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Release dependency caps for pandas 3 incompatibility#2

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jessegmeyerlab wants to merge 2 commits into
mainfrom
agent/fix-dependency-caps-issue-1
Draft

Release dependency caps for pandas 3 incompatibility#2
jessegmeyerlab wants to merge 2 commits into
mainfrom
agent/fix-dependency-caps-issue-1

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@jessegmeyerlab

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Closes #1.

Summary

  • bump Full-DIA from 1.0.2 to 1.0.3 so the existing package dependency caps can be published
  • add pandas<3.0.0 to the Conda environment
  • retain the existing numpy<2.0.0 constraints

Why

Pandas 3 changes GroupBy.apply behavior used during DIA window extraction. The grouping columns can be absent from the resulting frames, causing KeyError: 'quad_low_mz_values'. The released 1.0.2 metadata does not cap pandas, even though main now does.

No analysis logic is changed.

Validation

  • compared the branch against main
  • confirmed only full_dia/__init__.py and requirements/fulldia_cuda12.yml changed
  • branch is two commits ahead and zero commits behind main

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KeyError: 'quad_low_mz_values'

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