Create rmd.yml

.github/scripts/render.py

@@ -0,0 +1,84 @@
+"""
+Jupyter Notebook Batch Renderer
+
+Usage examples:
+    python render_notebook.py render config.json
+    python render_notebook.py render config.json --output_dir rendered
+"""
+
+from jinja2 import Environment, FileSystemLoader
+import json
+import fire
+from pathlib import Path
+from glob import glob
+
+
+class NotebookRenderer:
+    def render(self, config_file, output_dir="rendered"):
+        """
+        Render all Jupyter notebooks in current directory using configuration
+
+        Args:
+            config_file: Path to JSON configuration file
+            output_dir: Output directory path (default: "rendered")
+        """
+        root = Path(__file__).parent.parent.parent
+        print(f"Root directory: {root}")
+
+        # Setup paths
+        config_path = root / config_file
+        output_path = root / output_dir
+
+        # Create output directory if it doesn't exist
+        output_path.mkdir(exist_ok=True)
+
+        # Validate config file exists
+        if not config_path.exists():
+            raise FileNotFoundError(f"Config file '{config_path}' not found")
+
+        # Load configuration
+        try:
+            with open(config_path, 'r') as f:
+                context = json.load(f)
+        except json.JSONDecodeError as e:
+            raise ValueError(f"Invalid JSON in config file: {e}")
+        except Exception as e:
+            raise IOError(f"Error loading config file: {e}")
+
+        print(f"Loaded configuration: {context.keys()}")
+
+        # Setup Jinja2 environment
+        env = Environment(
+            loader=FileSystemLoader(root),
+            autoescape=False
+        )
+
+        # Find all .ipynb files in current directory
+        ipynb_files = glob(str(root / "*.ipynb"))
+        print(f"Found {len(ipynb_files)} notebook files to process")
+
+        # Process each file
+        success_count = 0
+        for file_path in ipynb_files:
+            try:
+                file_name = Path(file_path).name
+                print(f"\nProcessing: {file_name}")
+
+                template = env.get_template(file_name)
+                rendered_content = template.render(context)
+
+                output_file = output_path / file_name
+                with open(output_file, 'w') as f:
+                    f.write(rendered_content)
+
+                print(f"Successfully rendered to: {output_file}")
+                success_count += 1
+            except Exception as e:
+                print(f"Error processing {file_name}: {str(e)}")
+                continue
+
+        print(f"\nFinished. Successfully rendered {success_count}/{len(ipynb_files)} notebooks")
+
+
+if __name__ == '__main__':
+    fire.Fire(NotebookRenderer)

.github/workflows/rmd.yml

@@ -0,0 +1,67 @@
+name: Convert Notebooks to RMarkdown
+on:
+  push:
+  #  paths:
+  #    - '**.ipynb'
+  workflow_dispatch:  # Allow manual triggering
+
+permissions:
+  contents: write
+
+jobs:
+  convert:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install jupyter, jupytext, fire, loguru, jinja2
+      run: |
+        python -m pip install --upgrade pip
+        pip install nbformat jupytext fire loguru jinja2
+
+    - name: Create artifact directory
+      run: |
+        mkdir -p artifacts/rmd
+        rm -rf artifacts/rmd/*  # Clean any existing files
+
+    - name: Render all notebooks
+      run: |
+        python .github/scripts/render.py render config_rmd.json .
+
+    - name: Convert notebooks to RMarkdown
+      run: |
+        # Find all notebooks in the repository
+        NOTEBOOKS=$(find . -name "*.ipynb" -not -path "*/\.*" -not -path "*/artifacts/*")
+
+        # Convert each notebook
+        for nb in $NOTEBOOKS; do
+          echo "Converting $nb to Rmd..."
+          # Get the base name without path and extension
+          base_name=$(basename "$nb" .ipynb)
+
+          # Convert to Rmd in the artifacts directory
+          jupytext --to rmarkdown "$nb" --output "artifacts/rmd/${base_name}.Rmd"
+        done
+
+    - name: Copy data folder
+      run: |
+        cp -r data artifacts/rmd
+
+    #- name: Upload conversion results
+    #  if: always()
+    #  uses: actions/upload-artifact@v4
+    #  with:
+    #    name: rmd-files
+    #    path: artifacts/rmd/
+    #    retention-days: 1
+
+    - name: GitHub Pages action
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: rmd-files         # The branch the action should deploy to.
+        folder: artifacts/rmd     # The folder the action should deploy.

.gitignore

@@ -1,3 +1,6 @@
+# path for rendered notebooks
+rendered
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]