BUG: extensions are placed at top level and not under meta as Nextclade expects

[corneliusroemer]

#865 allows an extensions JSON object to be defined in auspice_config.json and passed through.

Unfortunately, I didn't realize that the current implementation places extensions at the top level and not under meta as Nextclade expects.

I had thought the discussion on Slack and my issue was clear about this expectation. But unfortunately it was nowhere mentioned that we had settled on meta.extensions.

Given that Nextclade is the only user of this feature so far and we have just released Augur 14.1, would it be possible to make a change from extensions to meta.extensions? @jameshadfield

Maybe we can squeeze this in with the next release? The change would be quite trivial I think.

Alternatively we could accept both - but that would be asking for trouble. Changing what Nextclade expects would be troublesome.

Given that we were undecided about extensions or meta.extensions I feel we should just stick with whatever convention Nextclade has adopted.

I'm sorry this slipped through - I should have checked the PR better 😬

[tsibley]

To clarify, extensions remains top-level in the Auspice config schema but would change to be within meta in the dataset schema?

[corneliusroemer]

Yes correct. I think this may also be what one naively expects, since all the other auspice config properties get moved into meta anyways.