diff --git a/.github/workflows/run_batch_script.yml b/.github/workflows/run_batch_script.yml index 4553393..5182ac3 100644 --- a/.github/workflows/run_batch_script.yml +++ b/.github/workflows/run_batch_script.yml @@ -40,6 +40,10 @@ jobs: cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH + - name: Pre-download necessary models + run: | + sct_deepseg spinalcord -install + - name: "Checkout '${{ github.event.repository.name }}'" uses: actions/checkout@v4 with: @@ -50,17 +54,27 @@ jobs: cd "${{ github.event.repository.name }}/multi_subject" sct_run_batch -script process_data.sh -config config.yml + - name: "Upload CSV files for easier tutorial updating" + uses: actions/upload-artifact@v4 + with: + name: Multi Subject CSV Files + path: ${{ github.event.repository.name }}/multi_subject/output/**/*.csv + - name: Output full log for sanity checking + if: always() run: | cd "${{ github.event.repository.name }}/multi_subject/output/log" - for logfile in process_data_sub-01.log err.process_data_sub-01.log; do - if [[ -e "${logfile}" ]]; then - echo "=== Contents of ${logfile} ===" - cat "${logfile}" - else - echo "=== No file ${logfile} ===" - fi - done + for subxx in sub-01 sub-03 sub-05; do + for logfile in process_data_${subxx}.log err.process_data_${subxx}.log; do + if [[ -e "${logfile}" ]]; then + echo "=== Contents of ${logfile} ===" + cat "${logfile}" + else + echo "=== No file ${logfile} ===" + fi + done + done + - name: Check results (no error logs) if: always() diff --git a/.github/workflows/run_script_and_create_release.yml b/.github/workflows/run_script_and_create_release.yml index 5633e6c..2851ad2 100644 --- a/.github/workflows/run_script_and_create_release.yml +++ b/.github/workflows/run_script_and_create_release.yml @@ -60,6 +60,12 @@ jobs: cd "${{ github.event.repository.name }}/single_subject" ./batch_single_subject.sh + - name: "Upload CSV files for easier tutorial updating" + uses: actions/upload-artifact@v4 + with: + name: Single Subject CSV Files + path: ${{ github.event.repository.name }}/single_subject/data/**/*.csv + - name: "Package data into tutorial-specific .zip files" run: | cd ${{ github.event.repository.name }}