Why I Moved My git Repos to Codeberg (and Left Github)

TLDR - I moved most of my github presence to codeberg. Including this page, my personal/professional website: https://groverj3.codeberg.page.

This is mostly just going to be a ramble. But probably not a very long one.

When I was in graduate school, pushing code to Github was a highly practical development solution for an asipring bioinformatician like myself. Not only did I get version control of the scripts and workflows I created for my doctoral work, but I also was showcasing that work by default. This also had the byproduct of learning git, and version control systems are a critical piece of technology which underpin all software development.

Github was acquired by Microsoft in 2018, and there was plenty of concern at the time. A platform known for hosting open-source projects being acquired by a company which, at least historically, has been hostile toward open source immediately raises questions about degrading the experience for open-source and academic users. However, I had been happily using it since, without any real issues.

When I was first looking for a job during grad school my github acted as a sort of portfolio. I will openly admit that nothing on it was all that impressive, but it still showed that I could learn basic software engineering and bioinformatics practices. I wasn't building huge software, but I was able to showcase a Snakemake workflow for processing small RNA sequencing, another for whole-genome bisulfite sequencing, and all my various small python scripts for working with NGS data. I have no doubt that this portfolio helped me get my first job at Seven Bridges.

Since then, I've changed jobs and thankfully been able to stay gainfully employed through subsequent volatile years in biotech. However, being employed in the private sector for quite some time means that the code I write and analyses I perform are property of my employer. I can no longer showcase my best work on an open platform. Therefore, my Github hasn't been a showcase for my best work since graduate school.

Over the past few years "AI" use in software development, and bioinformatics, has exploded. Of course the LLMs that power the plethora of chatbots, agentic coding systems, and simpler intelligent autocomplete system are trained on public code and all the text on the internet. Microsoft, owners of Github, have a large stake in OpenAI and also try to integrate their Copilot AI tools into seemingly every corner of every product they make. Naturally, this has meant AI tools for Github and available through VSCode. I'm not opposed to using these at all, if they can make me a better developer and automate away repetitive tasks. However, I still believe that I am ultimately responsible for the results I generate and code I write.

To satisfy the insatiable apetite for text (code or otherwise) that the companies training AI models have, everything on the internet is seemingly fair game. Including writing in your own voice. This creates a bit of a conflict for me about my modest presence of Github. Keep it there, and know that Github's mission has changed from facilitating open source software development, to feeding us more AI tools and text on which to train more AI models. Or, move things elsewhere and know that they may not be quite as discoverable, with a smaller community. I chose the latter, outside of some code I kept where it is due to being linked to publications from my grad school days.

I settled on Codeberg as a good location to put my personal projects and this website. It's a nonprofit rather than a big tech company, and works like a charm with the git command line utility. The platform is built around Forgejo which is also developed on the platform. Sure, it may not have all the bells and whistles of Github or GitLab, but I do find it to have all the features I need, which are few.

I'm not so naiive as to think that a big tech company isn't just going to scrape all of my public code off of here anyway. However, I get to feel all warm and fuzzy about supporting an open-source, non-profit, platform dedicated to hosting open-source projects themselves.

Now, I just need to update this static site more frequently and do some more personal projects again.