Improve error message when calling AtmGroup.unwrap() without bonds #4642

laksh-krishna-sharma · 2024-07-23T21:31:26Z

Fixes #4436: Improve error message when calling AtomGroup.unwrap() without bonds

This PR improves the error message that is raised when calling AtomGroup.unwrap() without defined bonds. The new message provides clearer guidance on how users can resolve the issue.

PR Checklist

Tests?
Issue raised/referenced?

Developers certificate of origin

I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

📚 Documentation preview 📚: https://mdanalysis--4642.org.readthedocs.build/en/4642/

pep8speaks · 2024-07-23T21:31:32Z

Hello @laksh-krishna-sharma! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file package/MDAnalysis/core/groups.py:

Line 1877:40: W291 trailing whitespace
Line 1879:80: E501 line too long (105 > 79 characters)
Line 1881:80: E501 line too long (90 > 79 characters)
Line 1882:80: E501 line too long (91 > 79 characters)

In the file testsuite/MDAnalysisTests/core/test_groups.py:

Line 1492:80: E501 line too long (84 > 79 characters)
Line 1494:80: E501 line too long (86 > 79 characters)
Line 1495:80: E501 line too long (87 > 79 characters)
Line 1499:36: W291 trailing whitespace

In the file testsuite/MDAnalysisTests/core/test_unwrap.py:

Line 341:80: E501 line too long (102 > 79 characters)
Line 343:80: E501 line too long (86 > 79 characters)
Line 344:80: E501 line too long (87 > 79 characters)

Comment last updated at 2024-07-28 09:21:18 UTC

github-actions

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.

github-actions · 2024-07-23T21:33:36Z

Linter Bot Results:

Hi @laksh-krishna-sharma! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/10130585219/job/28012143836

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

package/MDAnalysis/core/groups.py

orbeckst

@laksh-krishna-sharma looks good.

Could you please follow @tylerjereddy 's suggestion and find the place where we test for the exception being raised and then add a match for part of the message.

orbeckst

The tests are failing now, please fix. Perhaps you need to treat the match string more carefully. It would also be ok to just match the first line.

tylerjereddy · 2024-07-25T01:01:11Z

ya, just using a regex-style match on a sub-section of the message is usually what I see done

laksh-krishna-sharma · 2024-07-25T18:11:53Z

Thank you for your feedback, @orbeckst and @tylerjereddy. I have resolved the issue by carefully revising the match string. Please review the updated.

orbeckst · 2024-07-25T21:23:04Z

Tests are failing with something that looks related to your code

=================================== FAILURES ===================================
________________ TestAttributeGetting.test_unwrap_without_bonds ________________
[gw1] linux -- Python 3.10.14 /home/runner/micromamba/envs/mda/bin/python3.10

universe = <MDAnalysisTests.core.test_groups.TestAttributeGetting object at 0x7f6b8005f2e0>

    def test_unwrap_without_bonds(universe):
        with pytest.raises(NoDataError) as exc:
>           universe.atoms.unwrap()
E           AttributeError: 'TestAttributeGetting' object has no attribute 'atoms'

/home/runner/work/mdanalysis/mdanalysis/testsuite/MDAnalysisTests/core/test_groups.py:1485: AttributeError

Can you please check?

laksh-krishna-sharma · 2024-07-25T21:52:23Z

Thank you for letting me know, @orbeckst. I will investigate the issue and address the failing tests as soon as possible. I'll update once the problem is resolved.

codecov · 2024-07-26T09:52:42Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.59%. Comparing base (1bf58cc) to head (1898256).
Report is 41 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4642      +/-   ##
===========================================
- Coverage    93.61%   93.59%   -0.03%     
===========================================
  Files          171      183      +12     
  Lines        21250    22320    +1070     
  Branches      3936     3937       +1     
===========================================
+ Hits         19893    20890     +997     
- Misses         898      971      +73     
  Partials       459      459

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laksh-krishna-sharma · 2024-07-26T11:30:41Z

Thank you for your feedback, @orbeckst and @tylerjereddy. I have resolved the issue carefully . Please review the updated.

laksh-krishna-sharma · 2024-07-26T20:45:59Z

Please review the updated.

orbeckst

This looks functionality very good. I have one request for you to improve our existing code (see comment) and also

add yourself to the end of the file AUTHORS

update CHANGELOG: add an entry for the change in the CHANGELOG file to the top of Enhancements

mdanalysis/package/CHANGELOG

Lines 54 to 55 in 7302719

    
           Enhancements 
        
            * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)

and don't forget to add your GitHub handle at the end of the line of authors who contributed to the release

mdanalysis/package/CHANGELOG

Line 20 in 7302719

yuxuanzhuang, PythonFZ

That's all I see and then I can merge it.

testsuite/MDAnalysisTests/core/test_groups.py

laksh-krishna-sharma · 2024-07-27T08:41:01Z

Thank you for your review, @orbeckst. I'll complete all the tasks mentioned.

…unwrap(), rewrite test case

laksh-krishna-sharma · 2024-07-27T10:22:14Z

Thank you for your feedback, @orbeckst. I have made all the requested improvements, including updating the AUTHORS file, adding an entry to the CHANGELOG under Enhancements, and ensuring my GitHub handle is included with the contributors. I also revised the test using pytest.raises with the match parameter for message checking. Please review the updated.

orbeckst

Thanks, please see inline comments!

orbeckst · 2024-07-27T21:15:51Z

testsuite/MDAnalysisTests/core/test_groups.py

+            "2. Create a universe using a topology format where bonds are pre-defined."
+        )
+        expected_message_pattern = re.escape(expected_message)
+        assert re.fullmatch(expected_message_pattern, str(exc.value))


Sorry, my previous comment wasn't clear enough. What I would like you to do is to

add to the pytest.raises(NoDataError) above a match=expected_message_pattern)

remove the assert that checks for the message.

In this way we have all checks inside the pytest.raises.

package/CHANGELOG

laksh-krishna-sharma · 2024-07-28T09:57:32Z

@orbeckst thank you for clearly mentioning the issue again. I have resolved it carefully. Please review the updated.

orbeckst

All looking good, thanking you for patiently and promptly and addressing my comments.

I'll merge — thank you for your first contribution! I hope we see more from you!

orbeckst · 2024-07-28T18:36:55Z

Congratulations, @laksh-krishna-sharma , first merged contribution! 🎉

laksh-krishna-sharma · 2024-07-28T21:45:09Z

Thank you, @orbeckst! I am grateful for the opportunity to contribute and for your patient guidance. I would like to work more under your guidance in this repository. It would be great if you could help me with the environment setup, as I am looking to contribute more and learn from you. This being my first contribution, it has been an amazing experience, and I have learned a lot. I am excited to continue contributing and learning.

orbeckst · 2024-07-28T22:24:02Z

Thank you for your contribution, it was a pleasure working with you.

We only assign specific mentors for something like Google Summer of Code. When you're part of the MDAnalysis community you'll interact with many people — users, developers, documentation writers, instructors, ... I suggest you engage through the public forums (discussions, discord) if you have specific questions — typically there's someone there who can point you in the right direction.

laksh-krishna-sharma · 2024-07-28T22:27:15Z

Thank you @orbeckst . I understand the mentorship structure within the MDAnalysis community. I look forward to interacting with the community and continuing to contribute to the project.

Improve error message when calling AtmGroup.unwrap() without bonds

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Update AUTHORS and CHANGELOG for improved error message in AtomGroup.…

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…unwrap(), rewrite test case

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orbeckst merged commit d16b8d4 into MDAnalysis:develop Jul 28, 2024
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laksh-krishna-sharma deleted the fix/improve-error-message-when-calling-AtmGroup-unwrap-without-bonds branch July 29, 2024 07:36

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Improve error message when calling AtmGroup.unwrap() without bonds #4642

Improve error message when calling AtmGroup.unwrap() without bonds #4642

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	Enhancements
	* Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)

Improve error message when calling AtmGroup.unwrap() without bonds #4642

Improve error message when calling AtmGroup.unwrap() without bonds #4642

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