Add nbstripout to pre-commit

[e-koch]

Following #159, after the notebook content purge, we should add a pre-commit check that runs nbstripout. See details on this here: https://github.com/kynan/nbstripout

[Kitchi]

Here's a script that I've been using for the last few days - it runs black and nbstripout

#!/bin/bash
#
# Pre-commit hook to run black formatter on Python files and nbstripout on notebooks
# Location: .git/hooks/pre-commit

# Get the black and nbstripout paths
BLACK=$(which black)
NBSTRIPOUT=$(which nbstripout)

# Check if black is available
if [ ! -x "$BLACK" ]; then
    echo "Error: black not found at $BLACK"
    echo "Please install black in the astroviper environment:"
    exit 1
fi

# Check if nbstripout is available
if [ ! -x "$NBSTRIPOUT" ]; then
    echo "Error: nbstripout not found at $NBSTRIPOUT"
    echo "Please install nbstripout in the astroviper environment:"
    exit 1
fi

# Get list of staged Python files
PYTHON_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep '\.py$')

# Get list of staged Jupyter notebook files
NOTEBOOK_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep '\.ipynb$')

# Exit early if no Python files or notebooks are staged
if [ -z "$PYTHON_FILES" ] && [ -z "$NOTEBOOK_FILES" ]; then
    exit 0
fi

# Run black on staged Python files
if [ -n "$PYTHON_FILES" ]; then
    echo "Running black formatter on staged Python files..."
    for file in $PYTHON_FILES; do
        # Only process files that exist (not deleted)
        if [ -f "$file" ]; then
            echo "  Formatting: $file"
            $BLACK "$file"
            # Re-stage the file after formatting
            git add "$file"
        fi
    done
    echo "Black formatting complete."
fi

# Run nbstripout on staged notebook files
if [ -n "$NOTEBOOK_FILES" ]; then
    echo "Running nbstripout on staged notebook files..."
    for file in $NOTEBOOK_FILES; do
        # Only process files that exist (not deleted)
        if [ -f "$file" ]; then
            echo "  Stripping outputs: $file"
            $NBSTRIPOUT "$file"
            # Re-stage the file after stripping
            git add "$file"
        fi
    done
    echo "Nbstripout complete."
fi

exit 0

[Kitchi]

So looking more into this, looks like the best ways to do this is to use a pre-commit manager like pre-commit or prek that can manage multiple pre-commit steps in a YAML config. This is much more maintainable than the ad-hoc script I posted above.

This means carrying pre-commit as a dev dependency in the project, which I don't see as a problem. We will need to modify the build instructions to run pre-commit install or similar to deploy the pre-commit hooks after the git clone.

If this sounds reasonable I can open a PR in the next day or so.

[e-koch]

Is this already a dependency/somewhat setup already for black?

astroviper/.pre-commit-config.yaml

Line 47 in c1b5dc5

- repo: https://github.com/psf/black

[e-koch]

Though it looks like those have not been updated in some time

[Kitchi]

Oh excellent spot. Looks like it's already in place. I'll edit that to add an nbstripout hook, and add nbstripout as a dependency to pyproject.toml and we should be good to go.