C. Titus Brown

hackmd: [link](https://hackmd.io/EoYofvlFQ0SPF3wANO2w7Q?both) # gather benchmarking - sourmash v4.8.10 / branchwater plugin v0.9.5 Source repo: [sourmash-bio/2024-benchmark-gather](https://github.com/sourmash-bio/2024-benchmark-gather) ## sample SRR1976948 This sample contains 177 genomes. Benchmarking results with 64 threads (note pygather...

https://github.com/lskatz/dists2trees - make sure we are friendly with it

`pytest` is hanging at end of (successful) run on farm

2

when run as part of [the release procedure](https://sourmash.readthedocs.io/en/latest/release.html)

add some rust developer docs!

10

how to run the tests right: https://github.com/sourmash-bio/sourmash/pull/3138#issuecomment-2104746508

adjust default thresholding for prefetch and gather?

11

based on some of the results for the new long-read benchmarking paper Portik et al. ([link](https://www.biorxiv.org/content/10.1101/2022.01.31.478527v1) - not yet updated), @bluegenes and I were discussing ways to decrease the false...

https://github.com/sourmash-bio/sourmash/issues/3191 was partly caused by my failure to properly use the context manager for saving signatures. A patch fix and test were added in https://github.com/sourmash-bio/sourmash/pull/3214, but this should really be...

improve sourmash-rs core error reporting for bad/empty zip files

1

Extracting from issues reported in https://github.com/sourmash-bio/sourmash/issues/3191 and https://github.com/sourmash-bio/sourmash/issues/3190 - we get this error on empty zip files: ``` sourmash.exceptions.Panic: sourmash panicked: thread 'unnamed' panicked with 'called `Result::unwrap()` on an `Err`...

update docs with pretty pictures from `betterplot` plugin

2

the betterplot plugin (#3178 and https://github.com/sourmash-bio/sourmash_plugin_betterplot/) provides some nice additional visualization capabilities to sourmash. We should advertise those on the main sourmash docs, I think.

"upset" visualizations of intersections between genomes

4

this might be of use to people looking to grok genome overlaps etc. [notebook permalink](https://github.com/dib-lab/genome-grist/blob/051a96210958afcf7f1d61ce11537796339dc64e/hash-upsetr-example.ipynb) [notebook latest, but link may break ;)](https://github.com/dib-lab/genome-grist/blob/latest/hash-upsetr-example.ipynb)

Punted from https://github.com/sourmash-bio/sourmash/pull/3193 - > Right now we are calculating the intersection twice, once in `disk_revindex.rs` and once in `calculate_gather_stats` in `revindex/mod.rs`. This is unnecessary, of course. But the function...