Update ingest to pathogen-repo-template

nextstrain / mpox

Nextstrain build for mpox virus

https://nextstrain.org/mpox

MIT License

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Update ingest to pathogen-repo-template #234

Closed joverlee521 closed 5 months ago

joverlee521 commented 5 months ago

Description of proposed changes

Update ingest directory to match pathogen-repo-template layout.

This PR does not change any output data formats to not break any downstream uses of the data, i.e. the fields for the NDJSON and metadata.tsv were not changed.

Checklist

[ ] Checks pass
[x] Test run

joverlee521 commented 5 months ago

Not sure what's going on with the pre-commit.ci failure.

All tests pass when I run pre-commit run --all-files locally:

Screenshot 2024-01-30 at 2 57 01 PM

joverlee521 commented 5 months ago

Test run completed successfully and the metadata diff output to the test #scratch channel included the 10 new sequences that have become available since this morning's automated ingest run. No other data changes were reported.

joverlee521 commented 5 months ago

pre-commit.ci failure should be unrelated to changes in this PR. It is likely to be the same failure that is on the master branch. I see the same failure locally after rebasing this branch onto master.

I'm going to leave the pre-commit.ci failure in this PR alone since it will be fixed separately in https://github.com/nextstrain/mpox/pull/233 (or we can exclude .github/dependabot.yml in the .yamlfmt config)

joverlee521 commented 5 months ago

Merging since test run was successful. Will monitor automated runs the next couple of days.