quick fixes

Deep-MI · Aug 21, 2024 · a6da2e0 · a6da2e0
1 parent ffa1a6a
commit a6da2e0
Showing 1 changed file with 30 additions and 13 deletions.
diff --git a/.github/workflows/quicktest_runner.yaml b/.github/workflows/quicktest_runner.yaml
@@ -29,9 +29,26 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
+  check-output:
+    runs-on: self-hosted
+    steps:
+    - name: Check FastSurfer Output Directory
+      run: |
+        if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then
+          echo "FastSurfer output directory for subject1 exists. Finishing job..."
+          echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT
+          exit 0
+        else
+          echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..."
+          echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT
+
+        fi
+      id: check-fastsurfer-output
+
   # Create conda environment, install packages, and run Fastsurfer
   run-fastsurfer:
     runs-on: self-hosted
+    if: steps.check-fastsurfer-output.outputs.HAS_FASTSURFER == 'true'
     needs: checkout
     steps:
       # Check if the Environment Variables used in further steps are present
@@ -104,18 +121,18 @@ jobs:
         setuptools wheel
         python -m pip install --progress-bar off .[test]
       # Check if FastSurfer output already exists
-    - name: Check FastSurfer Output Directory
-      run: |
-        if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then
-          echo "FastSurfer output directory for subject1 exists. Finishing job..."
-          echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT
-          exit 0
-        else
-          echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..."
-          echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT
-
-        fi
-      id: check-fastsurfer-output
+#    - name: Check FastSurfer Output Directory
+#      run: |
+#        if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then
+#          echo "FastSurfer output directory for subject1 exists. Finishing job..."
+#          echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT
+#          exit 0
+#        else
+#          echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..."
+#          echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT
+#
+#        fi
+#      id: check-fastsurfer-output
       # Run FastSurfer
     - name: Run FastSurfer
       run: |
@@ -127,7 +144,7 @@ jobs:
         ./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \
                              --sd $RUNNER_FS_OUTPUT \
                              --parallel --threads 4 --3T --parallel_subjects surf
-      if: steps.check-fastsurfer-output.outputs.HAS_FASTSURFER == 'true'
+#      if: steps.check-fastsurfer-output.outputs.HAS_FASTSURFER == 'true'
 
   # Run pytest
   run-pytest: