sourmash

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https://github.com/sourmash-bio/pyo3_branchwater some benchmarks: https://github.com/sourmash-bio/pyo3_branchwater/issues/10

ctb

add tests for argparse features (e.g. `--help`)

1

#3031 is embarrasing, and we should add tests that avoid it. This could be made into a repeatable quest for new contributors.

ctb

it's incredibly fragile... ...and others think so too ;) https://hynek.me/articles/ditch-codecov-python/

ctb

sketch names in GTDB database use NCBI taxonomy

20

I am working on this pangenome database idea at https://github.com/ctb/2022-database-covers/. I may have found an error in the taxonomic classification while trying to figure some stuff out with the scripts....

ccbaumler

https://github.com/powturbo/TurboPFor-Integer-Compression highlighted in Tinted De Bruijn graphs tweet thread, https://twitter.com/BQPMalfoy/status/1760326415784747271?t=kqI2Ys_QXpvCTKDmGRUOOg ref https://github.com/spacegraphcats/spacegraphcats/issues/516

ctb

add docs about what the taxonomy input file format is

3

right now it's not really specified anywhere 😆 ``` ident,superkingdom,phylum,class,order,family,genus,species GCF_014075335.1,d__Bacteria,p__Proteobacteria,c__Gammaproteobacteria,o__Enterobacterales,f__Enterobacteriaceae,g__Escherichia,s__Escherichia flexneri GCF_000578955.1,d__Bacteria,p__Firmicutes,c__Bacilli,o__Staphylococcales,f__Staphylococcaceae,g__Staphylococcus,s__Staphylococcus aureus ```

ctb

support outputting manifests or manifest-like files as direct `-o` output.

2

In #1493, we added `sourmash_args.SaveSignaturesToLocation(...)` to support a wide variety of output formats. In #1891, we are adding the ability to read manifest files, as output by `sourmash sig manifest`....

ctb

Right now it's just @luizirber but maybe @bluegenes should be on there now?

ctb

add documentation for releasing new rust core

7

what I did for [r0.12.1](https://github.com/sourmash-bio/sourmash/releases/tag/r0.12.1), based on [r0.12.0](https://github.com/sourmash-bio/sourmash/releases/tag/r0.12.0) ``` # generate log of PRs git log --oneline r0.12.0..latest src/core | cut -d\ -f2- > /tmp/out.txt #edited src/core/CHANGELOG.md appropriately # tagged,...

ctb

move `signature::select` downsampling to `minhash()` or `get_sketch()`?

1

At the moment, we use `signature::select` to downsample minhashes if needed. However, this means we load the minhash during the `select`, which may happen during `sig_for_dataset`, for example, and then...

bluegenes