Notebook Cleaning

def nbdev_clean(fname: str = None, clear_all: bool = False, 
                disp: bool = False, read_input_dir: str = None, 
                write_input_dir: str = None):
    """
    Clean notebooks in project.
    
    Args:
        fname: Specific notebook file or glob pattern to clean
        clear_all: Remove all metadata and outputs (overrides settings)
        disp: Display cleaning progress and changes
        read_input_dir: Directory to read notebooks from
        write_input_dir: Directory to write cleaned notebooks to
        
    Removes unnecessary metadata, cell outputs, and execution counts
    from notebooks to make them git-friendly and reduce diff noise.
    """

def clean_nb(nb):
    """
    Clean a single notebook object.
    
    Args:
        nb: Notebook object to clean
        
    Returns:
        Cleaned notebook with metadata and outputs removed
        according to configuration settings.
    """

from nbdev.clean import nbdev_clean, clean_nb
from execnb.nbio import read_nb, write_nb

# Clean all notebooks in project
nbdev_clean()

# Clean specific notebook file
nbdev_clean('notebooks/01_core.ipynb')

# Clean with verbose output
nbdev_clean(disp=True)

# Clean and remove all metadata/outputs
nbdev_clean(clear_all=True)

# Clean notebook object directly
nb = read_nb('example.ipynb')
cleaned_nb = clean_nb(nb)
write_nb(cleaned_nb, 'cleaned_example.ipynb')

def nbdev_trust(fname: str = None, force_all: bool = False):
    """
    Trust notebooks matching fname pattern.
    
    Args:
        fname: Notebook name or glob pattern to trust
        force_all: Trust notebooks even if they haven't changed
        
    Trusts notebooks for execution by signing them with Jupyter's
    trust system. Only processes notebooks that have changed since
    last trust operation unless force_all is True.
    """

from nbdev.clean import nbdev_trust

# Trust all notebooks in project
nbdev_trust()

# Trust specific notebook
nbdev_trust('notebooks/analysis.ipynb')

# Force trust all notebooks regardless of change status
nbdev_trust(force_all=True)

# Trust notebooks matching pattern
nbdev_trust('notebooks/experimental/*.ipynb')

def nbdev_install_hooks():
    """
    Install git hooks for notebook processing.
    
    Installs pre-commit and other git hooks that automatically:
    - Clean notebooks before commits
    - Handle notebook merge conflicts
    - Process notebook metadata
    - Ensure consistent notebook formatting
    """

from nbdev.clean import nbdev_install_hooks

# Install git hooks for automatic cleaning
nbdev_install_hooks()
# Now git commits will automatically clean notebooks

def clean_jupyter():
    """
    Clean Jupyter-specific metadata and configuration.
    
    Removes Jupyter-specific metadata that can cause merge conflicts
    or unnecessary version control noise, including:
    - Kernel specifications that may vary between environments
    - Execution timing information
    - Widget state that doesn't serialize well
    """

def process_write(nb, fname: str):
    """
    Process and write notebook with cleaning.
    
    Args:
        nb: Notebook object to process
        fname: Output filename for processed notebook
        
    Applies all configured cleaning operations and writes
    the cleaned notebook to the specified file.
    """

# Remove cell IDs from notebooks
clean_ids = True

# Remove all metadata and outputs
clear_all = False

# Preserve specific metadata keys
allowed_metadata_keys = language_info,kernelspec
allowed_cell_metadata_keys = tags,id

# Enable Jupyter git hooks
jupyter_hooks = True

{
  "cell_type": "code",
  "execution_count": 42,
  "id": "a1b2c3d4-e5f6-7890",
  "metadata": {
    "scrolled": true,
    "execution": {"iopub.execute_input": "2023-01-01T12:00:00.000Z"}
  },
  "outputs": [{"output_type": "stream", "text": "Hello World"}],
  "source": "print('Hello World')"
}

{
  "cell_type": "code",
  "execution_count": null,
  "metadata": {},
  "outputs": [],
  "source": "print('Hello World')"
}

# Before each commit, hooks run:
nbdev_clean --clear_all  # Clean all notebooks
# Then proceed with commit

from nbdev.clean import nbdev_clean

# Clean only specific types of notebooks
nbdev_clean('notebooks/experiments/*.ipynb')

# Clean with custom settings
nbdev_clean(clear_all=True, disp=True)

from nbdev.clean import nbdev_clean, nbdev_trust
from nbdev.export import nb_export

# Complete workflow
def prepare_notebooks():
    """Prepare notebooks for version control and export."""
    # Clean notebooks
    nbdev_clean(disp=True)
    
    # Trust for execution
    nbdev_trust()
    
    # Export to modules
    nb_export()
    
    print("Notebooks prepared successfully")

prepare_notebooks()

from nbdev.clean import clean_nb, process_write
from execnb.nbio import read_nb
from pathlib import Path

def custom_clean_workflow(nb_path):
    """Custom cleaning with additional processing."""
    nb = read_nb(nb_path)
    
    # Apply standard cleaning
    cleaned_nb = clean_nb(nb)
    
    # Custom processing
    # Remove specific metadata, add custom fields, etc.
    
    # Write back
    process_write(cleaned_nb, nb_path)

# Apply to all notebooks
for nb_file in Path('notebooks').glob('*.ipynb'):
    custom_clean_workflow(nb_file)

# Add to your development workflow
nbdev_clean  # Before committing changes
nbdev_trust  # After pulling changes

# In GitHub Actions
- name: Clean notebooks
  run: nbdev_clean --clear_all
  
- name: Verify notebooks are clean  
  run: |
    nbdev_clean
    git diff --exit-code  # Fail if notebooks weren't already clean