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Update to Python 3.12+/pandas 3, expand README, simplify CI - #549

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aarmey merged 1 commit into
mainfrom
update-python-pandas-ci
Aug 21, 2026
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Update to Python 3.12+/pandas 3, expand README, simplify CI#549
aarmey merged 1 commit into
mainfrom
update-python-pandas-ci

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@aarmey

@aarmey aarmey commented Aug 21, 2026

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Summary

  • Bump requires-python to >=3.12 and pandas to >=3; update ruff/ty target versions to match. Ran the full lint/typecheck/test suite and several figure builds under pandas 3.0.5 on Python 3.14 with warnings-as-errors — no pandas 3 deprecations or breakage found in this codebase (a couple of unrelated pre-existing bugs were confirmed present on main too and left untouched).
  • Expanded the README with the citation and abstract for the paper this repo implements (Creixell & Meyer, Cell Rep Methods 2022), and removed the build/test status badges.
  • Removed the Build GitHub Actions workflow, switched the Test workflow from self-hosted to ubuntu-latest, and dropped the Codecov upload in favor of printing coverage to the console (make coverage).

Test plan

  • uv sync
  • make lint
  • make typecheck
  • make coverage (pytest with coverage printed to terminal)

🤖 Generated with Claude Code

https://claude.ai/code/session_01UiQSNu6WeCVKin3hccEQvT

- Bump requires-python to >=3.12 and pandas to >=3; update ruff/ty
  target versions to match. Verified via full test/lint/typecheck
  runs that no pandas 3 deprecations affect this codebase.
- Expand README with the paper citation and abstract this repo
  implements, and drop the build/test status badges.
- Remove the build workflow, run tests on github-hosted ubuntu-latest
  instead of self-hosted, and drop the Codecov upload in favor of
  printing coverage to the console.
@aarmey
aarmey merged commit 600ac75 into main Aug 21, 2026
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@aarmey
aarmey deleted the update-python-pandas-ci branch August 21, 2026 14:48
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