Marcus Fedarko

It looks like the build is failing for this -- since this PR only contains docs fixes, these failures are likely due to dependencies shifting. The build seems to be...

@wasade awesome, installing anndata via conda instead of via pip fixed the build! For now, the CI installs anndata from conda-forge instead of bioconda -- anndata is available on both...

The PR should be good to go. Thanks!

Just as a heads up, it looks like the Python 3.6 build began failing in recent months (although the Python 3.10 build is fine). As far as I can tell,...

It seems to be an explicitly optional dependency that's [just used in the `to_anndata()` function](https://github.com/biocore/biom-format/blob/5bf61d5d57864c5a4ae9c188a72133c7b655d06a/biom/table.py#L4270-L4319), so I don't think pinning `anndata` would be a big deal. But I guess it...

Eesh, that's annoying! It should be feasible to add this in. Looks like the lines causing the problem are here: https://github.com/biocore/empress/blob/e543610c5654399aa1dcbbede09b45b45c4170d0/empress/_plot_utils.py#L86-L101 ... So we can probably just add an `--overwrite...

FWIW, it looks like this currently breaks the interface because some code in the side panel assumes that the leaf sorting selector has already been assigned a value? Not sure...

Got it. Maybe 1000 x 1000 would be close enough.

It would also be nice to allow the user to specify certain values that should be excluded (and always included in `Other`) -- for example, `s__`, `Unspecified`, etc.

Hi @ggonnella, Thank you for the quick response! That's great news. I downloaded the `opt_ignore_seqs` branch, but it doesn't look like the `ignore_sequences` option is available -- as far as...