use action files filter

Author: chyumin

.github/workflows/test_changed_files.yml

@@ -6,42 +6,73 @@ on:
     types: [synchronize, opened, reopened, ready_for_review]
 
 jobs:
-  set-matrix-job:
-    name: Set jobs by changed Dockerfile
-    runs-on: ubuntu-latest
+  prepare-matrix-jobs:
+    name: Prepare Build and Test Jobs
+    runs-on: "ubuntu-latest"
     outputs:
-      sorters: ${{ steps.set-matrix.outputs.sorters }}
+      has_changed_files: ${{ steps.changed-files.outputs.any_changed }}
+      sorters: ${{ steps.get-changed-sorters.outputs.sorters }}
     steps:
-      - name: Checkount
+      - name: Checkout
         uses: actions/checkout@v3
 
       - name: Get changed files
         id: changed-files
         uses: tj-actions/changed-files@v23
+        with:
+          files: |
+            */Dockerfile
 
-      - name: Set jobs' matrix
-        id: set-matrix
+      - name: Prepare jobs matrix
+        id: get-changed-sorters
         run: |
+          # sorters variable will be a JSON-like array
           sorters="["
-          for file in /Dockerfilesabc/Dockerfiles def/Dockerfiles huea; do
-            if [[ "$file" == *"Dockerfile"* ]]; then
-              # Removing /Dockerfile from string
-              parsed=${file%*/Dockerfile*}
-
-              # Appending to sorters Array
-              sorters+="\"${parsed}\", "
-            fi
+
+          for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
+            # Removing /Dockerfile from string
+            parsed=${file%*/Dockerfile*}
+
+            # Appending to final string
+            sorters+="\"${parsed}\", "
           done
           sorters=${sorters%*, *}
           sorters+="]"
-          echo $sorters
 
+          echo ${sorters}
           echo "::set-output name=sorters::${sorters}"
-  test:
-    needs: set-matrix-job
-    runs-on: "ubuntu-latest"
+
+  build-and-test-image:
+    name: build (${{ matrix.sorter }})
+    if: needs.prepare-matrix-jobs.outputs.has_changed_files == 'true'
+    needs: prepare-matrix-jobs
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        sorter: ${{ fromJSON(needs.set-matrix-job.outputs.matrix) }}
+        # "macos-latest", "windows-latest"
+        os: ["ubuntu-latest", ]
+        sorter: ${{ fromJSON(needs.prepare-matrix-jobs.outputs.sorters) }}
     steps:
-      - run: echo ${{ matrix.sorter }}
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          python-version: 3.8
+
+      - name: Build ${{ matrix.sorter }} Docker image
+        run: |
+          cd ${{ matrix.sorter }}
+          bash build.sh
+          cd ..
+
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install dependencies & Test ${{ matrix.sorter }} image
+        run: |
+          if  [[ ${{ matrix.sorter }} == 'tridesclous' ]]
+            pip install tridesclous
+          fi
+          pip install -r requirements_test.txt
+          pytest -sv tests/test_singularity_containers.py::test_${{ matrix.sorter }}

spykingcircus/Dockerfile

@@ -14,3 +14,5 @@ RUN apt-get update && apt-get install -y packagekit-gtk3-module libcanberra-gtk-
 RUN pip install scikit-build
 RUN pip install cmake>=3.18
 RUN pip install spyking-circus==1.1.0
+
+# test

tests/test_singularity_containers.py

@@ -21,15 +21,15 @@ def run_kwargs(work_dir):
     test_recording, _ = se.toy_example(
         duration=30,
         seed=0,
-        num_channels=32,
+        num_channels=64,
         num_segments=1
     )
     test_recording = test_recording.save(name='toy')
     return dict(recording=test_recording, verbose=True, singularity_image=True)
 
 
-def test_spyking_circus(run_kwargs):
-    sorting = ss.run_spykingcircus(output_folder="spyking_circus", **run_kwargs)
+def test_spykingcircus(run_kwargs):
+    sorting = ss.run_spykingcircus(output_folder="spykingcircus", **run_kwargs)
     print(sorting)
 
 

tridesclous/Dockerfile

@@ -20,3 +20,5 @@ RUN pip install h5py
 RUN pip install loky packaging
 
 RUN pip install tridesclous==1.6.5
+
+# test