John Huddleston

Reposting [my comment from a Slack thread](https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1655333804924329?thread_ts=1655328567.263659&cid=C01LCTT7JNN): > Augur also already has a standard of supporting multiple output formats for a single command, depending on the user’s needs (augur filter...

I was really psyched about `curate`, but then the more I (over)thought about it, the more it seems that "curation" is more like "filtering" in that it describes carefully selecting...

Good call on clarifying the "data curation" context (`tidy` is another good option!), although that ambiguity is what concerned me in the first place (the determining "what information is worth...

> If a user provides both a metadata TSV and a FASTA file as inputs, I think we would only ever do an "inner" join that only keeps records that...

Thank you for the review, @tsibley! I'm rethinking my approach to this PR, actually, since I think it does too much at once. A simpler/clearer solution would be to: -...

It's the second case ("country" + "division"). In this specific case, creating custom columns in Excel is still a difficult task for this user group. I don't know that this...

@victorlin I like this idea of the `--engine` argument, as a general solution to how we add or remove support for different query syntax. Along the lines of @rneher's comment...

I agree, @tsibley, that we can't drop CSV support. The original context for the current implementation is described in https://github.com/nextstrain/augur/issues/574. There are two separate problems: 1. determining the delimiter of...

Playing with the measurements panel more today, I had a few comments/thoughts to add to the list above. 1. +1 for handling the long card titles. In [the example community...

From @rneher's review: > We don't seem to handle the case when the root node of the tree is not assigned to a clade explicitly. @jameshadfield, I understood this to...