C. Titus Brown

icon indicating a website link http://ivory.idyll.org/blog/ icon indicating an email [email protected]

icon company University of California, Davis icon location Davis, CA icon location Prof at UC Davis. Blogs at http://ivory.idyll.org/blog/ and uses bluesky under ctitusbrown.

Results 1175 comments of C. Titus Brown

update docs with pretty pictures from `betterplot` plugin

also wondering if maybe we want to split the sourmash docs from the sourmash code repository (I thought we had an issue about this somewhere, but can't find it). disadvantages:...

Solver improvements: meta issue

See also: https://github.com/bioconda/bioconda-recipes/issues/13774.

How to replicate sourmash hash function

hi @Adamtaranto, great question! The script you found is exactly the code we use internally (just, you know, faster). I would definitely apply "trust-but-verify" to my statement, but we put...

How to replicate sourmash hash function

ref https://github.com/sourmash-bio/sourmash/issues/3339

replace piz with rc-zip

(asking here, because it's relevant to some memory questions) - how are we feeling about Rust 1.74 these days?

proper compilation of `lib_lowlevel` is confusing

I've worked past this enough in the last few months that I'm not too worried about it any more. I think the major problem was that cbindgen outputs a lot...

Bump codecov/codecov-action from 3 to 4

@dependabot rebase

`samtools_mpileup_wc` rule fails for unclear reasons

`rm outputs.paper/genomes/.genomes.*` should be a way of resetting this.

why does `sig cat` use so much memory?

Looking into a few things - * `save_load.SaveSignatures_ZipFile`, which is used to save to a zip file, should not keep signatures in memory; * `sourmash_args.load_many_signatures` uses iterators/generators, should not keep...

why does `sig cat` use so much memory?

Main remaining thought is that we do keep zip files in memory in a weird way, see https://github.com/sourmash-bio/sourmash/issues/2340. Perhaps we need to close zip files when done.