git-add and git-diff use different diff tools?

Question

TL;DR I configured a difftool and git-diff gives "intelligent" diffs but git-add creates "stupid" hunks. Why?

I configured the difftool to use nbdime with nbdime config-git --enable --global which I think essentially just adds these lines to my .gitconfig:

[diff "jupyternotebook"]
    command = git-nbdiffdriver diff
[merge "jupyternotebook"]
    driver = git-nbmergedriver merge %O %A %B %L %P
    name = jupyter notebook merge driver
[difftool "nbdime"]
    cmd = git-nbdifftool diff \"$LOCAL\" \"$REMOTE\" \"$BASE\"
[difftool]
    prompt = false
[mergetool "nbdime"]
    cmd = git-nbmergetool merge \"$BASE\" \"$LOCAL\" \"$REMOTE\" \"$MERGED\"
[mergetool]
    prompt = false

Now git diff gives the good output I expect:

nbdiff /var/folders/6b/03yw1pts2nx_q8vftrh6fv140000gp/T//FILE.ipynb FOLDER/FILE.ipynb
--- /var/folders/6b/03yw1pts2nx_q8vftrh6fv140000gp/T//FILE.ipynb  2022-05-17 14:29:39.937318
+++ FOLDER/FILE.ipynb  2022-05-17 14:09:45.222229
## inserted before /cells/0:
+  code cell:
+    source:
+      ...
+  markdown cell:
+    source:
+      ...

## deleted /cells/0:
-  markdown cell:
-    source:
-      ...

## inserted before /cells/2:
+  code cell:
+    source:
+      ...

But if I do git add -e FOLDER/FILE.ipynb, it gives me a "really bad" diff:

diff --git a/FOLDER/FILE.ipynb b/FOLDER/FILE.ipynb
index 3a1540c..17363f8 100644
--- a/FOLDER/FILE.ipynb
+++ b/FOLDER/FILE.ipynb
@@ -1,621 +1,716 @@
 {
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    ...
-   ]
-  },
-  ... almost every line in the file is removed
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "j1qKT6qtAYEj"
+      },
+      "outputs": [],
+      "source": [
+        ...
+      ]
+    },
+    ... almost every line in the file is added back

I may have a fundamental misunderstanding of what git-add does, but why isn't git add using the nbdime diff tool? And is there a way I can add just the changes that I see in git-diff ?

Answer 1

Both git add -e and git add -p need to be able to understand an edited diff. They have a limited amount of comprehension of diffs in general, and require the "dumb" format from plain git diff. The nbdime tools take the original files apart, re-shuffle them into usable text, and diff that usable text,¹ but that's not what's actually in the files, and git add -e needs to work on what's in the files, not some cleaned-up presentation thereof.

---

¹What's in the files is machine-readable JSON. The result of the nbdime tools appears to be yaml. If Git had a native JSON diff engine, git add -p and company would be able to deal with the result, but Git doesn't, so it isn't. If Jupyter-notebooks used yaml, Git's line-oriented tools would be able to deal with them, but Jupyter-notebooks doesn't, so it isn't.