Skip y-axis stage coords flip for InCell reader #159
Workflow file for this run
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| name: CI | |
| on: | |
| # Don't trigger when only the docs are modified | |
| push: | |
| paths-ignore: | |
| - 'docs/**' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build the Docker container | |
| run: docker build -t ashlar:test . | |
| # Cache test data to avoid repeated download | |
| - uses: actions/cache@v3 | |
| id: cache-data | |
| with: | |
| path: | | |
| ~/data/ | |
| !~/data/exemplar-001.ome.tif | |
| key: testdata-2022-04-25 | |
| # Download exemplar-001 only if no cache is present | |
| - name: Exemplar-001 download | |
| if: steps.cache-data.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir ~/data | |
| cd ~/data | |
| curl -f -o exemplar-001.zip https://mcmicro.s3.amazonaws.com/exemplars/exemplar-001.zip | |
| unzip exemplar-001.zip | |
| mv exemplar-001/raw/*.ome.tiff . | |
| mv exemplar-001/illumination/*.tif . | |
| rm -r exemplar-001 | |
| rm exemplar-001.zip | |
| - name: Test the container | |
| run: | | |
| cd ~/data/ | |
| rm -f exemplar-001.ome.tif | |
| docker run -v "$PWD":/data ashlar:test /bin/bash -c "cd /data; \ | |
| ashlar $imgs -m 30 --dfp $dfp --ffp $ffp -o exemplar-001.ome.tif" | |
| env: | |
| imgs: 'exemplar-001-cycle-06.ome.tiff exemplar-001-cycle-07.ome.tiff exemplar-001-cycle-08.ome.tiff' | |
| dfp: 'exemplar-001-cycle-06-dfp.tif exemplar-001-cycle-07-dfp.tif exemplar-001-cycle-08-dfp.tif' | |
| ffp: 'exemplar-001-cycle-06-ffp.tif exemplar-001-cycle-07-ffp.tif exemplar-001-cycle-08-ffp.tif' | |
| # If the action is successful, the output will be available as a downloadable artifact | |
| - name: Upload processed result | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: exemplar-001 | |
| path: | | |
| ~/data/exemplar-001.ome.tif |