feat: add apptainer/singularity container definition #201
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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. |