runipynbs.py

#!/usr/bin/env python

# -----------------------------------------------------------------------------
# This work is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 4.0 International License. To view a
# copy of this license, visit
# http://creativecommons.org/licenses/by-nc-sa/4.0/.
# -----------------------------------------------------------------------------

import logging
import os
import sys

from runipy.notebook_runner import NotebookRunner, NotebookError
from IPython.nbformat.current import read

# Taken and modified from
# https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/blob/master/runipynbs.py
# See licenses/ directory for runipy license.
def main():
    log_format = '%(asctime)s %(message)s'
    log_datefmt = '%m/%d/%Y %I:%M:%S %p'
    ignore_dirs = ['.git', '.ipynb_checkpoints']

    logging.basicConfig(level=logging.DEBUG, format=log_format,
                        datefmt=log_datefmt)

    if len(sys.argv) > 1:
        start_path = sys.argv[1]
    else:
        start_path = '.'

    if not os.path.exists(start_path):
        logging.error("Directory or file '%s' does not exist.", start_path)
        sys.exit(1)

    if os.path.isfile(start_path):
        run_notebook(start_path)
    else:
        for root, dirs, files in os.walk(start_path):
            dirs.sort()
            for ignore_dir in ignore_dirs:
                if ignore_dir in dirs:
                    dirs.remove(ignore_dir)

            for name in sorted(files):
                if name.endswith('.ipynb'):
                    nbpath = os.path.normpath(os.path.join(root, name))
                    run_notebook(nbpath)


def run_notebook(nbpath):
    logging.info("Reading notebook '%s'", nbpath)
    with open(nbpath) as nbfile:
        notebook = read(nbfile, 'json')

    runner = NotebookRunner(notebook, mpl_inline=True)

    try:
        runner.run_notebook()
    except NotebookError:
        logging.error("An error occurred while executing notebook '%s'. "
                      "Exiting with nonzero exit status", nbpath)
        sys.exit(1)


if __name__ == '__main__':
    main()