align_tree cannot handle features with 0 counts

[dpear]

if a feature table has a feature with 0 sum, align_tree will throw an error stating that the id of the feature is not present in the table. (apologies for brevity, let me know and I can follow up with code examples etc.)

[mortonjt]

Hi, did you try this workaround : https://github.com/biocore/biom-format/issues/860 As @wasade and I discussed in previous iterations, if we explicitly store zeros in the biom table, it sort of thwarts bioms' ability to have memory efficient storage.

[wasade]

Thanks, @mortonjt! But there is an edge case here that needs to be fixed. sort_order based off the tree, but called after remove_empty which will raise if a feature is removed.

[wasade]

Fixed in #959, unsure why it didn't automatically close.