Conversion of a simple .ipynb to py then back to ipynb gives "KeyError: 'env'"

[liar666]

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "a=5\n",
    "print('hello',a)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "argv": [
    "python",
    "-m",
    "ipykernel_launcher",
    "-f",
    "{connection_file}"
   ],
   "display_name": "Python 3",
   "env": null,
   "interrupt_mode": "signal",
   "language": "python",
   "metadata": null,
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.4"
  },
  "name": "utils1.ipynb"
 },
 "nbformat": 4,
 "nbformat_minor": 2
}

First convertsion work:

$ jupytext --to py:percent --from ipynb utils1.ipynb
[jupytext] Reading utils1.ipynb in format ipynb
[jupytext] Updating the timestamp of utils1.py

Conversion back to original does not

$ jupytext --from py:percent --to ipynb utils1.py
[jupytext] Reading utils1.py in format py:percent
Traceback (most recent call last):
  File "/home/gmuller/Python/DataScience/bin/jupytext", line 8, in <module>
    sys.exit(jupytext())
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/cli.py", line 427, in jupytext
    exit_code += jupytext_single_file(nb_file, args, log)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/cli.py", line 494, in jupytext_single_file
    notebook = read(nb_file, fmt=fmt, config=config)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/jupytext.py", line 435, in read
    return read(stream, as_version=as_version, fmt=fmt, config=config, **kwargs)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/jupytext.py", line 444, in read
    return reads(fp.read(), fmt, config=config, **kwargs)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/jupytext.py", line 384, in reads
    format_name = read_format_from_metadata(text, ext) or fmt.get("format_name")
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/formats.py", line 280, in read_format_from_metadata
    metadata = read_metadata(text, ext)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/formats.py", line 259, in read_metadata
    metadata, _, _, _ = header_to_metadata_and_cell(lines, comment, ext)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/header.py", line 228, in header_to_metadata_and_cell
    recursive_update(metadata, yaml.safe_load("\n".join(jupyter))["jupyter"])
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/header.py", line 148, in recursive_update
    target[key] = recursive_update(target.get(key, {}), value)
  File "/home/gmuller/Python/DataScience/lib/python3.8/site-packages/jupytext/header.py", line 146, in recursive_update
    del target[key]
KeyError: 'env'

[mwouts]

Thanks @liar666 for reporting this.

Do you have any idea where this "env": null and "metadata": null in your kernelspec come from?

Anyway I agree they should not make Jupytext fail, I'll fix that part.

[mwouts]

Hi @liar666 , this should be fixed in the dev version. See https://jupytext.readthedocs.io/en/latest/developing.html for how to install it locally. Thanks for reporting this!

[liar666]

Do you have any idea where this "env": null and "metadata": null in your kernelspec come from?

I've tried to use EIN (Emacs Ipython Notebook package) on this source file, that might be the source of this problem :{
https://github.com/millejoh/emacs-ipython-notebook

Thanks for quick response and the patch I'll try it ASAP!!!
EDIT: Works perfectly on my notebooks! Thanks again !!!