A tool to run a Jupyter Notebook from a (partial) Github repository.
This description can be found on GitHub here
GitMiller is a tool for running Jupyter Notebooks from a (partial) Github repository. It downloads the repository in your temp folder, runs a designated notebook within it, and removes all downloaded files afterwards.
$ pip install gitmiller
After installation you can use the
gitmiller command-line tool to run your github notebooks.
The command-line interface takes the following input parameters:
|-u, --username||Username to gain access to GitHub repository|
|-p, --password||Password Github repository|
|-t, --token||Or use a Github token|
|-r, --repository||URL of GitHub repository (can be a subfolder)|
|-n, --notebook||filename of notebook you wish to execute, this file must exist in the root folder of the (partially) downloaded folder structure.|
|-o, --output||local path where GitMiller will put the executed version of your notebook|
|-c, --config||local path of YAML file in which you can add all mentioned paramaters|
GitMiller uses Papermill to run your remote notebook. Besides executing, Papermill also enables you to parameterize notebooks. If you would like to override certain variables in your notebook, add the variables and values in the config YAML file under the
papermill key. See example below.
This repository contains a folder
example in which a notebook
test.ipynb exists. If you would like to run this notebook with GitMiller, use either:
$ gitmiller -u <GITHUB USERNAME> -p <GITHUB PASSWORD>, -r https://github.com/UtrechtUniversity/GitMiller/tree/master/example, -n test.ipynb, -o <LOCAL OUTPUT-PATH>
or create the following YAML file:
repository: https://github.com/UtrechtUniversity/GitMiller/tree/master/example username: <GITHUB USERNAME> password: <GITHUB PASSWORD> notebook: test.ipynb output: <LOCAL OUTPUT-PATH> papermill: a: 10 b: 60
and run with:
$ gitmiller -c <PATH TO YAML-FILE>
Note for Windows users
The script isn't able to remove the temp-folder after the Notebook has been processed on Windows machines. I have tried a lot of things, but couldn't find a solution. Manually removing also turned out to be impossible when using a terminal. I give up. At the end a message is printed in which the path of the folder is mentioned so you can remove it yourself.
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