Leading comments for interpreter and encoding in scripts are not preserved

[matteoipri]

Hi,
I have a repository with Python scripts that I want to run as notebooks in JupyterLab.

My workflow with jupytext is the following:

1. pull the changes from the repository;
2. right-click on a script in the file browser and select "Open with Notebook";
3. run and edit the notebook/script and save;
4. commit the changed script in py:light format to the repository.

All my scripts begin with the following two lines:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

The Notebooks are opened exactly as I want them by jupytext, i.e. the cells are split at the points I want and those two lines are not present in the notebook.
Anyway, when I save my changes in the notebook those two lines are deleted from the python script, while I would like to still have them in the scripts.

Why are those two lines not preserved?
Is there a way to have them preserved?

Thanks

PS: this extension is awesome!

[mwouts]

Hello @matteoipri , thanks for reporting this.

I would have expected the two lines to be preserved by Jupytext, cf. this test.

Also, if I open in jupyter notebook a script test.py with the following content

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
a + 1

then I get a notebook with the following "jupytext" metadata (Edit / Edit notebook metadata):

"jupytext": {
    "executable": "/usr/bin/env python3",
    "encoding": "# -*- coding: utf-8 -*-",
    "notebook_metadata_filter": "-all",
    "cell_metadata_filter": "-all",
    "main_language": "python",
    "text_representation": {
      "extension": ".py",
      "format_name": "light"
    }
  },

Can you compare to what you get? Do you have any custom configuration option set on Jupytext?

[matteoipri]

Hi @mwouts, thanks for your reply. It triggered some more tests on my side.

I confirm that the test you suggest works as expected. The error is that I did not disclose my full test script. In order to avoid the pop-up asking for which kernel to use with the notebook, I add the YAML header to my scripts, like in the following:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# ---
# jupyter:
#   jupytext:
#     text_representation:
#       extension: .py
#       format_name: light
#       format_version: '1.4'
#       jupytext_version: 1.1.2
#   kernelspec:
#     display_name: Python 3
#     language: python
#     name: python3
# ---

a = 2

a + 1

This script, once opened as notebook and saved again looks like this:

# ---
# jupyter:
#   jupytext:
#     text_representation:
#       extension: .py
#       format_name: light
#       format_version: '1.4'
#       jupytext_version: 1.1.2
#   kernelspec:
#     display_name: Python 3
#     language: python
#     name: python3
# ---

a = 2

a + 1

I also just noticed that I am running two outdated versions: JupyterLab 0.35.5 (instead of 0.35.6) and jupytext 1.1.2 (instead of 1.1.3).
Can this be the root cause? I will upgrade as soon as possible and test again.

Thanks

[mwouts]

I see! Thanks for the additional details - I'll add one more test to be sure this gets fixed.
No need to upgrade now, you can wait for 1.1.4 instead!

[matteoipri]

Great, thanks!