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[MAJOR] deps: upgrade pandas 2.0 -> 3.0 [R PARITY REQUIRED] - #18

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upgrade/pandas-3.x
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[MAJOR] deps: upgrade pandas 2.0 -> 3.0 [R PARITY REQUIRED]#18
SHA888 wants to merge 1 commit into
mainfrom
upgrade/pandas-3.x

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@SHA888

@SHA888 SHA888 commented Apr 14, 2026

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Summary

Upgrade pandas from >=2.0 to >=3.0 (MAJOR version bump).

Risk Assessment

  • Level: HIGH - Core data structures
  • Breaking Changes:
    • NA handling changes (pd.NA behavior)
    • Index behavior modifications
    • StringDtype becomes default string type
    • concat() behavior changes for mismatched indices
  • R Parity Impact: CRITICAL - Data structure core to analysis pipeline

Checklist (MUST COMPLETE BEFORE MERGE)

  • Pre-commit checks pass (ruff, mypy)
  • CI tests pass (all Python versions)
  • R parity validation:
  • Numerical tolerance check: must match R within 1e-6
  • Validate DataFrame operations preserve R equivalence
  • Update CHANGELOG.md with breaking change notes

Validation Required

This PR is BLOCKED until R parity tests pass. See .

Notes

Dependabot ignores pandas major updates by design. Manual validation required.

- Update pandas requirement from >=2.0 to >=3.0
- Breaking changes: NA handling, Index behavior, StringDtype default
- REQUIRES R parity validation before merge
- Risk: HIGH - Core data structures

Blocked in dependabot.yml until validated.
@SHA888
SHA888 force-pushed the upgrade/pandas-3.x branch from 1bb461d to 84b70a3 Compare April 14, 2026 02:23
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