
| - name: Run Pipeline | |
| run: | | |
| echo "Current directory: $PWD" | |
| ymp make ${{matrix.target}} -j4 -p -vvv | |
| ## LOG ## | |
| - name: Save pipeline reports | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: results-${{ matrix.os }}-${{ matrix.target }} | |
| path: reports/ | |
| # Note: Not saving the actual test.generic directory because | |
| # it is a symlink and actions/upload-artifact@v2 has problems | |
| # with symlinks. |