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DOC: fix doctest output in transformations.py for newer NumPy#5283

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Kd1880:fix/doctest-transformations
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DOC: fix doctest output in transformations.py for newer NumPy#5283
Kd1880 wants to merge 5 commits intoMDAnalysis:developfrom
Kd1880:fix/doctest-transformations

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@Kd1880 Kd1880 commented Mar 6, 2026

Fixes part of #3925

Changes made in this Pull Request:

  • Fix doctest output in decompose_matrix() in transformations.py
  • Newer versions of NumPy return np.float64(0.123) instead of 0.123

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
(Claude by Anthropic was used to help identify and understand the fix. Actual code changes were made manually.)

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  • Issue raised/referenced?
  • Tests updated/added? (documentation-only change, no new tests needed)
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I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

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codecov bot commented Mar 6, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.82%. Comparing base (54d37c2) to head (044c5d5).
⚠️ Report is 4 commits behind head on develop.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #5283   +/-   ##
========================================
  Coverage    93.82%   93.82%           
========================================
  Files          180      182    +2     
  Lines        22477    22483    +6     
  Branches      3191     3195    +4     
========================================
+ Hits         21089    21095    +6     
  Misses         925      925           
  Partials       463      463           

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@IAlibay IAlibay left a comment

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You removed the AI and other declarations from the PR template. Please add them before we review this PR.

@Kd1880 Kd1880 requested a review from IAlibay March 9, 2026 16:13
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@BradyAJohnston BradyAJohnston left a comment

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Please use the template available in the repo (https://github.com/MDAnalysis/mdanalysis/blob/develop/.github/PULL_REQUEST_TEMPLATE.md).

It pre-fills when you open a PR on GitHub. Currently you have the changelog message from your other PR also in this PR. Please also update your other PR if you wish for us to review it.

@Kd1880 Kd1880 requested a review from BradyAJohnston March 11, 2026 17:40
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A couple changes needed.


Fixes
* Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)
* Fix doctest output in transformations.py for newer NumPy
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@jeremyleung521 jeremyleung521 Mar 16, 2026

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Your changes deleted someone else's line. Please restore that.

Also the two lines you added should be a single line.

- Kushagar Garg
- Jeremy M. G. Leung
- Harshit Gajjela
- Kriti Dogra
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Place your name at the bottom of the list.

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4 participants