Merge pull request #30 from berenslab/fix-ci-pipeline

Fix ci pipeline
berenslab · Oct 21, 2024 · 6d9d4a9 · 6d9d4a9
2 parents 77c8ace + c23c34f
commit 6d9d4a9
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Showing 5 changed files with 22 additions and 14 deletions.
diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
@@ -26,12 +26,10 @@ jobs:
 
     - name: Cache Singularity Image
       id: cache-singularity
-      uses: actions/cache@v4
+      uses: actions/cache/restore@v4
       with:
         path: ${{ env.sif_file }}
-        key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
-        restore-keys: |
-          ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        key: ${{ runner.os }}-singularity-${{ hashFiles('resources/retinal-rl.def') }}
 
     - name: Run Linter / Code check
       if: always() && steps.cache-singularity.outputs.cache-hit == 'true'

diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
@@ -15,15 +15,21 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
 
+    - name: Setup Apptainer
+      uses: eWaterCycle/setup-apptainer@v2
+      with:
+        apptainer-version: 1.3.0
+
     - name: Cache Singularity Image
       id: cache-singularity
       uses: actions/cache@v4
       with:
         path: ${{ env.sif_file }}
-        key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
-        restore-keys: |
-          ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        key: ${{ runner.os }}-singularity-${{ hashFiles('resources/retinal-rl.def') }}
 
     - name: Build Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: apptainer build ${{ env.sif_file }} resources/retinal-rl.def
+
+    - name: Show Versions
+      run: apptainer exec retinal-rl_singularity-image.sif pip freeze
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -21,14 +21,17 @@ jobs:
         needs: build
         runs-on: ubuntu-latest
         steps:
+
+        - name: Setup Apptainer
+          uses: eWaterCycle/setup-apptainer@v2
+          with:
+            apptainer-version: 1.3.0
         - name: Retrieve cached sif file
           id: cache-singularity
-          uses: actions/cache@v4
+          uses: actions/cache/restore@v4
           with:
             path: ${{ env.sif_file }}
-            key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
-            restore-keys: |
-                ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+            key: ${{ runner.os }}-singularity-${{ hashFiles('resources/retinal-rl.def') }}
         - name: Deployment / Push to ghcr.io
           run: |
             apptainer registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -28,6 +28,7 @@ jobs:
           else
             echo "changed=false" >> $GITHUB_OUTPUT
           fi
+          less $GITHUB_OUTPUT
 
   ensure_container: # main cache should provide the container if def file not changed
     name: Rebuild container

diff --git a/.github/workflows/update_cache.yml b/.github/workflows/update_cache.yml
@@ -55,9 +55,9 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ${{ env.sif_file }}
-        key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
-        restore-keys: |
-          ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        key: ${{ runner.os }}-singularity-${{ hashFiles('resources/retinal-rl.def') }}
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: apptainer pull ${{ env.sif_file }} ${{ env.singularity_image }}
+    - name: Show Versions
+      run: apptainer exec retinal-rl_singularity-image.sif pip freeze