Merge branch 'develop' into quarto-meta-analysis-demo

Author: AritraDey-Dev

.github/lychee.toml

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+# Lychee link checker configuration for PEcAn project
+# See https://lychee.cli.rs for more options
+
+# Don't fail on certificate issues (some sites have temporary cert problems)
+insecure = true
+
+
+# Exclude patterns (regex) - add domains/URLs that frequently have transient failures
+exclude = [
+  # Localhost URLs (local development only)
+  'localhost/*',
+  '127\.0\.0\.1/*',
+  'pecan\.localhost/*',
+]

.github/workflows/check-links.yml

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+name: Check Documentation Links (Periodic Checks)
+
+on:
+  # Run weekdays at 10:00 UTC
+  schedule:
+    - cron: '0 10 * * 1-5'
+  # Allow manual trigger
+  workflow_dispatch:
+  # Run on PR changes to link checker config
+  pull_request:
+    paths:
+      - '.github/lychee.toml'
+      - '.github/workflows/check-links.yml'
+
+jobs:
+  links-checker:
+    # Only run on main repository for scheduled runs
+    if: ${{ github.repository == 'PecanProject/pecan' || github.event_name != 'schedule' }}
+    
+    env:
+      ISSUE_NAME: 'Documentation: broken links automatic report'
+    
+    runs-on: ubuntu-latest
+    
+    permissions:
+      issues: write  # Required for creating/updating/closing issues
+    
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch all history for complete link checking
+      
+      - name: Links Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v2
+        with:
+          args: --config .github/lychee.toml './**/*.md' './**/*.html' './**/*.Rmd' './**/*.R' './**/*.qmd'
+          fail: false
+      
+      # Search for existing open issue to avoid creating duplicates
+      - name: Search for existing issue number
+        id: search-issue
+        run: |
+          encoded_issue_name=$(echo "$ISSUE_NAME" | sed 's/ /%20/g')
+          response=$(curl -s -X GET "https://api.github.com/search/issues?q=$encoded_issue_name+repo:PecanProject/pecan+state:open+label:automated-issue&type=Issues")
+          issue_number=$(echo "$response" | jq -r '.items[0].number // empty')
+          echo "issue_number=$issue_number" >> $GITHUB_OUTPUT
+      
+      # Create new issue or update existing one
+      - name: Create or update issue with report
+        uses: peter-evans/create-issue-from-file@v5
+        if: steps.lychee.outputs.exit_code != 0
+        with:
+          title: ${{ env.ISSUE_NAME }}
+          content-filepath: ./lychee/out.md
+          issue-number: ${{ steps.search-issue.outputs.issue_number }}
+          labels: automated-issue
+      
+      # Auto-close issue when all links are fixed
+      - name: Close automated issue
+        if: steps.lychee.outputs.exit_code == 0 && steps.search-issue.outputs.issue_number != ''
+        uses: peter-evans/close-issue@v3
+        with:
+          issue-number: ${{ steps.search-issue.outputs.issue_number }}
+          comment: '[Periodic links check](https://github.com/PecanProject/pecan/actions/workflows/check-links.yml) no longer finds broken links, closing issue.'

book_source/02_demos_tutorials_workflows/02_user_demos/02_Run_Demo01_Notebook.Rmd

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+## Running PEcAn Basic Run using Quarto {#run-demo-1}
+
+This guide explains how to run the **Basic Run** tutorial using the new Quarto notebook format.
+
+### Prerequisites
+
+To run this notebook interactively, you will need:
+
+[**RStudio**](https://posit.co/download/rstudio-desktop/): An integrated development environment for R.
+
+### Steps to Run
+
+1.  **Open in RStudio**:
+    Open the [`run_pecan.qmd`](https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd) file in RStudio.
+
+2.  **Run Interactively**:
+    You can run separate chunks and go through the comments of every section to understand the notebook better.
+
+3.  **Render the Notebook**:
+
+    To render the notebook to HTML, run the following command in your terminal:
+    ```bash
+    quarto render documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd
+    ```
+
+### View Generated Artifact
+
+If you prefer to view the pre-rendered output without running the code yourself, you can access the generated HTML artifact here:
+
+[**View Rendered Notebook (HTML)**](https://pecanproject.github.io/pecan-documentation/develop/rendered-demo-notebooks/run_pecan.html)

book_source/02_demos_tutorials_workflows/02_user_demos/03_Run_Demo02_Notebook.Rmd

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+## Running Uncertainty Analysis using Quarto {#run-demo-2}
+
+This guide explains how to run the **Uncertainty Analysis** tutorial using the new Quarto notebook format.
+
+### Prerequisites
+
+To run this notebook interactively, you will need:
+
+[**RStudio**](https://posit.co/download/rstudio-desktop/): An integrated development environment for R.
+
+### Steps to Run
+
+1.  **Open in RStudio**:
+    Open the [`uncertainty.qmd`](https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd) file in RStudio.
+
+2.  **Run Interactively**:
+    You can run separate chunks and go through the comments of every section to understand the notebook better.
+
+3.  **Render the Notebook**:
+    To render the notebook to HTML, run the following command in your terminal:
+    
+    ```bash
+    quarto render documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd
+    ```
+
+### View Generated Artifact
+
+If you prefer to view the pre-rendered output without running the code yourself, you can access the generated HTML artifact here:
+
+[**View Rendered Notebook (HTML)**](https://pecanproject.github.io/pecan-documentation/develop/rendered-demo-notebooks/uncertainty.html)