Modernize/cleanup 2 #3
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Once the repo modernization is complete, these files will be deleted; for the moment this allows them to be easily accessed.
Exclude the _LEGACY tree because there's no point in cleaning that stuff up; leave a comment so I remember to go back and remove it when `_LEGACY` goes away.
Also apply pre-commit cleanup
…/vendored subrepo: subdir: "ingest/vendored" merged: "5b74edc" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "5b74edc" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo/" commit: "73a0129"
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FWIW, the move of the top level auspice directory will break the link to the community build that can be viewed at https://nextstrain.org/community/nextstrain/yellow-fever.
Not sure how much it gets used since this build was updated ~5 years ago.
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Ah, you mean that community build is directly coming out of the GitHub repo?
In that case, what I might do instead is branch a new main off the current master, and then use that new main branch as the place where in-progress "modernization" work is collected, and then only loop back and remove master when the modernization work is complete and we're ready to move yellow-fever into the officially supported builds.
Thoughts?
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(I don't have insight into whether we want to maintain the community build here - for our canonical pathogen repos I wouldn't expect usage of /community URLs but 🤷 )
Community URLs will, in the absence of an explicit branch, use the default branch.
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for our canonical pathogen repos I wouldn't expect usage of /community URLs
Right, just wanted to point this out in case there was usage of it. I also didn't realize we had a yellow-fever build at https://nextstrain.org/yellow-fever (although it's two years older than the community URL).
Should we just upload this community dataset as a core yellow-fever dataset and remove from here? (Saying that with no historical context of who produced this community dataset)
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The community dataset links to http://evolve.zoo.ox.ac.uk/Evolve/Sarah_Hill.html -- which 404s -- but Google suggests that Sarah Hill is https://www.rvc.ac.uk/about/our-people/sarah-hill; there is at least yellow fever research in her publication trail.
I think (unless I'm very confused), my goal here is replacing/updating our yellow fever build.
I'm not sure what sort of guarantees we provide (or even should provide) to folks who have set up community builds, or what we do when a community build "breaks".
Guidance appreciated. 😁
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I think (unless I'm very confused), my goal here is replacing/updating our yellow fever build.
Totally, sorry for the confusion. Since the community build was within our Nextstrain repo, I had thought this was our yellow fever build and was wondering if we should upload it as an official Nextstrain build.
I'm not sure what sort of guarantees we provide (or even should provide) to folks who have set up community builds, or what we do when a community build "breaks".
You're right, we don't want to put any guarantees on community builds. I just thought it would nice to preserve this particular build if this was created by the Nextstrain team.
All that said, seems like we don't have to dwell on it now and just proceed with moving it to under _LEGACY. We can revisit what to do with it when the time comes to completely delete it from the repo.
Remove unused configuration files
Description of changes
This is the first several steps outlined in the "moderize repo" issue