Automatically upload CSV files as artifacts during CI runs (#31)

Author: joshuacwnewton

.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()

.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 }}