add steps for venv

InstituteforDiseaseModeling · Sep 25, 2024 · 0f5c234 · 0f5c234
1 parent 5bedf28
commit 0f5c234
Show file tree

Hide file tree

Showing 2 changed files with 22 additions and 15 deletions.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -25,30 +25,33 @@ jobs:
       run: |
         docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace demo-quarto-image bash -c "
           echo 'Creating gallery directory...'
-          mkdir -p gallery && \
+          mkdir -p gallery && chmod -R 777 gallery && \
           echo 'gallery directory created.'
-
-          FOLDERS=(python R)
-          echo 'Folders to process: ${FOLDERS[@]}'
+          
+          source /opt/venv/bin/activate
+          echo 'activated virtualenv.'
+          
+          FOLDERS=(python r)
+          echo 'Folders to process: \${FOLDERS[@]}'
 
           for FOLDER in \"\${FOLDERS[@]}\"; do
-            echo 'Searching for .qmd and .ipynb files in $FOLDER...'
-            find \"\$FOLDER\" \( -name '*.qmd' -o -name '*.ipynb' \) | while read file; do
+            echo \"Searching for .qmd and .ipynb files in \$FOLDER...\"
+            find \"\$FOLDER\" \( -name '*.qmd' -o -name '*.ipynb' \) | while read -r file; do
               
-              echo 'Processing file: $file'
-              target_dir='gallery/$(dirname \"$file\")'
-              echo 'Creating target directory: $target_dir'
-              mkdir -p \"\$target_dir\" && echo 'Directory $target_dir created.'
+              echo \"Processing file: \$file\"
+              target_dir=\"gallery/\$(dirname \"\$file\")\"
+              echo \"Creating target directory: \$target_dir\"
+              mkdir -p \"\$target_dir\" && echo \"Directory \$target_dir created.\"
 
-              echo 'Attempting to render $file with execution...'
+              echo \"Attempting to render \$file with execution...\"
               if quarto render \"\$file\" --to html --output-dir \"\$target_dir\"; then
-                echo 'Successfully rendered $file with execution.'
+                echo \"Successfully rendered \$file with execution.\"
               else
-                echo 'Failed to render $file with execution. Rendering without execution...'
+                echo \"Failed to render \$file with execution. Rendering without execution...\"
                 if quarto render \"\$file\" --to html --no-execute --output-dir \"\$target_dir\"; then
-                  echo 'Successfully rendered $file without execution.'
+                  echo \"Successfully rendered \$file without execution.\"
                 else
-                  echo 'Rendering failed for $file, even without execution.'
+                  echo \"Rendering failed for \$file, even without execution.\"
                 fi
               fi
 

diff --git a/Dockerfile b/Dockerfile
@@ -60,6 +60,10 @@ RUN dpkg -i quarto-1.5.57-linux-amd64.deb
 WORKDIR /app
 
 COPY r /app/r
+COPY python /app/python
+
+# Install python packages in venv
+RUN /opt/venv/bin/pip install -r python/requirements.txt
 
 EXPOSE 8787
 EXPOSE 8888