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Update pandas dependency for LDSC #28030

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merged 2 commits into from Apr 15, 2021
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jdblischak
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The version of LDSC pinned for the bioconda recipe (commit 12e2687) breaks starting with pandas version 0.21.0. For more details see bulik/ldsc#175 (comment)

This PR makes the following edits:

  • Constrains pandas to be less than 0.21.0 (effectively pinning it to version 0.20.3)
  • Updates the bundled setup.py to reflect the pandas constraint as well as removing the dev-only requirement nose
  • Updates the version in the bundled setup.py to match the version in meta.yaml as well as the version listed in the source code

Thinking more long-term: The current master branch of ldsc has merged a fix for pandas >=0.21.0. Ideally we will eventually update the bioconda recipe. But until the authors bump the version number (or even better tag a new release, as requested in bulik/ldsc#177), I'd prefer to not introduce the confusion of having a different versioning scheme between the source code and the bioconda recipe. Furthermore, both the requirements.txt and environment.yml files they provide still pin pandas to <0.21.0, so using this older version is still the safest option (since this is likely what the code was tested against).

xref: #18704, #27877


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@mbargull
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@BiocondaBot, please update

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I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

@BiocondaBot BiocondaBot merged commit 1672cb5 into bioconda:master Apr 15, 2021
@jdblischak
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@mbargull Thanks for the review and merge! I confirmed the recipe works for me locally.

@mbargull
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Perfect, thanks!

@jdblischak jdblischak deleted the ldsc-pandas branch April 16, 2021 01:35
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3 participants