replaced lib.transformations with transformations package

[orbeckst]

Fixes #5061

Changes made in this Pull Request:

• removed old lib.transformations code
• use transformations package instead (which is the updated version of our old vendored code)
• Makes transformations a core dependency.
• moved our only addition (transformations.rotaxis() to mdamath.rotaxis()) and left a deprecated version in lib.transformations

PR Checklist

• [x] Issue raised/referenced?
• [x] Tests updated/added?
• [x] Documentation updated/added?
• [x] package/CHANGELOG file updated?
• [x] Is your name in package/AUTHORS? (If it is not, add it!)

Developers Certificate of Origin

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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📚 Documentation preview 📚: https://mdanalysis--5062.org.readthedocs.build/en/5062/

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 94.11%. Comparing base (8b0be5f) to head (bd88561). Report is 2 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5062      +/-   ##
===========================================
+ Coverage    93.62%   94.11%   +0.48%     
===========================================
  Files          177      177              
  Lines        22001    21331     -670     
  Branches      3114     3021      -93     
===========================================
- Hits         20599    20075     -524     
+ Misses         947      847     -100     
+ Partials       455      409      -46     

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[orbeckst]

If you both think that’s feasible then it may still be a positive trade off for us: reduce code burden inside MDA (and magically increase coverage by 0.5%) and do something good for the community.  Who would start the process of getting on the cf feedstock recipe?Am 6/12/25 um 03:57 schrieb Irfan Alibay @.***>: @IAlibay commented on this pull request.

In .github/actions/setup-deps/action.yaml:

• transformations:

• default: 'transformations'

I agree with @RMeli - the recipe seems rather simple so it might not be too much of a hassle for us to take it on.

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[IAlibay]

Who would start the process of getting on the cf feedstock recipe?

I have opened an issue on the feedstock, let's see what happens.

[orbeckst]

Thanks!

-- Oliver Beckstein (he/his/him) @.***

On Jun 12, 2025, at 08:34, Irfan Alibay @.***> wrote:

IAlibay left a comment (MDAnalysis/mdanalysis#5062) https://github.com/MDAnalysis/mdanalysis/pull/5062#issuecomment-2967322563 Who would start the process of getting on the cf feedstock recipe?

I have opened an issue on the feedstock, let's see what happens.

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[RMeli]

I have opened an issue on the feedstock, let's see what happens.

Thanks @IAlibay! I'd be OK to be added as a maintainer if needed.

[hmacdope]

While we wait for the transformations people to respond so we can migrate, I have had a crack at updating the numpy C interface for transformations.c to modern NPY C API in #5068 such that things build correctly again.

Seems to be working?

[RMeli]

Thanks @hmacdope! Sounds good to me to fix the issue quickly with #5068 while we wait for the conda package to be sorted.