Seth Stadick
@ducktapeprogrammer.bsky.social
760 followers 390 following 190 posts
Bioinformatics. Rust. Mojo.
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ducktapeprogrammer.bsky.social
Have you started in on trying out openzl on an bfx formats? It looks very promising!
Reposted by Seth Stadick
curiouscoding.nl
Any recommendations for a github CI plugin for performance monitoring?

Thinking of using github-actions-bench [0] which makes decent plots, in combination with maybe iai [1] for measuring CPU cycles (wall-time is too flaky in GH actions).

0: github.com/benchmark-ac...
1: github.com/bheisler/iai
GitHub - benchmark-action/github-action-benchmark: GitHub Action for continuous benchmarking to keep performance
GitHub Action for continuous benchmarking to keep performance - benchmark-action/github-action-benchmark
github.com
Reposted by Seth Stadick
yminsky.bsky.social
Excited to say that we're looking to hire someone to focus on OxCaml education! We're doing enough to change the language that we have a pretty big internal education task ahead of us, and we want to hire someone to focus on it!

Please share this with others!

www.janestreet.com/join-jane-st...
OxCaml Educator :: Jane Street
Jane Street is a quantitative trading firm and liquidity provider with a unique focus on technology and collaborative problem solving.
www.janestreet.com
Reposted by Seth Stadick
bedec.bsky.social
Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...
ducktapeprogrammer.bsky.social
Perl 👀 x.com/jxmnop/statu...

To be fair, Perl was the OG write only vibe coding language.
Reposted by Seth Stadick
prefix.dev
Another deep dive in the technology behind Conda package managers: file linking! Did you know that there are symlinks, hardlinks and reflinks? Reflinks are the best – copy on write is space efficient and isolates the cache.

Learn more: prefix.dev/blog/what-l...
What linking means when installing a Conda package
Package managers face a fundamental challenge: how to efficiently place files from a package cache into multiple environments without excessive disk usage or compromising isolation.
prefix.dev
Reposted by Seth Stadick
curiouscoding.nl
Sassy is out now!

Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!

Available now wherever you get your code

With @rickbitloo.bsky.social

curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Sassy solves approximate string matching: finding all matches of a pattern in a text.
ducktapeprogrammer.bsky.social
It’s come up for me! As a link specifically.
ducktapeprogrammer.bsky.social
I’ve been wondering how Perl would fair with an llm. It manages to pack so much context into so few characters, it kind of seems like it should be great for llms?

I have no idea how to go about proving it is “good” or “bad” for an LLM though.
ducktapeprogrammer.bsky.social
That’s fair! And I don’t have any better solutions.

Based on the linked AVX2 feature share in my other reply, hopefully we can widen the “generic” simd support in compilers here at some point
ducktapeprogrammer.bsky.social
They support/ run CI for the large Hw groups like Linux-64, linux-aarch, osx-64, etc.

Some good HW stats: firefoxgraphics.github.io/telemetry/#v...

Sites here: linebender.org/blog/a-plan-...

If v3 is around 75% in consumer PC, it’s got to be 90%+ for the HW for BFX
Graphics Survey
firefoxgraphics.github.io
ducktapeprogrammer.bsky.social
That compiles it on the CI machine I believe, so you can’t target the end user CPU features :(

You kind of can with conda features, but it’s a big pain and not standard that I can tell.

It causes me great pain that all these tools we install with conda are basically stuck with sse only
ducktapeprogrammer.bsky.social
I was trying to be gracious by calling them "user thoughts". reddit's gonna reddit
ducktapeprogrammer.bsky.social
It might have been about array/range and their relationship with Iterator/IntoIterator
ducktapeprogrammer.bsky.social
Thanks for the reply! I'll keep digging.
ducktapeprogrammer.bsky.social
@steveklabnik.com Did you write an article about ways you wish Rust Iterators had evolved differently? Or remember who wrote that?

Mojo is about to start in on its iterator abstraction and I was looking for lessons learned from Rust, but can't find that article.

I might be imagining this it 😬
Reposted by Seth Stadick
curiouscoding.nl
Looking for papers to cite for tight definitions of global alignment, semi-global alignment, and mapping...

I would probably be the person to ask, yet here we are.