adding script to bu used in the workflow

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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