So I committed to something I've been meaning to explore for a while: Jupyter + JupyterBook. If you aren't familiar, Jupyter is a "notebook" system where you write narrative and executable code in one document. Think Rmarkdown/Quarto but more what-you-see-is-what-you-get, and results get embedded. - ThreadSky

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pvdimens.bsky.social • 93 days ago

So I committed to something I've been meaning to explore for a while: Jupyter + JupyterBook. If you aren't familiar, Jupyter is a "notebook" system where you write narrative and executable code in one document. Think Rmarkdown/Quarto but more what-you-see-is-what-you-get, and results get embedded.

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pvdimens.bsky.social•93 days ago

Embedded is great b/c it saves output in the doc (text, plots, etc). Jupyter = JUlia PYThon R, the languages it was initially conceived for. It also works with bash, which rocks. So you write a narrative, with notes, and code that gets executed, with results that get embedded. Awesome.

pvdimens.bsky.social•93 days ago

But here's where it gets awesomer. You can set up a GH repo to automatically build your notebooks into a *nice* website (via JupyterBook). Your repository, your work, code, results, and narrative *as a website*. Automatically. Automagically. The sims project? https://pdimens.github.io/haplotagging_simulations/

pvdimens.bsky.social•93 days ago

And that was automatically built from https://github.com/pdimens/haplotagging_simulations whenever I make a push. The *totality* of this project is that repo/site. And it'll be in that state when I go on to publish it. You won't have to rummage around the repo if you don't want to-- the site is the public-face of that work.

pvdimens.bsky.social•93 days ago

And, you can use Jupyter from VScode (like I do, see screenshot) if you don't want to bother with the native browser-based UIs. It's amazing. My mental overhead is so much less for organization. It looks NICE. It's TRANSPARENT. It's REPRODUCIBLE.

pvdimens.bsky.social•93 days ago

I don't hoard knowledge. Here's a template repo I made to quickly set this up for yourself for any project:
https://github.com/therkildsen-lab/jupyter-workflow

Here's a guide I wrote to do it:
https://therkildsen-lab.github.io/user-guide/docs/programming/jupyter/

We can take steps towards being sincere when we write "all code available at xxx" 🤓

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