update quicktest.yaml

.github/workflows/quicktest.yaml

@@ -55,54 +55,38 @@ jobs:
           cd $PYTHONPATH
         fi
 
-  # Run FastSurfer on MRI data
-  run-fastsurfer:
-    runs-on: self-hosted
-    needs: build-singularity-image
-    steps:
-    - name: Run FastSurfer
-      run: |
-        cd $RUNNER_FS_OUTPUT
-        DIRECTORY="subjectX"
-        echo "pwd: $(pwd)"
-        if [ ! -d "$DIRECTORY" ]; then
-        # if the directory does not exist, run FastSurfer
-          echo "Output directory does not exist. Running FastSurfer."
-          singularity exec --nv \
-                        --no-home \
-                        --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
-                        --env FASTSURFER_HOME=/fastsurfer-dev \
-                        -B $RUNNER_FS_MRI_DATA:/data \
-                        -B $RUNNER_FS_OUTPUT:/output \
-                        -B $RUNNER_FS_LICENSE:/fs_license \
-                        $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
-                        /fastsurfer/run_fastsurfer.sh \
-                        --fs_license /fs_license/.license \
-                        --t1 /data/subjectx/orig.mgz \
-                        --sid subjectX --sd /output \
-                        --parallel --3T
-        else
-          echo "Output directory already exists. Deleting directory and running FastSurfer."
-          rm -rf $DIRECTORY
-          singularity exec --nv \
-            --no-home \
-            --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
-            --env FASTSURFER_HOME=/fastsurfer-dev \
-            -B $RUNNER_FS_MRI_DATA:/data \
-            -B $RUNNER_FS_OUTPUT:/output \
-            -B $RUNNER_FS_LICENSE:/fs_license \
-            $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
-            /fastsurfer/run_fastsurfer.sh \
-            --fs_license /fs_license/.license \
-            --t1 /data/subjectx/orig.mgz \
-            --sid subjectX --sd /output \
-            --parallel --3T
-        fi
+#  # Run FastSurfer on MRI data
+#  run-fastsurfer:
+#    runs-on: self-hosted
+#    needs: build-singularity-image
+#    steps:
+#    - name: Run FastSurfer
+#      run: |
+#        cd $RUNNER_FS_OUTPUT
+#        DIRECTORY="subjectX"
+#        echo "pwd: $(pwd)"
+#        if [ -d "$DIRECTORY" ]; then
+#          # if output already exists, delete it and run again
+#          echo "Output already exists. Deleting output directory and running FastSurfer again."
+#          rm -rf $DIRECTORY
+#        singularity exec --nv \
+#                      --no-home \
+#                      --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
+#                      --env FASTSURFER_HOME=/fastsurfer-dev \
+#                      -B $RUNNER_FS_MRI_DATA:/data \
+#                      -B $RUNNER_FS_OUTPUT:/output \
+#                      -B $RUNNER_FS_LICENSE:/fs_license \
+#                      $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
+#                      /fastsurfer/run_fastsurfer.sh \
+#                      --fs_license /fs_license/.license \
+#                      --t1 /data/subjectx/orig.mgz \
+#                      --sid subjectX --sd /output \
+#                      --parallel --3T
 
   # Test file existence
   test-file-existence:
     runs-on: self-hosted
-    needs: run-fastsurfer
+#    needs: run-fastsurfer
     steps:
     - name: Test File Existence
       run: |
@@ -111,7 +95,7 @@ jobs:
   # Test for errors in log files
   test-error-messages:
     runs-on: self-hosted
-    needs: [run-fastsurfer, test-file-existence]
+#    needs: [test-file-existence]
     steps:
     - name: Test Log Files For Error Messages
       run: |
@@ -120,9 +104,8 @@ jobs:
   # Test seg_stats
   test-seg-stats:
     runs-on: self-hosted
-    needs: [run-fastsurfer, test-file-existence, test-error-messages]
+#    needs: [test-error-messages]
     steps:
     - name: Test seg_stats
       run: |
-        pip install pandas
         python3 test/quick_test/test_stats.py $RUNNER_FS_REF_STATS $RUNNER_FS_OUTPUT_STATS