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April 9, 2022 16:51
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run and validate a notebook
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#!/usr/bin/env python | |
""" | |
simple example script for running notebooks and reporting exceptions. | |
Usage: `checkipnb.py foo.ipynb [bar.ipynb [...]]` | |
Each cell is submitted to the kernel, and checked for errors. | |
""" | |
import os,sys,time | |
from Queue import Empty | |
try: | |
from IPython.kernel import KernelManager | |
except ImportError: | |
from IPython.zmq.blockingkernelmanager import BlockingKernelManager as KernelManager | |
from IPython.nbformat.current import reads, NotebookNode | |
def run_notebook(nb): | |
km = KernelManager() | |
km.start_kernel(stderr=open(os.devnull, 'w')) | |
try: | |
kc = km.client() | |
except AttributeError: | |
# 0.13 | |
kc = km | |
kc.start_channels() | |
shell = kc.shell_channel | |
# simple ping: | |
shell.execute("pass") | |
shell.get_msg() | |
cells = 0 | |
failures = 0 | |
for ws in nb.worksheets: | |
for cell in ws.cells: | |
if cell.cell_type != 'code': | |
continue | |
shell.execute(cell.input) | |
# wait for finish, maximum 20s | |
reply = shell.get_msg(timeout=20)['content'] | |
if reply['status'] == 'error': | |
failures += 1 | |
print "\nFAILURE:" | |
print cell.input | |
print '-----' | |
print "raised:" | |
print '\n'.join(reply['traceback']) | |
cells += 1 | |
sys.stdout.write('.') | |
print "ran notebook %s" % nb.metadata.name | |
print " ran %3i cells" % cells | |
if failures: | |
print " %3i cells raised exceptions" % failures | |
kc.stop_channels() | |
km.shutdown_kernel() | |
del km | |
if __name__ == '__main__': | |
for ipynb in sys.argv[1:]: | |
print "running %s" % ipynb | |
with open(ipynb) as f: | |
nb = reads(f.read(), 'json') | |
run_notebook(nb) |
@twiecki @kayhan-batmanghelich did you fix the issue?
Our solution
import os
import glob
import time
import sys
import traceback
import nbconvert
import nbformat
ep = nbconvert.preprocessors.ExecutePreprocessor(
extra_arguments=["--log-level=40"],
timeout=300,
)
def run_notebook(path):
path = os.path.abspath(path)
assert path.endswith('.ipynb')
nb = nbformat.read(path, as_version=4)
try:
ep.preprocess(nb, {'metadata': {'path': os.path.dirname(path)}})
except Exception as e:
print("\nException raised while running '{}'\n".format(path))
traceback.print_exc(file=sys.stdout)
sys.exit(1)
if __name__ == '__main__':
print('Running notebooks might take a long time...')
print('===========================================\n')
for path in glob.iglob('notebooks/**/*.ipynb', recursive=True):
root, ext = os.path.splitext(os.path.basename(path))
if root.endswith('_'):
continue
s = time.time()
sys.stdout.write('Now running ' + path)
sys.stdout.flush()
run_notebook(path)
sys.stdout.write(' -- Finish in {}s\n'.format(int(time.time()-s)))
print('\n\033[92m'
'==========================='
' Notebook testing done '
'==========================='
'\033[0m')
Just incase someone runs into the same issue as me:
> reply = shell.get_msg(timeout=20)['content']
E TypeError: 'coroutine' object is not subscriptable
This was solved for me by replacing shell.get_msg
with kc.get_shell_msg
as mentioned in a note on the 6->7 migration guide.
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@minrk Second that request. Tried to run but got a: