C. Titus Brown

consider adding dendrogram clustering/cut code into sourmash

3

the dendrogram annotation, display, and cut code [here](https://github.com/ctb/2017-sourmash-cluster/blob/master/species-clustering.ipynb) is proving to be both robust and useful; should probably just add it in to base sourmash.

separate out load_signatures code to distinguish loading-from-file and parsing-from-string

3

per https://github.com/dib-lab/sourmash/issues/875#issuecomment-583783495 this would be an API change to a frequently used function, so gotta be careful and do this for a major version change.

work in progress ;) Related issues: * https://github.com/sourmash-bio/sourmash/issues/2717 quickstart/tutorial: https://hackmd.io/mtWXjcWdRb-860RkeTevXQ?view repo: https://github.com/ctb/2024-human-contam

Fixes https://github.com/simonw/datasette/issues/1459 Adds support for `--open --get /path` to be used in combination. If `--open` is provided alone, datasette will open a web page to a default URL. If `--get...

khmer is unmaintained. what now?

4

ref discussion in: https://github.com/dib-lab/khmer/issues/1927 hi folks, I'm afraid we aren't able to maintain khmer at all moving forward - it's basically been in unmaintained mode since 2018 at the latest....

tackling https://github.com/dib-lab/genome-grist/issues/312 current status: `make` works :)

- [ ] switch to pyproject.toml

is it possible to do binderhub-style RStudioWeb reverse proxying?

17

e.g. support RStudio inside of this JupyterHub a la https://github.com/binder-examples/r inquiring minds would like to know ;) ## Status update 1 (added by CH) Currently it is not possible to...

EXP: debug multisigfile loading

1

code to support https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/445

per comment on #3342, https://github.com/sourmash-bio/sourmash/pull/3342#discussion_r1801549808 @luizirber speaketh: >I wonder if we can do (in a future PR, not this one) a new `.downsampled_iter(scaled)` for operations like `count_common`, and avoid the...