Merge branch 'develop' of https://github.com/PecanProject/pecan into SDA_data

Author: Dongchen Zhang

.github/workflows/book.yml

@@ -12,7 +12,11 @@ on:
   workflow_dispatch:
 
 jobs:
+  call-render-quarto:
+    uses: ./.github/workflows/render-quarto.yml
+
   bookdown:
+    needs: call-render-quarto
     runs-on: ubuntu-latest  
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -45,6 +49,11 @@ jobs:
       run: |
         cd book_source
         Rscript -e 'options(bookdown.render.file_scope=FALSE); bookdown::render_book("index.Rmd", "bookdown::gitbook")'
+    # download quarto artifacts
+    - uses: actions/download-artifact@v4
+      with:
+        name: quarto-html
+        path: book_source/_book/
     # save artifact
     - uses: actions/upload-artifact@v4
       with:

.github/workflows/render-quarto.yml

@@ -4,6 +4,7 @@ on:
   push:
   pull_request:
   workflow_dispatch:
+  workflow_call:
 
 jobs:
   render-notebook:
@@ -39,13 +40,24 @@ jobs:
             }
           '"
 
-      - name: Render Demo 1 notebook to HTML
+      - 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_1_Basic_Run/run_pecan.qmd --to html &&
+            quarto render /work/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd --to html
           "
-      - name: Render Demo 2 notebook to HTML
+
+      - name: Prepare HTML artifacts
         run: |
-          docker run --rm -v ${{ github.workspace }}:/work pecan-base-ci:latest bash -c "
-            quarto render /work/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd --to html
-          "
+          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/
+
+      - name: Upload rendered HTML as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: quarto-html
+          path: quarto_html_build/
+          retention-days: 90

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

@@ -6,8 +6,11 @@ There are two ways of using PEcAn, via the web interface and directly within R.
 
 The following Tutorials assume you have installed PEcAn. If you have not, please consult the [PEcAn Installation Section](#pecan-manual-setup).
 
-|Type|Title|Web Link| Source Rmd|
-|:--:|:---:|:------:|:---------:|
+
+|Type|Title|Web Link| Source Rmd/qmd|
+|:--:|:---:|:------:|:-------------:|
+|Demo| Basic Run (Quarto)| <a href="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="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| 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> |

book_source/index.Rmd

@@ -1,6 +1,5 @@
 --- 
 title: "The Predictive Ecosystem Analyzer"
-date: "`r Sys.Date()`"
 site: bookdown::bookdown_site
 documentclass: book
 biblio-style: apalike