Mastering GitHub Pages (Jekyll and GitHub Pages)

Bayesvl is R package for visually learning the graphical structures of Bayesian networks, and performing Hamiltonian Markov chain Monte Carlo (MCMC) with 'Stan'. ***** For more information, please visit: https://mindsponge.info/posts/14 *****

Quarto makes it very easy to publish a website via GitHub Pages: It is as simple as running quarto publish gh-pages. Here we explore a slightly different method that uses a GitHub Action to publish the website automatically every time it is updated. Classic GitHub Pages The classic way to publish a website via GitHub pages is to maintain a separate branch gh-pages.

Set up ssh keys to make login to the HPC easy!

I saw this Tweet a few days ago from Jeremy Leipzig counting the number of GitHub repositories that sequencing-related companies have on their organization page, but was immediately curious how many of these had an open-source license versus a restrictive or unknown license. I tried to one-shot this with GPT-5 given a screenshot of Jeremy's Tweet and a few instructions. It got me 90% of the way but I had to make a few tweaks here and there.

Donald Hobern drew my attention to nice the way iNaturalist displays taxonomic splits: In this example, observations identified as Rhipidura fuliginosa are being split into Rhipidura fuliginosa and Rhipidura albiscapa . This immediately reminds me of the idea which keeps circulating around, namely using version control tools to manage taxonomic classification.

I'm teaching a class on quantitative methods in linguistics, and after getting tired, over the years, of debugging everyone's computer before we could get to the content of learning R (much less quantitative methods), I decided to seize control. I'm running the course through GitHub Classroom which comes with an educational allowance for using GitHub codespaces.

If you're doing any kind of scientific computing and not using version control, you're doing it wrong. The git version control system and GitHub, a web-based service for hosting and collaborating on git-controlled projects, have both become wildly popular over the last few years.