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| -rw-r--r-- | bin/run_notebooks.py | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/bin/run_notebooks.py b/bin/run_notebooks.py new file mode 100644 index 0000000..ea7e8ee --- /dev/null +++ b/bin/run_notebooks.py @@ -0,0 +1,67 @@ +# ! python +# coding: utf-8 +# From https://gist.github.com/tpogden/ec79f2ebe2baf45655445b575dc7f540 +# with some more context at https://ogden.eu/run-notebooks +# Thanks to @tpogden for his gist + +import os +import sys +import argparse +import glob + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + +# Parse args +parser = argparse.ArgumentParser(description="Runs a set of Jupyter \ + notebooks.") +file_text = """ Notebook file(s) to be run, e.g. '*.ipynb' (default), +'my_nb1.ipynb', 'my_nb1.ipynb my_nb2.ipynb', 'my_dir/*.ipynb' +""" +parser.add_argument('file_list', metavar='F', type=str, nargs='*', + help=file_text) +parser.add_argument('-t', '--timeout', help='Length of time (in secs) a cell \ + can run before raising TimeoutError (default 600).', default=600, + required=False) +parser.add_argument('-p', '--run-path', help='The path the notebook will be \ + run from (default pwd).', default='.', required=False) +args = parser.parse_args() +print('Args:', args) +if not args.file_list: # Default file_list + args.file_list = glob.glob('*.ipynb') + +# Check list of notebooks +notebooks = [] +print('Notebooks to run:') +for f in args.file_list: + # Find notebooks but not notebooks previously output from this script + if f.endswith('.ipynb') and not f.endswith('_out.ipynb'): + print(f[:-6]) + notebooks.append(f[:-6]) # Want the filename without '.ipynb' + +# Execute notebooks and output +num_notebooks = len(notebooks) +print('*****') +for i, n in enumerate(notebooks): + n_out = n + '_out' + with open(n + '.ipynb') as f: + nb = nbformat.read(f, as_version=4) + ep = ExecutePreprocessor(timeout=int(args.timeout), kernel_name='python3') + try: + print('Running', n, ':', i, '/', num_notebooks) + out = ep.preprocess(nb, {'metadata': {'path': args.run_path}}) + except CellExecutionError: + out = None + msg = 'Error executing the notebook "%s".\n' % n + msg += 'See notebook "%s" for the traceback.' % n_out + print(msg) + sys.exit(1) + except TimeoutError: + msg = 'Timeout executing the notebook "%s".\n' % n + print(msg) + sys.exit(110) + finally: + # Write output file + with open(n_out + '.ipynb', mode='wt') as f: + nbformat.write(nb, f)
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