CI/CD update (#12)

* Building parallel Docker images

* CI rough draft

* Updated Dockerfile for the large container image

.github/workflows/ci.yml

@@ -0,0 +1,57 @@
+name: CI
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    env:
+      IMG: exemplar-001-cycle6.ome.tif
+      PMAP: exemplar-001-cycle6_Probabilities_1.tif
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build the Docker container
+        run: |
+          docker build -t s3seg:test .
+          docker build -t s3seg:test-large large/
+
+      # Cache test data to avoid repeated download
+      - uses: actions/cache@v3
+        id: cache-data
+        with:
+          path: ~/data/*.tif
+          key: testdata-2022-05-12
+
+      # Download test data only if no cache is present
+      - name: Test data download
+        if: steps.cache-data.outputs.cache-hit != 'true'
+        run: |
+          mkdir ~/data
+          cd ~/data
+          curl -f -o $IMG "https://mcmicro.s3.amazonaws.com/ci/$IMG"
+          curl -f -o $PMAP "https://mcmicro.s3.amazonaws.com/ci/$PMAP"
+
+      - name: Test the default container
+        run: |
+          cd ~/data
+          rm -rf exemplar-001-cycle6
+          docker run -v "$PWD":/data s3seg:test /bin/bash -c "cd /data; \
+            python /app/S3segmenter.py --imagePath $IMG --stackProbPath $PMAP --outputPath ."
+
+      - name: Test the large container
+        run: |
+          cd ~/data
+          rm -rf large
+          mkdir large
+          docker run -v "$PWD":/data s3seg:test-large /bin/bash -c "cd /data; \
+            python /app/S3segmenter.py --imagePath $IMG --stackProbPath $PMAP --outputPath large"
+
+      # 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: ex001-s3seg
+          path: |
+            ~/data/exemplar-001-cycle6/**
+            ~/data/large/**
+  

.github/workflows/dockerhub.yml

@@ -21,12 +21,22 @@ jobs:
           username: ${{ secrets.MCMICRO_USERNAME }}
           password: ${{ secrets.MCMICRO_TOKEN }}
       -
-        name: Build and push
-        id: docker_build
+        name: Build and push the standard image
+        id: docker_build_standard
         uses: docker/build-push-action@v2
         with:
           push: true
           tags: labsyspharm/s3segmenter:${{ github.event.release.tag_name }}
+      -
+        name: Build and push the large-scale image
+        id: docker_build_large
+        uses: docker/build-push-action@v2
+        with:
+          context: large
+          push: true
+          tags: labsyspharm/s3segmenter:${{ github.event.release.tag_name }}-large
       -
         name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: |
+          echo ${{ steps.docker_build_standard.outputs.digest }}
+          echo ${{ steps.docker_build_large.outputs.digest }}

large/Dockerfile

@@ -1,6 +1,15 @@
 FROM python:3.10
 
-RUN pip install scikit-learn scikit-image opencv-python tifffile imagecodecs dask-image zarr ome_types
+RUN python -m pip install \
+    dask[dataframe] \
+    scikit-learn \
+    scikit-image \
+    opencv-python-headless \
+    tifffile \
+    imagecodecs \
+    dask-image \
+    zarr \
+    ome_types
 
 COPY S3segmenter.py ./app/S3segmenter.py
 COPY save_tifffile_pyramid.py ./app/save_tifffile_pyramid.py