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fix: add DeprecationWarning to geneset() and snp_dataset()#1286

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Tanisha127:fix/deprecation-warnings-geneset-snp-dataset
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fix: add DeprecationWarning to geneset() and snp_dataset()#1286
Tanisha127 wants to merge 3 commits intomalariagen:masterfrom
Tanisha127:fix/deprecation-warnings-geneset-snp-dataset

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@Tanisha127
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Fixes #1285

What changed

  • Added warnings.warn(..., DeprecationWarning) to geneset() in genome_features.py
  • Added warnings.warn(..., DeprecationWarning) to snp_dataset() in snp_data.py

Why

Both methods were silently deprecated with no runtime warning to users.

Testing

  • geneset() — DeprecationWarning raised correctly
  • snp_dataset() — DeprecationWarning raised correctly
    All existing tests pass.

@Tanisha127
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Hi @jonbrenas,
Kindly take a look at this PR.
Thanks!

@ZiadXI
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ZiadXI commented Apr 13, 2026

Hey, Thanks for working on this.

I actually opened a PR earlier addressing the same issue (#1273), but it hasn’t been reviewed yet. I wanted to ask, does your implementation introduce anything different in terms of approach or behavior compared to what was previously proposed?

Just trying to understand if there are key differences or improvements so we can avoid duplicating effort.

Appreciate it

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fix: geneset() and snp_dataset() are deprecated but emit no DeprecationWarning

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