WIP foreground model for sensor noise bypass #139
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: | |
| # 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 |