Jupyter Notebooks with Git

Problems with version control of Jupyter Notebooks

There are several issues to manage Jupyter Notebooks with Git:

  • Jupyter Notebooks cell metadata changes even when no content changes have been made to the cells. This makes Git diffs unnecessarily complicated.

  • The lines that Git writes to the *.ipynb files in case of merge conflicts cause the notebooks to no longer be valid JSON and therefore cannot be opened by Jupyter: you will then get the Error loading notebook message when opening them.

    Conflicts are especially common in notebooks because Jupyter changes the following each time a notebook is run:

    • Each cell contains a number that indicates the order in which it was executed. If team members execute the cells in different order, every single cell has a conflict! To fix this manually would take a very long time.

    • For each image, such as a plot, Jupyter records not only the image itself in the notebook, but also a simple text description containing the ID of the object, for example <matplotlib.axes._subplots.AxesSubplot at 0x7fbc113dbe90>. This will change every time you run a notebook, and therefore will conflict every time two people run that cell.

    • Some output can be non-deterministic, such as a notebook that uses random numbers or interacts with a service that provides different output over time.

    • Jupyter adds metadata to the notebook that describes the environment in which it was last run, such as the name of the kernel. This often varies between different installations, and so two people saving a notebook (even without other changes) will often have a conflict in the metadata.

nbdev2

nbdev2 has a set of git hooks that provide clean git diffs that automatically resolve most git conflicts and ensure that any remaining conflicts can be fully resolved within the standard Jupyter notebook environment:

  • A new git merge driver provides notebook-native conflict markers that result in notebooks opening directly in Jupyter, even if there are Git conflicts. Local and remote changes are each shown as separate cells in the notebook, so you can simply delete the version you don’t want to keep or combine the two cells as needed.

    See also

    nbdev.merge docs

  • Resolving git merges locally is extremely helpful, but we also need to resolve them remotely. For example, if a merge request is submitted and then someone else submits the same notebook before the merge request is merged, it could cause a conflict:

       "outputs": [
        {
    <<<<<< HEAD
         "execution_count": 8,
    ======
         "execution_count": 5,
    >>>>>> 83e94d58314ea43ccd136e6d53b8989ccf9aab1b
         "metadata": {},
    

    The save hook of nbdev2 automatically removes all unnecessary metadata (including execution_count) and non-deterministic cell output; this means that there are no pointless conflicts like the one above, since this information is not stored in the commits in the first place.

To get started, follow the instructions in Git-Friendly Jupyter.

jq

The results of the calculations can also be saved in the notebook file format nbformat. These can also be Base-64-coded blobs for images and other binary data that should not normally be included in a version management. These can be removed manually with Cell ‣ All Output ‣ Clear, but you have to carry out these steps before every git add, and it also does not solve a second cause of the noise in git diff, namely some in the metadata.

In order to get systematically comparable versions of notebooks in the version management, we can use jq, a lightweight JSON processor. It takes some time to set up jq because it has its own query/filter language, but the default settings are usually well chosen.

Installation

jq can be installed with:

$ sudo apt install jq
$ brew install jq

Example

A typical call is:

jq --indent 1  \
  '(.cells [] | select (has ("output")) | .outputs) = []
  | (.cells [] | select (has ("execution_count")) | .execution_count) = null
  | .metadata = {"language_info": {"name": "python", "pygments_lexer": "ipython3"}}
  | .Cells []. metadata = {}
  '  example.ipynb

Each line within the single quotation marks defines a filter – the first selects all entries from the cells list and deletes the output. The next entry resets all outputs. The third step deletes the notebook’s metadata and replaces it with a minimum of necessary information so that the notebook can still be run without complaints. The fourth filter line .cells []. metadata = {}, deletes all meta information. If you want to keep certain meta information, you can indicate this here.

Set up

  1. To make your work easier, you can create an alias in the ~/.bashrc file:

    alias nbstrip_jq="jq --indent 1 \
        '(.cells[] | select(has(\"outputs\")) | .outputs) = []  \
        | (.cells[] | select(has(\"execution_count\")) | .execution_count) = null  \
        | .metadata = {\"language_info\": {\"name\": \"python\", \"pygments_lexer\": \"ipython3\"}} \
        | .cells[].metadata = {} \
        '"
    
  2. Then you can conveniently enter the following in the terminal:

    $ nbstrip_jq example.ipynb > stripped.ipynb
    
  3. If you start with an existing notebook, you should first add a filter commit by simply reading in the newly filtered version of your notebook without the unwanted metadata. After you have added the notebook with git add, you can see whether the filter has really worked with git diff --cached before you do git commit -m 'filter'.

  4. If you want to use this filter for all Git repositories, you can also configure your Git globally:

    1. First you add the following to your ~/.gitconfig file:

      [core]
      attributesfile = ~/.gitattributes
      
      [filter "nbstrip_jq"]
      clean = "jq --indent 1 \
              '(.cells[] | select(has(\"outputs\")) | .outputs) = []  \
              | (.cells[] | select(has(\"execution_count\")) | .execution_count) = null  \
              | .metadata = {\"language_info\": {\"name\": \"python\", \"pygments_lexer\": \"ipython3\"}} \
              | .cells[].metadata = {} \
              '"
      smudge = cat
      required = true
      
      clean

      is applied when adding changes to the stage area.

      smudge

      is used when resetting the workspace by changes from the stage area.

    2. Then you have to specify the following in the ~/.gitattributes file:

      *.ipynb filter=nbstrip_jq
      
  5. If you then use git add to add your notebok to the stage area, the nbstrip_jq filter will be applied.

    Note

    However, git diff will not show you any changes between the working and stage areas. Only with git diff --staged you can see that only the filtered changes have been applied.

    Warning

    clean and smudge filters often do not play well with git rebase across such filtered commits. Then you should disable these filters before rebasing.

  6. And there is another problem: If such a notebook is run again, git diff will not show any changes, but git status will. Therefore, the following should be entered in the ~/.bashrc file to be able to quickly clean the respective working directory:

    function nbstrip_all_cwd {
        for nbfile in *.ipynb; do
            echo "$( nbstrip_jq $nbfile )" > $nbfile
        done
        unset nbfile
    }
    

ReviewNB

ReviewNB solves the problem of doing Merge requests with notebooks. GitLab’s code review GUI only works with line-based file formats, such as Python scripts. Most of the time, however, I prefer to check the source code notebooks because:

  • I want to check the documentation and the tests, not just the implementation

  • I want to see the changes to the cell output, like charts and tables, not just the code.

For this purpose ReviewNB is perfect.

nbdime

nbdime is a GUI for nbformat diffs and replaces nbdiff. It attempts content-aware diffing locally as well as merging notebooks, is not limited to displaying diffs, but also prevents unnecessary changes from being checked in. However, it is not compatible with nbdev2.

nbstripout

nbstripout automates Clear all outputs. It uses nbformat and a few auto magic to set up .git config. In my opinion, however, it has two drawbacks:

  • it is limited to the problematic metadata section

  • it is slow.