Derive jupytext cm from app cm

[mwouts]

Jupytext's CM is derived directly from the NotebookApp (or ServerApp)'s contents manager.
This should allow Jupytext to be used with Voila - see #270
(@SylvainCorlay, what else do we need to do for this?)

[mwouts]

@153957, @fool65c, when this gets ready I will prepare a release candidate and make sure you can test it, as you reported using a CM derivated from Jupytext's TextFileContentsManager...

[codecov]

Codecov Report

Merging #275 into master will increase coverage by <.01%.
The diff coverage is 98.17%.

@@            Coverage Diff             @@
##           master     #275      +/-   ##
==========================================
+ Coverage   99.19%   99.19%   +<.01%     
==========================================
  Files          68       68              
  Lines        6612     6617       +5     
==========================================
+ Hits         6559     6564       +5     
  Misses         53       53

Impacted Files	Coverage Δ
jupytext/__init__.py	100% <100%> (ø)	⬆️
jupytext/version.py	100% <100%> (ø)	⬆️
jupytext/contentsmanager.py	98.44% <98.14%> (+0.01%)	⬆️

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[lgtm-com]

This pull request introduces 1 alert when merging 04894ff into 872c658 - view on LGTM.com

new alerts:

• 1 for Unused import

[153957]

Thanks for the heads up, I will have a look.

[mwouts]

There is a release candidate for this:

pip install jupytext==1.2.0rc1

@153957, @fool65c, could you please test that this is compatible with your own content manager?

Also, I would be curious to know whether this would work:

from jupytext.contentsmanager import build_jupytext_contents_manager_class
c.NotebookApp.contents_manager_class = build_jupytext_contents_manager_class(base_cm_class)

where base_cm_class if your base cm class (in case you have one that is not based on the Jupytext cm).

[lgtm-com]

This pull request introduces 1 alert when merging 611c7e2 into 12c7dea - view on LGTM.com

new alerts:

• 1 for Unused import

[fool65c]

@mwouts I was able to test and it worked as expected thanks for pushing it through

[153957]

It correctly detects my custom class being a subclass. and seems to work fine.

I also tried

from jupytext.contentsmanager import build_jupytext_contents_manager_class
c.NotebookApp.contents_manager_class = build_jupytext_contents_manager_class(base_cm_class)

And made my base_cm_class a subclass of LargeFileManager, however, I then ran into some issues like Config option 'default_jupytext_formats' not recognized by 'base_cm_class'. It did seem to use my custom class: Deriving a JupytextContentsManager from base_cm_model. So that seems to happen in the wrong order.

[mwouts]

Thanks @fool65c and @153957 , it's great that you could test this. Thank you so much!

however, I then ran into some issues like Config option 'default_jupytext_formats' not recognized by 'base_cm_class'. It did seem to use my custom class: Deriving a JupytextContentsManager from base_cm_model. So that seems to happen in the wrong order.

Interesting. The message Deriving a JupytextContentsManager from base_cm_model is printed by Jupytext's server extension. But this should only occur when the notebook app's contents manager is not already supercharged with Jupytext's one. Maybe I could have been clearer - my question was whether something like the below in your jupyter_notebook_config.py does work (it does locally here):

from jupytext.contentsmanager import build_jupytext_contents_manager_class
from notebook.services.contents.largefilemanager import LargeFileManager


class UserSpecificContentsManagerClass(LargeFileManager):
    """A CM defined by the user"""
    pass


c.NotebookApp.contents_manager_class = build_jupytext_contents_manager_class(UserSpecificContentsManagerClass)
c.ContentsManager.default_jupytext_formats = "ipynb,md"

[lgtm-com]

This pull request introduces 1 alert when merging a89d2b0 into 9bda1f8 - view on LGTM.com

new alerts:

• 1 for Unused import

[mwouts]

With the latest commit I now see the server extension setting Jupytext's contents manager on Jupyter Server:

(python3) C:\Users\Marc\Documents\GitHub\jupytext>jupyter server
[I 21:12:47.182 ServerApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 21:12:47.183 ServerApp] Serving notebooks from local directory: C:\Users\Marc\Documents\GitHub\jupytext
[I 21:12:47.183 ServerApp] The Jupyter Server is running at:
[I 21:12:47.183 ServerApp] http://localhost:8888/?token=...

So I think we're good to go!