C. Titus Brown comments

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                                            C. Titus Brown

consider how to support more flexible `Collection` in `RevIndex` for external storage

File types that can be loaded as a single collection, per https://github.com/sourmash-bio/sourmash_plugin_branchwater/blob/fa7ab221baa9a8437353f2e894892fbd7545a479/src/utils.rs#L660 (which, yes, is potentially not inclusive of everything sourmash can actually do, but seems like a good starting...

EXP: debug multisigfile loading

@luizirber @bluegenes thoughts welcome!

EXP: debug multisigfile loading

@luizirber bump!

EXP: debug multisigfile loading

🙏

containment search tutorial: searching for genomes in metagenomes

This tutorial needs to be fixed to use `manysearch`.

explore extending branchwater plugin to load zip files for prefetch and gather, entirely on rust side?

I think an additional/different reason to implement something like this is we could also easily support the RocksDB index here as well.

explore extending branchwater plugin to load zip files for prefetch and gather, entirely on rust side?

I looked into this a bunch, and it is essentially impossible (or at least complicated, and very ill advised) to share objects between pyo3 and FFI. So we would not...

explore extending branchwater plugin to load zip files for prefetch and gather, entirely on rust side?

ref https://github.com/sourmash-bio/sourmash/issues/3595 as a better idea for zip.

WIP: adjust warnings around tax abund and provide v5 upgrades to `tax metagenome`

See new validation workflow here: https://github.com/sourmash-bio/2025-validate-sourmash-tax-formats.

WIP: adjust warnings around tax abund and provide v5 upgrades to `tax metagenome`

Ready for review @bluegenes! This got really complicated from a code and testing perspective. My suggestion for detailed review efforts are to confirm that the various `test_metagenome_abund_reporting_*` tests match the...