fix: removing duplicates in conditions JSONL #192
Workflow file for this run
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: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Cancel-Previous: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/[email protected] | |
| with: | |
| workflows: "main.yml" | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| Formatting-Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup formatting environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: none # breaks otherwise | |
| - name: Check formating | |
| run: | | |
| make ci | |
| shell: bash -el {0} | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/[email protected] | |
| with: | |
| message: | | |
| Please check for formatting and linting issues. You can use `make lint` to: | |
| - Check your Bash style with `beautysh` and formatting with `shellcheck`. | |
| - Check your Python style with `black`, linting with `flake8`. | |
| - Check your Snakemake style with `snakefmt`. | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| Run-Test-Mode: | |
| needs: Formatting-Linting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Setup formatting environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: none # breaks otherwise | |
| - name: Install qsv (not in conda-forge yet) | |
| run: | | |
| cd /tmp | |
| wget https://github.com/jqnatividad/qsv/releases/download/0.112.0/qsv-0.112.0-x86_64-unknown-linux-musl.zip | |
| unzip qsv-0.112.0-x86_64-unknown-linux-musl.zip | |
| cp qsv_musl-1.2.3 /usr/local/bin/qsv | |
| - name: Install python package | |
| run: | | |
| pip install -e . | |
| shell: bash -el {0} | |
| - name: Run in test mode | |
| run: | | |
| CI=true snakemake --cores=1 -p all | |
| shell: bash -el {0} | |
| env: | |
| QSV_NO_UPDATE: "1" |