Thomas Sibley

A config file with each step's args/params could absolutely be the "syntax TBD" I mentioned for multiple transforms "chained together in the same process". :-) It would be important that...

@ammaraziz Thanks for your comment! It's nice to have more people thinking about this. I think there's a number of downsides to the syntax you propose (some of which you...

@ammaraziz Not intruding at all. :-) It's good to get feedback and input and questions from outside the core team. To answer your question about handling of sequences, our thinking...

Re: names: `augur curate` is my current frontrunner as the concept of _curation_ encompasses all of the subcommands we've talked about. It occurred to me earlier this week when talking...

+1 for @huddlej's thoughts on I/O. They match how I imagined the framework that individual commands plug into (regardless of whether Augur-provided or user-provided). Re: `--output-metadata /dev/stdout` being non-ideal, a...

A few quick notes I had during our call just now: 1. Much of the templated SQL seems to interpolate values directly without proper quoting. If interpolation is used, quoting...

> Could you clarify what you mean by using interpolation vs. placeholders? ``` cur.execute(f"select * from x where y = '{z}'") # interpolation (problematic) cur.execute("select * from x where y...

@victorlin Ok, sounds good. These are great candidates for caching, indeed. That example SQL is a little more tortuous than I was expecting, which was using a date/time function or...

> …but for that I think it's easier to just create copies of the database file rather than sharing a single one: > > 1. Current SQLite logic relies on...

See also [Slack discussion](https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1644484579232879), including ideas about how to re-use doc in various places.