fix(?): code check comparison to master

make init/get singularity action do only the caching/pulling

.github/workflows/code_check.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   init:
-    uses: ./.github/workflows/setup.yml
+    uses: ./.github/workflows/get_singularity.yml
     with:
       singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
       sif_file: retinal-rl_singularity-image-latest.sif
@@ -19,12 +19,13 @@ jobs:
     needs: init
     runs-on: ubuntu-latest
     steps:
-    - name: list directory
-      run: ls
-    - uses: actions/checkout@v4
-    - name: list directory
-      run: ls
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Fetch all branches
+      run: git fetch --all
     - name: Run Pylint
       run: |
         singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
-        pylint $(git diff --name-only origin/master HEAD -- '*.py')
+        pylint $(git diff --name-only origin/master...HEAD -- '*.py')

.github/workflows/config_scan.yml

@@ -3,7 +3,7 @@ on: [pull_request,workflow_dispatch]
 
 jobs:
   init:
-    uses: ./.github/workflows/setup.yml
+    uses: ./.github/workflows/get_singularity.yml
     with:
       singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
       sif_file: retinal-rl_singularity-image-latest.sif
@@ -12,7 +12,9 @@ jobs:
     needs: init
     runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4
     - name: Scan classification config
       run: |
+        cp -r resources/config_templates/* config/
         singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
         python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu

.github/workflows/setup.yml → .github/workflows/get_singularity.yml

@@ -1,4 +1,4 @@
-name: Pull Singularity container & Setup Repository
+name: Get Singularity Container
 
 on:
   workflow_call:
@@ -13,10 +13,7 @@ on:
 jobs:
   init:
     runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
+    steps:      
       - name: Setup Apptainer
         uses: eWaterCycle/setup-apptainer@v2
         with: