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: Lint and test workflow | |
| on: | |
| push: | |
| workflow_dispatch: | |
| jobs: | |
| quality: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone repo | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha || github.base_ref }} | |
| - name: Setup Python environment | |
| uses: prefix-dev/setup-pixi@v0.8.14 | |
| with: | |
| environments: >- | |
| dev-only | |
| activate-environment: dev-only | |
| - name: isort | |
| run: isort workflow/scripts/*.py -c --profile black | |
| - name: Black | |
| run: black . --check | |
| - name: snakefmt | |
| run: snakefmt . --check | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: ["quality"] | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Pixi environment | |
| uses: prefix-dev/setup-pixi@v0.8.14 | |
| with: | |
| activate-environment: true | |
| - name: Test lighsheet-example | |
| run: | | |
| ./run.py --input-path $(pwd)/testing/dryrun_tests/lightsheet-example/ --subject M4A1Te3 --stains Abeta PI Lectin --output-bids-dir test_out/mouse_appmaptapoe --use-conda -np |