# Jupyter notebook continuous integration with github actions

**URL:** <https://discourse.julialang.org/t/jupyter-notebook-continuous-integration-with-github-actions/118479>\
**Category:** Jupyter-Notebook\
**Created:** [August 22, 2024, 11:19am UTC](https://discourse.julialang.org/t/jupyter-notebook-continuous-integration-with-github-actions/118479 "2024-08-22T11:19:53Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [August 22, 2024, 11:19am UTC](https://discourse.julialang.org/t/jupyter-notebook-continuous-integration-with-github-actions/118479/1 "2024-08-22T11:19:53Z")

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What’s the current best way of setting up CI with github actions for Jupyter notebooks containing Julia code?

I’ve found some blog posts, github actions and similar, proposing some solutions, e.g. [(1)](https://github.com/marketplace/actions/run-notebook), [(2)](https://forem.julialang.org/sosiristseng/publishing-julia-notebooks-with-docker-and-github-actions-ii-github-actions-3ajm), [(3)](https://github.com/sosiristseng/template-juliabook-matrix), [(4)](https://medium.com/@liljess981/automating-my-jupyter-notebook-with-github-actions-40336139e86b), [(5)](https://discourse.julialang.org/t/testing-jupyter-notebooks-ci/28599), [(6)](https://github.com/JuliaInterop/NBInclude.jl), etc…

I’m just having trouble figuring out which one of these I should be using. Some of these discussions or codes are years old, so I don’t know if they’re still maintained. A lot of these discussions are mostly snippets of github actions various people have put together for this, but I’m not sure if these are robust.

The end goal would be to set up a [Binder](https://mybinder.org/) repo with a bunch of examples on how to use [my library](https://github.com/sloisel/MultiGridBarrier.jl). I would ideally like to do a bit of CI by having github actions run all my notebooks and make sure they don’t error out.

Thanks,

S

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**Author:** ![Wen-Wei\_Tseng](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/wen-wei_tseng/32/28839_2.png) [@Wen-Wei\_Tseng](https://discourse.julialang.org/u/Wen-Wei_Tseng)\
**Post date:** [August 22, 2024, 12:01pm UTC](https://discourse.julialang.org/t/jupyter-notebook-continuous-integration-with-github-actions/118479/2 "2024-08-22T12:01:17Z")

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Hello Sébastien,

I’m the author of (2), but I haven’t updated the forem post for a while. You can checkout [my current template repository](https://github.com/sosiristseng/template-juliabook), grab a copy, and try it out.  
The workflow currently:

- executes both Literate.jl (`.jl` ) and Jupyter (`.ipynb`) notebooks in parallel (since GitHub action runners have 4 CPU cores),
- caches executed notebooks to save execution time
- publishing a [jupyterbook](https://jupyterbook.org/) website with Binder support
- automatic updates GitHub actions (via dependabot) and Julia dependencies (needs a PAT)

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**Author:** ![loisel](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/loisel/32/50626_2.png) [@loisel](https://discourse.julialang.org/u/loisel)\
**Post date:** [August 22, 2024, 12:30pm UTC](https://discourse.julialang.org/t/jupyter-notebook-continuous-integration-with-github-actions/118479/3 "2024-08-22T12:30:37Z")

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Hello Wen-Wei Tseng (apologies, I’m not sure which part is your first name!)

Thanks for your insightful reply, I am reading all this carefully.

It seems like your solution does a tremendous amount of stuff, far beyond what I am asking, so I’m trying to understand some bits.

1. You say your thing produces a `jupyterbook` with Binder support. I clicked around on your github link, and found [this](https://sosiristseng.github.io/template-juliabook/). I must admit I’ve never used Binder but my intention was to have a jupyterlab session with my notebooks opened so that people can play around with it. Is this not what Binder does? Can I do that from your `jupyterbook`?
2. I took a brief look at `jupyterbook` and `Literate.jl`, both look slightly tangential to what I’m trying to achieve. Do I have to use those?
3. Your solution also uses `Kodiak`, `linkcheck.yml`, `update-manifest.yml`. Now I must admit I’m a bit of a beginner with Github Actions, and I’ve previously failed twice to set up Github Branch Protection, which the Kodiak web site says is a requirement. I’ve also previously failed to setup `update-manifest.yml`. Are these all requirements?

Thanks again for your help,

S

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**Author:** ![Wen-Wei\_Tseng](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/wen-wei_tseng/32/28839_2.png) [@Wen-Wei\_Tseng](https://discourse.julialang.org/u/Wen-Wei_Tseng)\
**Post date:** [August 22, 2024, 1:42pm UTC](https://discourse.julialang.org/t/jupyter-notebook-continuous-integration-with-github-actions/118479/4 "2024-08-22T13:42:06Z")

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Hello Sébastien,

Binder support is disable by default, you can activate it by editing `docs/_config.yml`

```yaml
launch_buttons:
   binderhub_url: "https://mybinder.org" # The URL of the BinderHub (e.g., https://mybinder.org)

```

You don’t have to use Literate notebooks (just putting Jupyter notebooks is OK). The Literate notebooks option is just an additional format the workflow supports. The workflow will try to find and execute `jl` and `ipynb` files in the `docs` folder. (You can see the code in [run.jl](https://github.com/sosiristseng/template-juliabook/blob/main/run.jl))

Kodiak (`.kodiak.toml`), `linkcheck.yml`, and `update-manifest.yml` are optional. You can delete them if you don’t need them. Kodiak bot is for automerging updates. `linkcheck.yml` is for checking http links in notebooks.  
`update-manifest.yml` is for automatically updating Julia dependencies every week.

Hope the information helps.