Dev umi #19
Workflow file for this run
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: MONSDA CI | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened, labeled, unlabeled] | |
| workflow_dispatch: | |
| inputs: | |
| run_full_pipeline: | |
| description: "Run full pipeline integration test" | |
| required: false | |
| default: false | |
| type: boolean | |
| jobs: | |
| tests: | |
| name: Unit tests (pytest) | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: monsda-test | |
| environment-file: environment.yml | |
| python-version: 3.12.2 | |
| channels: conda-forge,bioconda | |
| allow-softlinks: true | |
| channel-priority: flexible | |
| show-channel-urls: true | |
| use-only-tar-bz2: false | |
| auto-activate-base: false | |
| - name: build and install MONSDA | |
| run: | | |
| cd ${{ github.workspace }} | |
| python -m pip install --upgrade pip | |
| python -m pip install -e . | |
| python -m pip install pytest | |
| - name: run unit tests | |
| run: | | |
| cd ${{ github.workspace }} | |
| pytest -q tests/test_Utils.py | |
| full-pipeline: | |
| name: Full pipeline integration test | |
| runs-on: ubuntu-latest | |
| needs: tests | |
| if: >- | |
| (github.event_name == 'workflow_dispatch' && inputs.run_full_pipeline) || | |
| (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'full-pipeline')) | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: monsda-test | |
| environment-file: environment.yml | |
| python-version: 3.12.2 | |
| channels: conda-forge,bioconda | |
| allow-softlinks: true | |
| channel-priority: flexible | |
| show-channel-urls: true | |
| use-only-tar-bz2: false | |
| auto-activate-base: false | |
| - name: build and install MONSDA | |
| run: | | |
| cd ${{ github.workspace }} | |
| python -m pip install --upgrade pip | |
| python -m pip install -e . | |
| - name: prepare integration test config | |
| run: | | |
| cd ${{ github.workspace }} | |
| VERSION=$(monsda --version 2>&1 | sed 's/MONSDA version //g') | |
| sed -i "s/\"VERSION\": \"FIXME\"/\"VERSION\": \"${VERSION}\"/g" tests/data/config_Test.json | |
| - name: run full pipeline test | |
| run: | | |
| cd ${{ github.workspace }}/tests | |
| ln -fs data/* . | |
| mkdir -p CONDALIB | |
| monsda -j 6 -c config_Test.json --directory ${PWD} --use-conda --conda-prefix CONDALIB --save | |
| - name: upload test logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: full-pipeline-debug-artifacts | |
| path: | | |
| ${{ github.workspace }}/tests/LOGS | |
| ${{ github.workspace }}/tests/SUBSNAKES | |
| ${{ github.workspace }}/tests/FASTQ | |
| ${{ github.workspace }}/tests/MAPPED | |
| ${{ github.workspace }}/tests/QC | |
| ${{ github.workspace }}/tests/COUNTING | |
| ${{ github.workspace }}/tests/PEAKS | |
| ${{ github.workspace }}/tests/TRACKS |