Sharing notebooks¶

Objectives

Instructor note

Sharing dynamic notebooks on Binder ¶

Exercise (20 min): Making your notebooks reproducible by anyone via Binder

Create a new GitHub repository.
Commit and push the notebook which we have created earlier to this repository. If you got stuck earlier, you can download this notebook (right-click, “Save as …”). You can also try Binder with a different notebook.
Create a requirements.txt file which contains (adapt this if your notebook has other dependencies):
```
matplotlib==3.4.1
```
Commit and push also this file to your notebook repository.
Visit https://mybinder.org:

Screenshot of Binder web interface.¶
Copy-paste the markdown text for the mybinder badge into a README.md file in your notebook repository.
Check that your notebook repository now has a “launch binder” badge in your README.md file on GitHub.
Try clicking the button and see how your repository is launched on Binder (can take a minute or two). Your notebooks can now be expored and executed in the cloud.
Enjoy being fully reproducible!
Even better would be to get a DOI to your notebook and point Binder to the DOI.

More examples with Binder:

(Optional) Exercise: what happens without requirements.txt?

Start the repository in Binder
fig3/fig3bc.ipynb is a Python notebook, so works in Binder. Most others are in R, which also works in Binder. But how? Try to run the notebook - can you make it work?
Install the missing requirements with pip. Does it work now? Why or why not?
How could this be better?

(Optional) Exercise: share an interactive (ipywidgets) notebook via Binder

Take the solution from the exercise “Widgets for interactive data fitting” in the Examples of Jupyter features episode and paste it into a notebook.
Push the notebook to a GitHub/GitLab repository.
Create a requirements.txt file in your notebook repository, e.g.:
```
ipywidgets==7.4.2
numpy==1.16.4
matplotlib==3.1.0
```
Try to deploy this example via Binder in the same way as the above exercise.

(Optional) Exercise: share R Markdown/R Studio project via Binder

This exercise is for those who use Rmd files instead of Jupyter notebooks.

Put your Rmd file into a GitHub repository.
To this repository add a file runtime.txt which specifies the R version you want to use:
```
r-3.6-2020-10-13
```
To this repository add a file install.R which lists the dependencies, for instance:
```
install.packages(c("readr", "ggplot2"))
```
After you have done that, visit https://mybinder.org/v2/gh/myuser/myrepo/mybranch?urlpath=rstudio (adapt “myuser”, “myrepo”, and “mybranch”).
For more information, see this guide.

You can enter a URL, GitHub repo or username, or GIST ID in nbviewer and view a rendered Jupyter notebook
Read the Docs can render Jupyter Notebooks via the nbsphinx package
Binder creates live notebooks based on a GitHub repository
EGI Notebooks (see also https://egi-notebooks.readthedocs.io)
JupyterLab supports sharing and collaborative editing of notebooks via Google Drive. Recently it also added support for Shared editing with collaborative notebook model.
Notedown, Jupinx and DocOnce can take Markdown or Sphinx files and generate Jupyter Notebooks
Voilà allows you to convert a Jupyter Notebook into an interactive dashboard
The jupyter nbconvert tool can convert a (.ipynb) notebook file to:
- python code (.py file)
- an HTML file
- a LaTeX file
- a PDF file
- a slide-show in the browser

These platforms can be used free of charge but have paid subscriptions for faster access to cloud resources:

CoCalc (formerly SageMathCloud) allows collaborative editing of notebooks in the cloud
Google’s colaboratory lets you work on notebooks in the cloud, and you can read and write to notebook files on Drive
Microsoft Azure Notebooks also offers free notebooks in the cloud
Deepnote allows real-time collaboration

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