---
title: Cleaning Jupyter Notebook Cell Output for Git Repos
permalink: /futureproof/cleaning-noteboook-cell-output-git/
description: Switching between my Mac and NixOS setups constantly challenges my workflow, but I strive to make my environments portable. While tools like Nix and Vim help bridge the gap, I hit a snag with Jupyter Notebooks polluting my Git history differently on each OS. I discovered my usual tool, `nbstripout`, was breaking because it stored absolute paths in the local `.git/config`. The real fix, making it truly 'set-it-and-forget-it' across machines, is using `nbstripout --install --attributes` to leverage the portable `.gitattributes` file, ensuring clean notebook commits no matter where I'm working.
meta_description: Ensure clean, portable Git commits for Jupyter Notebooks by using nbstripout with .gitattributes to eliminate absolute paths across OSs.
meta_keywords: nbstripout, Jupyter Notebook cleaning, Git clean commits, portable gitattributes, absolute path removal, cross-platform Git, Mac, NixOS, notebook output stripping, version-controlled attributes
layout: post
sort_order: 1
---

{% raw %}


Okay, I am in the office. I am on the Mac. All that muscle memory stuff comes
into effect. I have to do the real-time remapping sufficient so that flow state
can still be achieved. Switching hardware, especially between different desktop
OSes is very disruptive. But being able to do so is one of the most fundamental
skills to future-proofing. They are trying to tie you to their particular
hardware and OS, making switching hard.

It's interesting that my first steps are now intuitively opening the terminal,
going to a repo, doing git pull and then `nix develop` to ensure my `nvim`
environment is the same. This is a powerful technique to make muscle memory
portable. But it can't do much about the host OS or the kooky key-swapping the
Mac does. Vim is an interoperable haven. 

Okay, now focus on Notebook. I need to grab a code example from a notebook to
complete this, and I'm going to be doing a lot more Notebook work directly in
the Pipulate repo now in general. And I might be doing it from the Mac or my
NixOS machine at home. And I don't want to pollute the Pipulate repo with
`.ipynb` meta garbage, so it's time to make sure nbstripout is working. I just
made a change to a notebook and did a `git diff` and saw all the ugly cell
output! That's a surprise because I thought I already had my favorite notebook
meta information scrubbing tool, `nbstripout` turned on in the repo...

But it was using absolute paths, and switching between Linux and Mac made it
break, because my `/home/user/` folder is different! On Mac it's `/Users/user/`
And `nbstripout` uses absolute paths in the repo's `.git/config` file.

Okay, if you're here for the tool in the first place, this one is different from
the others because it's (supposed to be) set-it and forget-it. Once you `pip
install nbstripout` to get it on your machine, then you just `cd` into your repo
and:

```bash
nbstripout --install --attributes .gitattributes
```
This ensures that `nbstripout` works across different machines **without absolute paths** by using `.gitattributes` instead of `.git/config`.

Now, every time a Jupyter Notebook (`.ipynb`) is committed, its output cells will be stripped automatically, keeping your repo clean across Mac, Linux, or any other environment you sync with.

Want to double-check if it's working? Run:
```bash
git check-attr filter -- *.ipynb
```
It should return:
```
*.ipynb: filter: nbstripout
```

Then do another `git diff` after modifying a notebook—you should no longer see output metadata polluting the diff.

This is **the** way to make `nbstripout` truly cross-platform and set-it-and-forget-it. 🚀

Now just in case you happen to pull a repo that already has absolute paths in
its `.git/config` like I just did, you can make sure your own global
configuration is clean and fix the repo by doing the following:

### **Step 1: Remove Absolute Paths from `.git/config`**
If `nbstripout` was previously installed with absolute paths, clean them out with:
```bash
git config --unset filter.nbstripout.clean
git config --unset filter.nbstripout.smudge
git config --unset filter.nbstripout.required
```
This ensures that the repo no longer has a broken absolute path reference.

### **Step 2: Enable Global `nbstripout` (Optional)**
If you want `nbstripout` to work **across all repos on your machine**, install it globally:
```bash
nbstripout --install --global
```
This avoids repo-specific configuration issues.

### **Step 3: Ensure Portable `.gitattributes` Usage**
For maximum portability, ensure `nbstripout` is applied using `.gitattributes` instead:
```bash
nbstripout --install --attributes
```
This will create a `.gitattributes` file containing:
```
*.ipynb filter=nbstripout
```
which is **version-controlled** and travels with the repo.

### **Step 4: Verify It's Working**
Test if `nbstripout` is correctly applied:
```bash
git check-attr filter -- *.ipynb
```
It should return:
```
*.ipynb: filter: nbstripout
```
Then modify a notebook and run:
```bash
git diff
```
You should **no longer see** unwanted cell output in the diff.

Now, you're fully future-proofed across Mac, NixOS, or any other machine you pull this repo on. 🚀

---

## Double Checking WHY This Works

> I confirmed that this works with a git diff, but I'm clarifying for myself
> double-checking with Gemini 2.5 exactly why this works.

Okay, let's break down how the method described in the article avoids using absolute paths for `nbstripout`:

1.  **The Problem with the Old Method:**
    * The author initially had `nbstripout` configured directly within the repository's local Git configuration file (`.git/config`).
    * This configuration likely involved specifying the *exact path* to the `nbstripout` executable or related scripts.
    * These paths are *absolute*, meaning they start from the root directory of the filesystem (e.g., `/Users/user/...` on Mac or `/home/user/...` on Linux).
    * Because these paths are different on different operating systems (Mac vs. Linux), the configuration stored in `.git/config` would work on one machine but be broken on the other. The `.git/config` file is specific to that local clone of the repository and isn't typically shared or version-controlled.

2.  **The Solution Using `.gitattributes`:**
    * The command `nbstripout --install --attributes` changes *how* Git is told to use `nbstripout`.
    * Instead of putting absolute paths into the local `.git/config`, it modifies (or creates) a file named `.gitattributes` directly within the repository.
    * Inside `.gitattributes`, it adds a line like: `*.ipynb filter=nbstripout`
    * **Crucially, this line does *not* contain an absolute path.** It simply tells Git: "For any file ending in `.ipynb`, apply a filter named `nbstripout`."

3.  **How Git Finds `nbstripout`:**
    * The `.gitattributes` file tells Git *which* filter to use (by name: "nbstripout"), but not *where* that filter command is located.
    * Git finds the *actual command* for the "nbstripout" filter by looking in its configuration (often set up globally or locally by running `nbstripout --install` or `nbstripout --install --global` previously).
    * This setup relies on the `nbstripout` command being available in the system's `PATH` on *whatever machine you are currently using*.
    * When you run a Git command (like `git commit` or `git diff`), Git sees the instruction in `.gitattributes`, looks up the "nbstripout" filter definition, finds the `nbstripout` command in the current system's `PATH`, and executes it.

4.  **Why This is Portable:**
    * The `.gitattributes` file is part of the repository and is version-controlled, so it's identical on every machine (Mac, Linux, etc.) that clones the repo.
    * It contains only the *name* of the filter, not a system-specific path.
    * The responsibility of *finding* the `nbstripout` executable is shifted to the Git installation on the *local machine*, which uses the local system's `PATH`.
    * As long as `nbstripout` is installed and accessible on each machine you work on, Git can find and run it correctly using the portable instructions from `.gitattributes`.

In essence, the `.gitattributes` file provides a portable, repository-level instruction ("use the nbstripout filter"), while the actual execution relies on the `nbstripout` tool being correctly installed and findable on the specific machine where the Git commands are being run, thus avoiding hardcoded, OS-dependent absolute paths within the shared repository configuration.

## An AI's Summary

Here's the summary from the author's perspective:

[Moved to top]

---

**Title/Headline Ideas:**

* Make `nbstripout` Truly Cross-Platform with `.gitattributes`
* Solving `nbstripout` Absolute Path Issues Between Mac and Linux
* Set-and-Forget Jupyter Notebook Cleaning in Git Across Any OS
* Portable `nbstripout`: Stop Committing Notebook Output Metadata
* Fixing Broken `nbstripout` Configs for Multi-OS Development
* Keep Your Jupyter Notebook Diffs Clean Everywhere with `nbstripout` and `.gitattributes`
* The Right Way to Install `nbstripout` for Cross-Platform Repos

---

**AI Opinion:**

This article provides a practical and valuable solution to a common frustration
for developers working with Jupyter Notebooks in Git repositories across
different operating systems (like macOS and Linux). The author effectively uses
a personal narrative about switching machines to frame the technical problem –
`nbstripout` failing due to absolute path configurations in `.git/config`. The
explanation of *why* this happens and the clear, step-by-step instructions on
using `.gitattributes` for a portable, repository-level solution are excellent.
Including commands for verification and troubleshooting existing configurations
adds significant utility. It's a well-focused piece that directly addresses a
specific technical pain point with an actionable fix.

{% endraw %}