Sharing your Jupyter notebook#
One neat way of sharing your research workflow - whether that is your data cleaning process, the statistical modelling that you have applied to your data set, or how you have visualised your results - is through Jupyter notebooks.
Working with sensitive data may, however, create barriers to sharing your Jupyter notebook: you do not want to commit a Jupyter notebook containing sensitive data to GitHub.
You can get around this hurdle by manually clearing your notebookâs output before each Git commit you do.
This process is, however, time-consuming, cumbersome and - most importantly - extremely error-prone.
You only need to forget to clear the output once to inadvertently expose your data.
Another, much more efficient (and failsafe!) way of doing this is by using nbstripout.
nbstripout#
nbstripoutis a utility that - when used as a git filter or pre-commit hook - automatically strips the Jupyter (or IPython/Zeppelin) notebook output before Git even gets the chance to see it.
In other words, it simulates the Clear All Output procedure in the Jupyter notebook user interface.
Installing nbstripout#
The latest version of nbstripout can be installed from PyPI (The Python Package Index) using the command pip install --upgrade nbstripout.
If you are using Anaconda, you can install nbstripout via the conda package manager: conda install -c conda-forge nbstripout.
Setting up the git filter and attributes#
Once nbstripout is installed, you need to add it to your local Git repository.
Start by creating a new repository or navigating to one that you are already using. Once there, add nbstripout using the command nbstripout --install.
You can check that nbstripout has successfully been applied as a filter by running the command cat .git/config, or checking git attributes by running the commandcat .git/info/attributes.
Removing the git filter and attributes#
If you decide that you would like to remove nbstripout, simply run nbstripout --uninstall whilst in the repository.
Installing nbstripout globally#
nbstripout is generally installed in one local Git repository at a time, so that you can control when it is applied as a filter.
However, if all of your notebooks deal with sensitive data, it might be a good idea to install nbstripout globally across all of your Git repositories.
This way, no notebooks risk slipping under the radar.
To install nbstripout globally, run the command: nbstripout --install --global