differences show up as if the file was deleted

[parmentelat]

Description

the extension mostly works fine for me, except when it comes to displaying the actual differences;
the extension actually computes the exact set of modified files, that is fine, but when I click the +/- icon to display the actual differences, the 'new file' always comes empty - as if the file had been deleted or completely emptied - like in the following example

where in reality a cell was added to the previous release, as can be seen here:

(base) root@4a9011c1fdff:~/work/notebooks# git diff
diff --git a/notebooks/0-00-intro.md b/notebooks/0-00-intro.md
index 5306863..aa4094a 100644
--- a/notebooks/0-00-intro.md
+++ b/notebooks/0-00-intro.md
@@ -15,3 +15,8 @@ puis le corpus principal:
 * numpy: le tableau homogène , pour le calcul scientifique;
 * pandas: la dataframe (similaire à une table SQL), pour le traitement de données;
 * matplotlib: pour les affichages de données scientifiques.
+
+```python
+import sys
+sys.version_info
+```

we exclusively use jupytext-encoded notebooks, I figured maybe that could be the problem ? here this notebook uses markdown:myst as its underlying format

Reproduce

From a freshly cloned repo, containing a markdown:myst simply add a single cell to one of the notebooks, and display the differences from the git extension

Expected behavior

The differences should be displayed as the addition of that single cell; what I see is as if the file had been deleted

Context

this runs in a docker image built FROM jupyter/scipy-notebook:latest

• Python package version:

$ pip show jupyterlab-git
Version: 0.38.0

• Extension version:

$ jupyter labextension list
JupyterLab v3.4.5
/opt/conda/share/jupyter/labextensions
        jupyterlab_pygments v0.2.2 enabled OK (python, jupyterlab_pygments)
        jupyterlab-jupytext v1.3.8+dev enabled OK (python, jupytext)
        nbdime-jupyterlab v2.1.1 enabled OK
        @jupyter-widgets/jupyterlab-manager v3.1.1 enabled OK (python, jupyterlab_widgets)
        @jupyterlab/git v0.38.0 enabled OK (python, jupyterlab-git)

• Git version:

git --version
git version 2.34.1

• Operating System and its version:

$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.1 LTS"
$ uname -a
Linux 4a9011c1fdff 5.16.12-200.fc35.x86_64 #1 SMP PREEMPT Wed Mar 2 19:06:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

Command Line Output

Paste the output from your command line running `jupyter lab` here, use `--debug` if possible.

relevant section seems to be this:

^@^@!^A^@^@^@^@^@^@3^Y^@^@^@^@^@^@{\254\341\311\324\273\317\205:27.573 NotebookApp] 200 GET /49267/static/components/jquery-ui/themes/smoothness/jquery-ui.\
min.css?v=fb45616eef2c454960f91fcd2a04efeda84cfacccf0c5d741ba2793dc1dbd6d3ab01aaae6485222945774c7d7a9a2e9fb87e0d8ef1ea96893aa6906147a371bb (10.88.0.1) 0.88\
0000ms
^@^@^@^@^@^@^@^@^@^@!^@^@^@^@^@^@^@p>\223^A^@^@^@^@0=\223^A^@^@^@^@ ^@^@^@^@^@^@^@ ^A^@^@^@^@^@^@S!\223^A^@^@^@^@{\254\341\311\324\273\317\205:27.583 Noteb\
ookApp] 200 GET /49267/static/components/jquery-typeahead/dist/jquery.typeahead.min.css?v=5edf53bf6bb9c3b1ddafd8594825a7e2ed621
    Error:
[D 14:32:01.653 NotebookApp] 200 POST /49267/git/status?1660746721231 (10.88.0.1) 165.060000ms
[D 14:32:02.603 NotebookApp.jupyterlab_git] Execute ['git', 'diff', '--numstat', '4b825dc642cb6eb9a060e54bf8d69288fbee4904', 'HEAD', '--', 'notebooks/0-00-\
intro.md'] in /home/jovyan/work/.
[D 14:32:02.607 NotebookApp.jupyterlab_git] Code: 0
    Output: 17  0       notebooks/0-00-intro.md

    Error:
[D 14:32:02.607 NotebookApp.jupyterlab_git] Execute ['git', 'show', 'HEAD:notebooks/0-00-intro.md'] in /home/jovyan/work/.
[I 14:32:02.613 NotebookApp] Refusing to serve hidden file or directory '/home/jovyan/work/./notebooks/0-00-intro.md', via 404 Error
[D 14:32:02.614 NotebookApp] 200 POST /49267/git/content?1660746722337 (10.88.0.1) 2.220000ms
[D 14:32:02.615 NotebookApp.jupyterlab_git] Code: 0
    Output: Licence CC BY-NC-ND, Val\303\251rie Roy & Thierry Parmentelat



    # Python num\303\251rique: numpy, pandas et matplotlib


    Contenu de ce module:

    * un petit test pour \303\251valuer les comp\303\251tences moyennes sur Python de base (c'est-\303\240-dire: hors numpy/pandas/matplotlib)
    * un module optionnel, et tr\303\250s court, qui contient des rappels essentiels sur, justement, Python de base

    puis le corpus principal:

    * numpy: le tableau homog\303\250ne , pour le calcul scientifique;
    * pandas: la dataframe (similaire \303\240 une table SQL), pour l...
    Error:
[D 14:32:02.615 NotebookApp] 200 POST /49267/git/content?1660746722336 (10.88.0.1) 13.700000ms
[D 14:32:03.233 NotebookApp] 204 PUT /49267/lab/api/workspaces/default?1660746722968 (10.88.0.1) 1.830000ms
[D 14:32:04.485 NotebookApp.jupyterlab_git] Execute ['git', 'fetch', '--all', '--prune'] in /home/jovyan/work/.
[D 14:32:04.505 NotebookApp.jupyterlab_git] Code: 0
    Output: Fetching origin

Web Browser Output

Paste the output from your browser web console here.

*nothing seems to be relevant in the browser console*

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[fcollonval]

@parmentelat thanks for reporting. Would you mind running jupyterlab in debug mode (CLI option --debug) and report here the log you get when opening the diff?

Related question, if you open the diff for a commit in the history panel, do you see the same error?

It is probably related to jupytext. But maybe not 😉