diff --git a/.github/workflows/quicktest_runner.yaml b/.github/workflows/quicktest_runner.yaml index 3d105b2f..c0139702 100644 --- 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: