Annot demux refactor #88
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| name: Run Pytest | |
| on: | |
| push: | |
| branches: [main, dev, annot_demux_refactor] | |
| pull_request: | |
| branches: [main, dev, annot_demux_refactor] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: tranquillyzer | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 22.9.0-2 | |
| use-mamba: true | |
| python-version: "3.10.12" | |
| - name: Install Python packages (extra) | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| pip install pytest pytest-order pytest-cov | |
| - name: Download model and reference | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p tests/10x3p/data tests/references | |
| curl -L "https://www.dropbox.com/scl/fi/gmmifxp964fe66qvv3nfk/10x3p_sc_ont_016.h5?rlkey=vqqob3hxrqsuq8540su1aw985&st=bwk2kblf&dl=0" -o models/10x3p_sc_ont_016.h5 | |
| curl -L "https://www.dropbox.com/scl/fi/7almukao9vykewf4p73eg/10x3p_sc_ont_016_params.yaml?rlkey=ge8fhouxvvya3umlzryk8mvtq&st=zn01vxqc&dl=0" -o models/10x3p_sc_ont_016_params.yaml | |
| curl -L "https://www.dropbox.com/scl/fi/4wvup62v1sgh7v84899ud/10x3p_sc_ont_016_lbl_bin.pkl?rlkey=m0xt4vzdpfc0ztj91zw93ko8p&st=y5skyjsq&dl=0" -o models/10x3p_sc_ont_016_lbl_bin.pkl | |
| curl -L "https://www.dropbox.com/scl/fi/9203pc2gz45u419kze446/hg38_gencode_chr21.fa?rlkey=k1co80pso7zsvb8oiqqc1o1dy&st=e0e92h5h&dl=1" -o tests/references/hg38_gencode_chr21.fa | |
| curl -L "https://www.dropbox.com/scl/fi/9zvh26moro7frfho818ko/hg38_gencode_chr21.gtf?rlkey=v3s05m9ap3srpjhvl5yfjfeq7&st=hn6mufoq&dl=0" -o tests/references/hg38_gencode_chr21.gtf | |
| curl -L "https://www.dropbox.com/scl/fi/98ykmaori9zrqf0q1qn36/hg38.HouseKeepingGenes.bed.gz?rlkey=dqjabcby9b9owso30njfpauyt&st=zmvxk4pp&dl=0" -o tests/references/hg38.HouseKeepingGenes.bed.gz | |
| - name: Run Pytest with coverage | |
| shell: bash -l {0} | |
| run: | | |
| pytest --maxfail=1 -q \ | |
| --cov=. \ | |
| --cov-report=term-missing \ | |
| --cov-report=xml:coverage.xml | |
| - name: Combine coverage (explicit) | |
| shell: bash -l {0} | |
| run: | | |
| python - <<'PY' | |
| import coverage | |
| cov = coverage.Coverage(data_file=".coverage") | |
| cov.load() | |
| cov.combine() | |
| cov.xml_report(outfile="coverage.xml") | |
| PY | |
| - name: Upload coverage to Codecov | |
| if: always() | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |