Run And Save A Ipynb File From The Command Line. This Script Is ...

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damianavila/ipynb_run_save.py Created March 20, 2013 20:49 Show Gist options

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Learn more about clone URLs Clone this repository at <script src="https://gist.github.com/damianavila/5208296.js"></script> Save damianavila/5208296 to your computer and use it in GitHub Desktop. Download ZIP Run and save a ipynb file from the command line. This script is working in dev version (1.0) of IPython (for previous version you have to tweak it). It will generate a new "run & saved" notebook. Raw ipynb_run_save.py This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters Show hidden characters

#!/usr/bin/env python

"""

Script for running and save notebooks from command line.

How to use: `ipynb_run_save.py foo.ipynb

Some tweaks over ipydoctest.py from minrk

by @damianavila

"""

import io

import os

import sys

from Queue import Empty

from IPython.kernel.blockingkernelmanager import BlockingKernelManager

from IPython.nbformat.current import read, write, NotebookNode

def run_cell(km, cell):

shell = km.shell_channel

iopub = km.iopub_channel

# print "\n\ntesting:"

# print cell.input

shell.execute(cell.input)

# wait for finish, maximum 20s

shell.get_msg(timeout=20)

outs = []

while True:

try:

msg = iopub.get_msg(timeout=0.2)

except Empty:

break

msg_type = msg['msg_type']

if msg_type in ('status', 'pyin'):

continue

elif msg_type == 'clear_output':

outs = []

continue

content = msg['content']

# print msg_type, content

out = NotebookNode(output_type=msg_type)

if msg_type == 'stream':

out.stream = content['name']

out.text = content['data']

elif msg_type in ('display_data', 'pyout'):

for mime, data in content['data'].iteritems():

attr = mime.split('/')[-1].lower()

# this gets most right, but fix svg+html, plain

attr = attr.replace('+xml', '').replace('plain', 'text')

setattr(out, attr, data)

if msg_type == 'pyout':

out.prompt_number = content['execution_count']

elif msg_type == 'pyerr':

out.ename = content['ename']

out.evalue = content['evalue']

out.traceback = content['traceback']

else:

print "unhandled iopub msg:", msg_type

outs.append(out)

return outs

def test_notebook(nb):

km = BlockingKernelManager()

km.start_kernel(extra_arguments=['--pylab=inline'], stderr=open(os.devnull, 'w'))

km.start_channels()

# run %pylab inline, because some notebooks assume this

# even though they shouldn't

km.shell_channel.execute("pass")

km.shell_channel.get_msg()

while True:

try:

km.iopub_channel.get_msg(timeout=1)

except Empty:

break

errors = 0

cells = 0

for ws in nb.worksheets:

for cell in ws.cells:

if cell.cell_type != 'code':

continue

cells += 1

try:

outs = run_cell(km, cell)

except Exception as e:

print "failed to run cell:", repr(e)

print cell.input

errors += 1

continue

cell.outputs = outs

if errors:

print " %3i cells failed to complete" % errors

if cells:

print "%i code cells from notebook %s" % (cells, nb.metadata.name)

km.shutdown_kernel()

del km

if __name__ == '__main__':

for ipynb in sys.argv[1:]:

print "running %s" % ipynb

with io.open(ipynb, encoding='utf8') as f:

nb = read(f, 'json')

test_notebook(nb)

base, ext = os.path.splitext(ipynb)

new_ipynb = "%s_run_saved%s" % (base, ext)

with io.open(new_ipynb, 'w', encoding='utf8') as f:

write(nb, f, 'json')

print "wrote %s" % new_ipynb

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