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Fix broken links in docs#4941

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orbeckst merged 6 commits intoMDAnalysis:developfrom
namiroues:fix-broken-links
Mar 13, 2025
Merged

Fix broken links in docs#4941
orbeckst merged 6 commits intoMDAnalysis:developfrom
namiroues:fix-broken-links

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@namiroues
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@namiroues namiroues commented Mar 1, 2025

Fixes #4940

Changes made in this Pull Request:

Identified broken links in docs were fixed.

PR Checklist

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

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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.


📚 Documentation preview 📚: https://mdanalysis--4941.org.readthedocs.build/en/4941/

@namiroues
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Hi @micaela-matta and @orbeckst. Could you please review this PR? Thanks.

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codecov bot commented Mar 1, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.41%. Comparing base (6a75df0) to head (90f5d6c).
Report is 27 commits behind head on develop.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #4941      +/-   ##
===========================================
- Coverage    93.66%   93.41%   -0.26%     
===========================================
  Files          177      189      +12     
  Lines        21850    22925    +1075     
  Branches      3079     3078       -1     
===========================================
+ Hits         20466    21415     +949     
- Misses         933     1059     +126     
  Partials       451      451              

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THanks for the work. Minor comments inline.

Please also add yourself to AUTHORS.

Comment thread package/MDAnalysis/coordinates/MMTF.py
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/selections/gromacs.py Outdated
Comment thread package/MDAnalysis/coordinates/GRO.py Outdated
@orbeckst orbeckst self-assigned this Mar 1, 2025
@namiroues namiroues changed the title Fix broken links Fix broken links in docs Mar 4, 2025
@namiroues
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Hi @orbeckst. Thanks for the comments. Only one change was needed at the end.

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lgtm, thanks!

Comment thread package/MDAnalysis/coordinates/GRO.py Outdated
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/selections/gromacs.py Outdated
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
Comment thread package/MDAnalysis/coordinates/TRJ.py Outdated
orbeckst and others added 3 commits March 10, 2025 20:31
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
@orbeckst orbeckst enabled auto-merge (squash) March 11, 2025 03:37
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@IAlibay could you have a quick look again? Thank you for finding the correct AMBER pages.

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IAlibay commented Mar 13, 2025

/azp run

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IAlibay commented Mar 13, 2025

@IAlibay could you have a quick look again? Thank you for finding the correct AMBER pages.

Ah sorry, I saw you set auto-merge so I assumed you were dismissing my request changes.

@orbeckst orbeckst merged commit 8fb40ad into MDAnalysis:develop Mar 13, 2025
15 of 24 checks passed
Abdulrahman-PROG pushed a commit to Abdulrahman-PROG/mdanalysis that referenced this pull request Apr 13, 2025
* Fixes MDAnalysis#4940
* Fix broken links
* docs: address review comments
* use new genuine AMBER TRJ specs
* link to GMX current docs

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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Fix broken links in docs

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