episode about sharing notebooks

Author: bast

content/index.md

@@ -66,7 +66,7 @@ them to own projects**.
 - 12:45-13:30 - Working with Notebooks
   - Notebooks and version control
   - Other tooling
-  - Sharing notebooks
+  - {doc}`notebooks/sharing`
 
 - 13:30-14:15 - Other useful tools for Python development
   - {doc}`good-practices`
@@ -128,6 +128,7 @@ documentation
 collaboration
 dependencies
 testing
+notebooks/sharing
 refactoring-concepts
 good-practices
 profiling

content/notebooks/binder.jpg

@@ -0,0 +1,83 @@
+# Sharing notebooks
+
+:::{objectives}
+- Know about good practices for notebooks to make them reusable
+- Have a recipe to share a dynamic and reproducible visualization pipeline
+:::
+
+[this lesson is adapted after <https://coderefinery.github.io/jupyter/sharing/>]
+
+
+## Document dependencies
+
+- If you import libraries into your notebook, note down their versions.
+  Document the dependencies as discussed in section {doc}`../dependencies`.
+
+- Place either `environment.yml` or `requirements.txt` in the same folder as
+  the notebook(s).
+
+- If you publish the notebook as part of a publication, it is probably a good
+  idea to **pin the versions** of the libraries you use.
+
+- This is not only useful for people who will try to rerun this in future, it
+  is also understood by some tools (e.g. [Binder](https://mybinder.org/)) which we
+   will see later.
+
+
+## Different ways to share a notebook
+
+We need to learn how to share notebooks. At the minimum we need
+to share them with our future selves (backup and reproducibility).
+
+- You can enter a URL, GitHub repo or username, or GIST ID in [nbviewer](https://nbviewer.jupyter.org/) and view a rendered Jupyter notebook
+- Read the Docs can render Jupyter Notebooks via the [nbsphinx package](https://nbsphinx.readthedocs.io/)
+- [Binder](https://mybinder.org/) creates live notebooks based on a GitHub repository
+- [EGI Notebooks](https://notebooks.egi.eu) (see also <https://egi-notebooks.readthedocs.io>)
+- [JupyterLab](https://github.com/jupyterlab/jupyterlab) supports sharing and collaborative editing of notebooks via Google Drive. Recently
+  it also added support for [Shared editing with collaborative notebook model](https://github.com/jupyterlab/jupyterlab/pull/10118).
+- [JupyterLite](https://jupyterlite.readthedocs.io/en/latest/) creates a Jupyterlab environment in the browser and can be hosted as a GitHub page.
+- [Notedown](https://github.com/aaren/notedown), [Jupinx](https://github.com/QuantEcon/sphinxcontrib-jupyter) and [DocOnce](https://github.com/hplgit/doconce) can take Markdown or Sphinx files and generate Jupyter Notebooks
+- [Voilà](https://voila.readthedocs.io/en/stable/) 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
+
+
+The following platforms can be used free of charge but have **paid subscriptions** for
+faster access to cloud resources:
+- [CoCalc](https://cocalc.com/) (formerly SageMathCloud) allows collaborative editing of notebooks in the cloud
+- [Google Colab](https://colab.research.google.com/) lets you work on notebooks in the cloud, and you can [read and write to notebook files on Drive](https://colab.research.google.com/notebooks/io.ipynb)
+- [Microsoft Azure Notebooks](https://notebooks.azure.com/) also offers free notebooks in the cloud
+- [Deepnote](https://deepnote.com/) allows real-time collaboration
+
+
+## Sharing dynamic notebooks using [Binder](https://mybinder.org/)
+
+::::{challenge} Exercise/demo: Making your notebooks reproducible by anyone (15 min)
+Instructor demonstrates this:
+- First we look at the statically rendered version of the [example
+  notebook](https://github.com/workshop-material/classification-task/blob/main/example.ipynb)
+  on GitHub and also [nbviewer](https://nbviewer.jupyter.org/).
+- Visit [https://mybinder.org](https://mybinder.org):
+  :::{figure} binder.jpg
+  :alt: Screenshot from mybinder.org user interface
+  :::
+- 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
+  explored and executed in the cloud.
+- Enjoy being fully reproducible!
+::::
+
+
+## How to get a digital object identifier (DOI)
+
+- [Zenodo](https://zenodo.org/) is a great service to get a
+  [DOI](https://en.wikipedia.org/wiki/Digital_object_identifier) for a notebook
+  (but **first practice** with the [Zenodo sandbox](https://sandbox.zenodo.org/)).
+- [Binder](https://mybinder.org/) can also run notebooks from Zenodo.
+- In the supporting information of your paper you can refer to its DOI.