John Huddleston

Ah, I see. That example clears it up. I think what @rneher is recommending looks like this instead: ```json { "nodes": { "ARG/Cordoba-12873-61/2020": { "clade_membership": "20A" } }, "branches": {...

I'm just now looking at this issue in preparation for reviewing @victorlin's PR #756. The most recent version of Augur includes some more realistic metadata in the functional test suite,...

I just ran into this problem, too, trying to build a tree for the country of Chad which has 9 sequences all of which have an ambiguous date of `2021`....

@elebow This is an excellent direction. One feature of augur filter we have discussed in the past is [how to enable generic queries of metadata using AND/OR logic like with...

This is a great idea! We should also consider linking out to examples of ISO 8601 dates, since users may not be familiar with this term (or will not know...

One way to think about incomplete dates like `YYYY` and `YYYY-MM` would be to standardize/sanitize these to `YYYY-XX-XX` and `YYYY-MM-XX`, respectively, early in a workflow. This could be part of...

I'm most familiar with seasonal flu data where I've never seen dates with the kind of partial ambiguity described above. I agree that these should be treated as a data...

I haven't had a chance to do a full review yet, but at first glance, this is a really cool feature! It seems pretty helpful for situations like H3N2 where...

@rneher may have a preference about my recommended solution to this issue, but I still stand by the plan to: 1. include cvxopt as a primary dependency 2. drop matplotlib...

I just ran into this issue, too, trying to use the Nextclade gene map GFF as an input to augur translate. After thinking about this more and reading the comments...