C. Titus Brown
C. Titus Brown
in favor of `ingest`, which causes fewer Python issues 😅 - see code in `cli/__init__.py`. Or, just remove the functionality altogether - see https://github.com/sourmash-bio/sourmash/issues/2786
PR https://github.com/sourmash-bio/sourmash/pull/3072 is a proposed step along the road to support a sourmash v5 release :tada:. PR https://github.com/sourmash-bio/sourmash/pull/3074 tries the same test infrastructure out on a second fix. Specifically, #3072...
This PR adds `--v5` functionality to `sig collect` and `sig check`, switching the default behavior (when `--v5` is specified) over to the new `--relpath` functionality per https://github.com/sourmash-bio/sourmash/issues/3071. This PR is...
NOTE: PR into https://github.com/sourmash-bio/sourmash/pull/3072 This PR changes the default behavior of `sig manifest` for sourmash v5 to, by default, _not_ rebuild the manifest for collections. This is also further exploration...
the code cov estimates on https://github.com/sourmash-bio/sourmash/pull/3072 are clearly wrong, and this popped up elsewhere too - https://github.com/sourmash-bio/sourmash/pull/3066#issuecomment-1986880433 maybe we need to pay attention to https://github.com/sourmash-bio/sourmash/pull/2980?
per https://github.com/sourmash-bio/sourmash/pull/3054 and https://github.com/sourmash-bio/sourmash/issues/3008#issuecomment-1975174211, we'd like relative paths to be the default manifest output behavior in sourmash v5.
per conversation here: https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/163 and also we should recommend `fastmultigather` as [here](https://github.com/sourmash-bio/sourmash/issues/1614#issuecomment-1971378076) and deprecate `multigather` ;)
over in In https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/213, I tried to describe standalone manifests and their benefits for lazy loading. I wrote: > > There are various places where we recommend using manifests instead...
The discussion around lazy loading, manifests, and so on is converging, for me, on recommending .zip files and standalone manifests as being the Right Set of Output Files for lazy...
over in https://github.com/ctb/2024-calc-full-gather/ I have implemented a simple script that takes fastgather output (from https://github.com/sourmash-bio/sourmash_plugin_branchwater/) and turns it into full gather output without redoing the searches - it literally just...