Update README.md (#47) #80
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| name: Run tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: build conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: seqneut-pipeline | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| auto-update-conda: true | |
| channel-priority: strict | |
| - name: lint with ruff | |
| # NOTE: must specify the shell so that conda init updates bashrc see: | |
| # https://github.com/conda-incubator/setup-miniconda#IMPORTANT | |
| shell: bash -el {0} | |
| run: ruff check . | |
| - name: check code format with black | |
| shell: bash -el {0} | |
| run: black --check . | |
| - name: check snakemake files format with snakefmt | |
| shell: bash -el {0} | |
| run: snakefmt --check . | |
| - name: lint snakemake files with snakemake --lint | |
| shell: bash -el {0} | |
| run: cd test_example && snakemake --lint && cd .. | |
| - name: run pipeline on test example | |
| shell: bash -el {0} | |
| run: > | |
| rm -rf docs | |
| && cd test_example | |
| && rm -rf results | |
| && snakemake --software-deployment-method conda -j 2 | |
| && cd .. | |
| - name: test titers as expected | |
| shell: bash -el {0} | |
| run: cd test_example && python test_titers_as_expected.py && cd .. | |
| - name: upload results in case of error | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: results | |
| path: test_example/results | |
| retention-days: 7 |