ci.yml

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