tests: no unbound variable without --quick #243
This file contains 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: Workflow CI | |
| on: | |
| push: | |
| branches: "main" | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| jobs: | |
| run_workflow: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: setup-mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: 3.11 | |
| mamba-version: "*" | |
| channels: bioconda,conda-forge | |
| channel-priority: true | |
| auto-update-conda: true | |
| activate-environment: true | |
| - name: Cache generated inputs | |
| id: cache-inputs | |
| uses: actions/cache@v3 | |
| with: | |
| path: tests/rawdata | |
| key: rawdata-${{ hashFiles('tests/Snakefile.generate-rawdata') }}-${{ hashFiles('acanthophis/template/environment.yml') }}-${{ hashFiles('acanthophis/template/workflow/rules/envs/*.yml') }} | |
| - name: setup data | |
| shell: bash -el {0} | |
| run: | | |
| mamba info | |
| pushd tests | |
| bash -el setup.sh | |
| popd | |
| - name: run workflow | |
| shell: bash -el {0} | |
| run: | | |
| pushd tests | |
| bash -el test.sh --quick | |
| popd | |
| - name: cat all log files on failure | |
| if: ${{ failure() }} | |
| run: | | |
| find tests/ -name '*.log' -exec tail -n 1000 {} \; |