CI: add meta-analysis notebook and modularize rendering workflow

.github/notebooks.yaml

@@ -0,0 +1,4 @@
+notebooks:
+  - path: documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd
+  - path: documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd
+  - path: documentation/tutorials/Demo_03_Meta_Analysis/meta_analysis.qmd

.github/workflows/render-quarto.yml

@@ -28,13 +28,35 @@ jobs:
         with:
           version: '1.8.17'
 
+      - name: Parse notebook configuration
+        id: config
+        run: |
+          # Extract paths from yaml using grep and sed
+          # Assumes simple format: "  - path: some/path.qmd"
+          paths=$(grep "path:" .github/notebooks.yaml | sed 's/.*path: *//')
+
+          # 1. r_files: \"/work/path1\", \"/work/path2\"
+          # escape quotes for R vector
+          r_files_raw=$(echo "$paths" | awk '{printf "\\\"/work/%s\\\", ", $0}')
+          r_files=${r_files_raw%, }
+
+          # 2. render_cmd: quarto render /work/path1 --to html && ...
+          render_cmd_raw=$(echo "$paths" | awk '{printf "quarto render /work/%s --to html && ", $0}')
+          render_cmd=${render_cmd_raw% && }
+
+          # 3. paths (space separated) for artifact loop
+          paths_out=$(echo "$paths" | tr '\n' ' ')
+
+          echo "r_files=$r_files" >> $GITHUB_OUTPUT
+          echo "render_cmd=$render_cmd" >> $GITHUB_OUTPUT
+          echo "paths=$paths_out" >> $GITHUB_OUTPUT
+
       - name: Check R code style with styler
         run: |
           docker run --rm -v ${{ github.workspace }}:/work pecan-base-ci:latest bash -c "Rscript -e '
             if (!requireNamespace(\"styler\", quietly = TRUE)) install.packages(\"styler\");
             files_to_check <- c(
-              \"/work/documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd\",
-              \"/work/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd\"
+              ${{ steps.config.outputs.r_files }}
             );
             unstyled <- styler::style_file(files_to_check);
             if (is.data.frame(unstyled) && \"changed\" %in% names(unstyled) && any(unstyled\$changed == TRUE)) {
@@ -48,17 +70,26 @@ jobs:
       - name: Render Quarto notebooks to HTML
         run: |
           docker run --rm -v ${{ github.workspace }}:/work pecan-base-ci:latest bash -c "
-            quarto render /work/documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd --to html &&
-            quarto render /work/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd --to html
+            ${{ steps.config.outputs.render_cmd }}
           "
 
       - name: Prepare HTML artifacts
         run: |
           mkdir quarto_html_build
-          cp documentation/tutorials/Demo_1_Basic_Run/run_pecan.html quarto_html_build/
-          cp -r documentation/tutorials/Demo_1_Basic_Run/run_pecan_files quarto_html_build/
-          cp documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.html quarto_html_build/
-          cp -r documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty_files quarto_html_build/
+          for p in ${{ steps.config.outputs.paths }}; do
+            html_file="${p%.qmd}.html"
+            files_dir="${p%.qmd}_files"
+
+            if [ -f "$html_file" ]; then
+              cp "$html_file" quarto_html_build/
+            else
+              echo "Warning: $html_file not found"
+            fi
+
+            if [ -d "$files_dir" ]; then
+              cp -r "$files_dir" quarto_html_build/
+            fi
+          done
 
       - name: Upload rendered HTML as artifacts
         uses: actions/upload-artifact@v4

book_source/02_demos_tutorials_workflows/02_user_demos/01_introductions_user.Rmd

@@ -11,6 +11,7 @@ The following Tutorials assume you have installed PEcAn. If you have not, please
 |:--:|:---:|:------:|:-------------:|
 |Demo| Basic Run (Quarto)| <a href="rendered-demo-notebooks/run_pecan.html" target = "_blank">html</a> | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd" target = "_blank">qmd</a> |
 |Demo| Uncertainty Analysis (Quarto)| <a href="rendered-demo-notebooks/uncertainty.html" target = "_blank">html</a> | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd" target = "_blank">qmd</a> |
+|Demo| Meta Analysis (Quarto)| <a href="rendered-demo-notebooks/meta_analysis.html" target = "_blank">html</a> | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/Demo_03_Meta_Analysis/meta_analysis.qmd" target = "_blank">qmd</a> |
 |Demo| Basic Run| [html](#demo-1) | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd" target = "_blank">Rmd</a> |
 |Demo| Uncertainty Analysis| [html](#demo-2)| <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/02_Demo_Uncertainty_Analysis/Demo02.Rmd" target = "_blank">Rmd</a> |
 |Demo| Output Analysis|html | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/AnalyzeOutput/modelVSdata.Rmd" target="_blank">Rmd</a> |

documentation/tutorials/Demo_03_Meta_Analysis/meta_analysis.qmd

@@ -2,12 +2,13 @@
 title: "Demo 03: Meta Analysis"
 author: "Aritra Dey"
 format:
-  pdf:
-    toc: true
-    number-sections: true
-    fig-width: 10
-    fig-height: 6
-    fig-dpi: 300
+  html: default
+  pdf: default
+toc: true
+number-sections: true
+fig-width: 10
+fig-height: 6
+fig-dpi: 300
 ---
 
 # Introduction {#introduction}