Example of problems with versioning and cell ID in Jupyter notebooks

.gitignore

.ipynb_checkpoints/

README.md

Known Issue

Since creating this Gist I've found out that this is a known issue and being worked on in JupyterLab Issue #9729.

A temporary work around until the next release of JupyterLab would be to downgrade nbformat to v5.0.8 (at the time the last non-yanked release before v5.1.2) which sidesteps the problem by not supporting cell IDs (and removing them from the notebook).

Versioning problem example

With the addition of cell IDs to Jupyter notebooks (c.f. JEP 62) the ability to cleanly version them, even with all output cleaned from them, has become even harder given that subsequent runs of the notebooks change the cell ID and create a non-empty diff.

Note that this only seems to be a problem in JupyterLab. :?

Also reproducible in

Environment setup

$ pyenv virtualenv 3.8.7 example
$ pyenv activate example
(example) $ pip install --upgrade pip setuptools wheel
(example) $ pip install -r requirements.txt
(example) $ jupyter lab

Example of non-issue in Jupyter Notebook

1. Run jupyter notebook
2. Open example.ipynb
3. Kernel -> Restart & Run All
4. Kernel -> Restart & Clear Output
5. Save example.ipynb
6. Shutdown the running instance of Jupyter
7. git diff

Reproduction steps of problem in JupyterLab

This only seems to be a problem in JupyterLab, interestingly enough.

1. Run jupyter lab
2. Open example.ipynb
3. Kernel -> Restart Kernel and Run All Cells
4. Kernel -> Restart Kernel and Clear All Outputs
5. Save example.ipynb
6. Shutdown the running instance of Jupyter
7. git diff

An example diff is included in clean_run.diff.

clean_run.diff

diff --git a/example.ipynb b/example.ipynb
index 66713cf..89cc325 100644
--- a/example.ipynb
+++ b/example.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "expanded-samoa",
+   "id": "satisfied-forth",
    "metadata": {},
    "source": [
     "# Example of problems with cell names and version control"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "powerful-reverse",
+   "id": "royal-lottery",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "tropical-woman",
+   "id": "naked-quarter",
    "metadata": {},
    "outputs": [],
    "source": [

example.ipynb

requirements.txt

numpy
jupyter
jupyterlab==3.0.12