changing singularity to apptainer

.github/workflows/quicktest.yaml

@@ -1,5 +1,16 @@
 name: quicktest
 
+"""
+File: quicktest.yaml
+Author: Taha Abdullah
+Created on: 2023-03-04
+Functionality: This workflow runs some quick integration tests on FastSurfer commits. It checks out the new 
+                FastSurfer repo, sets up Python, builds a Singularity image, runs FastSurfer on sample MRI data, and 
+                runs pytest to check if the results are acceptable
+Usage: This workflow is triggered on a push or pull-request to the dev and main branch of DeepMI/FastSurfer. It can also
+        be triggered manually with workflow-dispatch
+"""
+
 on:
 #  pull_request:
   workflow_dispatch:
@@ -28,10 +39,14 @@ jobs:
 #      uses: actions/setup-go@v5
 #      with:
 #        go-version: '^1.13.1' # The Go version to download (if necessary) and use.
+#    - name: Set up Singularity
+#      uses: eWaterCycle/setup-singularity@v7
+#      with:
+#        singularity-version: 3.8.7
     - name: Set up Apptainer
       uses: eWaterCycle/setup-apptainer@v2
       with:
-        apptainer-version: 1.3.0
+        apptainer-version: 1.3.3
 
   # Build Docker Image and convert it to Apptainer
   build-apptainer-image:
@@ -45,14 +60,13 @@ jobs:
         if [ ! -f "$FILE" ]; then
         # If the file does not exist, build the file
           echo "SIF File does not exist. Building file."
-          PYTHONPATH=$PYTHONPATH
-          cd $PYTHONPATH
+          cd $FASTSURFER_HOME
           python3 Docker/build.py --device cuda --tag fastsurfer_gpu:cuda
           cd $RUNNER_FASTSURFER_IMGS
           apptainer build --force fastsurfer-gpu.sif docker-daemon://fastsurfer_gpu:cuda
         else
           echo "File already exists"
-          cd $PYTHONPATH
+          cd $FASTSURFER_HOME
         fi
 
   # Run FastSurfer on MRI data