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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Top-level utils package causes ncov-ingest to break #415

Closed jgadling closed 2 years ago

jgadling commented 2 years ago

I realize this isn't entirely the responsibility of the Pangolin team, but it's a simple fix and I believe it improves the clarity and manageability of this package, so here's the story:

Nextstrain's tools and ecosystem have been integrating with Pangolin more deeply recently. It's common to need to run ncov and/or ncov-ingest alongside a pangolin installation.

The pango-designation package as it stands right now installs a top-level module called utils when installed via pip. As far as I can tell the modules in this package aren't referenced by anything else in the ecosystem, and the presence of this top-level module breaks several of the tools in the ncov-ingest package which has its own internal utils module.

I think that moving the pango-designation utils module under the pango-designation module, or not installing it at all will help improve interoperability with other tools, and reduce confusion about where a system-wide package called utils is coming from.

corneliusroemer commented 2 years ago

Thanks, I removed the utils/__init__.py so with next release this should be resolved