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refactor: hiv #42

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@tristan-f-r tristan-f-r commented Jul 30, 2025 •
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Adds documentation back to the HIV dataset, and:

  • Does offline UniProt mapping. This drops a significant part of the code.
  • Drops KEGG gold standard generation, since it wasn't sufficient. Note that we now include a Prior work section in datasets/README.md, so this will never be actually lost.

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agitter reviewed Aug 8, 2025
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I left some initial comments that mostly pertain to my different expectations for what can go in the dataset readmes. I am finding it hard to review the new script-based pipeline with respect to the original notebooks. I'm not sure if it is a pure port or a complete rewrite.

@tristan-f-r tristan-f-r mentioned this pull request Aug 11, 2025
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tristan-f-r commented Jan 23, 2026

The kegg_orthology.py is a port. Every other file has been substantially rewritten, especially name_mapping.py, though for the better: this entire pipeline is now just 90 lines of Python.

@tristan-f-r tristan-f-r changed the title docs: hiv refactor: hiv Jan 23, 2026
@tristan-f-r tristan-f-r added the dataset Mutating datasets in any way. label Jan 23, 2026
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tristan-f-r commented Jan 23, 2026

I'm going to separate the miscellaneous cache changes over to make this an easier diff to read.

@tristan-f-r tristan-f-r mentioned this pull request Jan 23, 2026
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@tristan-f-r tristan-f-r force-pushed the hiv-clean branch 3 times, most recently from bd99a25 to e2afb83 Compare January 23, 2026 21:43
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