daanvanhauwermeiren / nbdime-tutorial

tutorials for usage of nbdime

nbdime-tutorial

tutorial for usage of nbdime

nbdime Tools for diffing and merging of Jupyter notebooks. https://github.com/jupyter/nbdime

dependencies

This tutorial is written and tested on the following versions:

python      3.6.6
notebook    5.7.0
nbdime      1.0.3

This does not work with the following combination:

python      2.7.12
notebook    4.2.3
nbdime      1.0.3

reference

why

Jupyter notebooks are useful, rich media documents stored in a plain text JSON format. This format is relatively easy to parse. However, primitive line-based diff and merge tools do not handle well the logical structure of notebook documents

nbdime, on the other hand, provides “content-aware” diffing and merging of Jupyter notebooks. It understands the structure of notebook documents. Therefore, it can make intelligent decisions when diffing and merging notebooks, such as:

• eliding base64-encoded images for terminal output
• using existing diff tools for inputs and outputs
• rendering image diffs in a web view
• auto-resolving conflicts on generated values such as execution counters

reference

installation

pip install nbdime

Note: when using anaconda as your python installation toolbox, make sure you install it in the desired environment. Because of integration into the jupyter extensions, installation in the same environment as your jupyter notebook installation is strongly advised. If you are unsure which environment this is, it is probably the base environment. If needed, switch to the desired environment by:

source activate ENV_NAME #linux, macos
activate ENV_NAME #windows

reference

console commands

nbdime provides the following CLI commands:

nbshow
nbdiff
nbdiff-web
nbmerge
nbmerge-web
mergetool
config-git

nbshow

nbshow gives you a nice, terminal-optimized summary view of a notebook. You can use it to quickly peek at notebooks without launching the full notebook web application.

available options:

ignorables:
Set which parts of the notebook (not) to show.

-s, --sources, -S, --ignore-sources
    show/ignore sources.

-o, --outputs, -O, --ignore-outputs
    show/ignore outputs.

-a, --attachments, -A, --ignore-attachments
    show/ignore attachments.

-m, --metadata, -M, --ignore-metadata
    show/ignore metadata.

-d, --details, -D, --ignore-details
    show/ignore details not covered by other options.

quickref:

# view code, ignoring output and any metadata:
nbshow -M -O THE_NOTEBOOK.ipynb

# view output, ignoring code and metadata
nbshow -M -S -D THE_NOTEBOOK.ipynb

diffing

nbdime offers two commands for viewing the diff between two notebooks:

• nbdiff for command-line diffing
• nbdiff-web for rich web-based diffing of notebooks

nbdiff

nbdiff does a terminal-optimized rendering of notebook diffs. Pass it the two notebooks you would like to compare, and it returns a nice, readable presentation of the changes in the notebook.

available options: see nbshow

quickref:

# purely compare code, ignoring output and metadata changes
nbdiff -M -O -D THE_NOTEBOOK_1.ipynb THE_NOTEBOOK_2.ipynb

# look for code and output changes, ignoring metadata changes
nbdiff -M -D THE_NOTEBOOK_1.ipynb THE_NOTEBOOK_2.ipynb

# look for output changes, ignoring metadata and code changes
nbdiff -M -S -D THE_NOTEBOOK_1.ipynb THE_NOTEBOOK_2.ipynb

nbdiff-web

Like nbdiff, nbdiff-web compares two notebooks.

Instead of a terminal rendering, nbdiff-web opens a web browser, compares the two notebooks, and displays the rich rendered diff of images and other outputs.

available options: see nbshow

quickref: see nbdiff (replace nbdiff with nbdiff-web)

merging

possibly redundant: check git integration?

reference

notebook extensions

To install and enable the nbdime jupyter extensions, run:

nbdime extensions --enable --sys-prefix

After installing the extensions, one or two buttons should show up in the notebook toolbar.

Clicking the git button will open a new tab showing the diff between the last commit and the currently saved version of the notebook. Note that this button will only be visible if the notebook is currently in a git repository.

Clicking the checkpoint button will similarly show the diff between the checkpointed and currently saved versions of the notebook.

reference

version control integration (GIT)

Git integration of nbdime is supported in two ways:

• through drivers for diff and merge operations, where nbdime takes on the responsibility for performing the diff/merge:

  • Diff driver
  • Merge driver

• through defining nbdime as diff and merge tools, which allow nbdime to display the diff/merge to the user without having to actually depend on git:

Diff web tool Merge web tool

Configure git integration by editing the .gitconfig (or .git/config) and .gitattributes in each git repository or in the home/etc directory for global effect.

To configure all diff/merge drivers and tools, simply call:

# locally in one git repo
nbdime config-git --enable
# global / system configuration
nbdime config-git --enable --global|--system

Once configured, the diff/merge drivers should simply work out of the box. For example, the normal git diff command should give you the standard diff for any non-notebook files, but use nbdime’s command-line diff for all .ipynb files. Nbdime will also be used for all merges on notebook files (no specific commands needed).

For more details, see the reference

reference

configuration

https://nbdime.readthedocs.io/en/latest/config.html

glossary

https://nbdime.readthedocs.io/en/latest/glossary.html