Programmatically run nbstripout and output new file.

[stanleyng8]

I am trying to run nbstripout programmatically within a Python script and create a new file from the input file (and not in-place). The documentation doesn't have this use case covered. Is there a way I can do it?

[kynan]

There is a (as you rightly point out undocumented) way of doing it programmatically - do what is done in main(). Something like this (untested):

import io
from nbstripout import strip_output, read, write, NO_CONVERT

if __name__ == '__main__':
    filename = ...
    outfile = ...
    with io.open(filename, 'r', encoding='utf8') as f:
        nb = read(f, as_version=NO_CONVERT)
    nb = strip_output(nb)
    with io.open(outfile, 'w', encoding='utf8') as f:
        write(nb, f)

[stanleyng8]

I tried the above in Python3.6 with Anaconda on Mac OsX and with just the import statement, I am getting the following error.

File "/Users/stanley/anaconda3/envs/py36/lib/python3.6/site-packages/nbstripout.py", line 96, in <module>
  output_stream = io.TextIOWrapper(sys.stdout.buffer, encoding='utf-8')

AttributeError: 'OutStream' object has no attribute 'buffer'

I looked at the nbstripout.py code and the code is specifically for Python3 yet this is where the error is coming from. Any ideas for a fix?

[kynan]

Are you trying the import from within a notebook? This will not work because sys.stdout is a ipykernel.iostream.OutStream in that case.

[psthomas]

I was trying to do something similar and might have a solution. If you want to do this from within a notebook, it's possible to run nbstripout as a part a bash command in a cell:

# Both original and the cleaned example are in the current working directory
notebook_path = './notebook.ipynb'
cleaned_path = './notebook_clean.ipynb'

# Bash commands within notebooks are preceeded by "!"
!cat {notebook_path} | nbstripout > {cleaned_path}

I've been running a command like this in a cell to make it more versatile and provide some feedback:

import os
from datetime import datetime

notebook_path = os.path.join(os.getcwd(),'notebook.ipynb')
cleaned_path = os.path.join(os.getcwd(),'notebook_clean.ipynb')

!cat {notebook_path} | nbstripout > {cleaned_path}

date_str = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
print('{0} Cleaned file created at: {1}'.format(date_str, cleaned_path))

2017-06-23 12:57:40 Cleaned file created at: <current directory>/notebook_clean.ipynb

Note: I think there might be an error in readme.rst because the shell pipeline example doesn't use cat while the docstring in nbstripout.py does. I can open a separate issue if needed.

[stanleyng8]

Thanks for the comments. I was running nbstripout with Python 3.6 as a script and not a notebook.

[kynan]

@stanleyng8 I can not reproduce this issue: have tried with Python 3.6 from anaconda. Which nbstripout version are you using?

[stanleyng8]

Thanks Florian but I have decided not to pursue this avenue any further.