sourmash

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refactor duplicate code in test_sourmash.py

2

per [@LilyAnderssonLee review](https://github.com/pyOpenSci/software-submission/issues/129#issuecomment-1838233643) >Refactoring duplicate code into helper functions to avoid redundancy and improve maintainability.

ctb

address pyopensci review comments for sourmash v4

2

our reviews are in over at https://github.com/pyOpenSci/software-submission/issues/129!!! this is a placeholder that will (eventually) contain a checklist for addressing all of the reviewer comments.

ctb

release checklist for sourmash v4.8.6

1

Release candidate testing: - [x] Command line tests pass for a release candidate - [x] All eight release candidate wheels are built Releasing to PyPI: - [x] RC tag(s)s deleted...

ctb

notes on developer installation, as of aug 2023

9

per https://sourmash.readthedocs.io/en/latest/developer.html, * it's not clear that the "general instructions" come after/are an ALTERNATIVE to the mamba install stuff * the mamba install stuff doesn't actually install tox, although tox-conda...

ctb

Add k-mer positions while sketching

3

I have a suggestion that may be considered for a future version of sourmash. The current Minhash includes `hashes` and `abundances`. I propose adding an optional array called `positions`, which...

mr-eyes

What about using different hash functions (reversible, rolling, etc.) with sourmash?

7

I have a simple/naive thought re reverse-hashing the kmers. We can provide an option to Minhash `reversible = True` to use a reversible hashing function like the Integer Hashing to...

mr-eyes

should sourmash gather insist on uniform scaling?

2

thinking through some of the gather issues revealed/discussed in https://github.com/sourmash-bio/sourmash/issues/2950, and also the bug in https://github.com/sourmash-bio/sourmash/issues/2825, and also worrying that branchwater fastgather/fastmultigather don't handle adaptive downsampling properly, I'm wondering if...

ctb

Now that we have `Select` implemented, deprecate and remove usage of rust `sig.select_sketch`, per https://github.com/sourmash-bio/sourmash/issues/1292

bluegenes

EXP: try out some new manifest methods

1

Note: PR into https://github.com/sourmash-bio/sourmash/pull/2598.

ctb

per @luizirber (paraphrased) -- we should find a replacement for `.sketches` as it clones all sketch data https://github.com/sourmash-bio/sourmash/blob/latest/src/core/src/signature.rs#L480-L482 ``` pub fn sketches(&self) -> Vec { self.signatures.clone() } ``` Note: `sig.iter()`...

bluegenes