Fix DeprecationWarning by using np.arctan2 for element-wise array ope…

[laksh-krishna-sharma]

Fixs #4339 : DeprecationWarning in nuclinfo.py for NumPy 1.25+ Compatibility

This commit resolves a DeprecationWarning related to NumPy's handling of arrays with ndim > 0, which will raise an error in future releases. Specifically, the calculation of phase_ang has been updated to use np.arctan2, ensuring element-wise array operations are handled correctly.

Changes made in this Pull Request:

• Replaced the deprecated atan2(D, C) with np.arctan2(D, C) to avoid scalar conversion issues.
• Maintained the same logic for converting the angle to degrees.

This update ensures the codebase is future-proof for upcoming versions of NumPy.

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.

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📚 Documentation preview 📚: https://mdanalysis--4730.org.readthedocs.build/en/4730/

[pep8speaks]

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/analysis/nuclinfo.py:

Line 237:80: E501 line too long (95 > 79 characters)
Line 256:1: W293 blank line contains whitespace
Line 265:80: E501 line too long (104 > 79 characters)
Line 271:80: E501 line too long (84 > 79 characters)
Line 285:1: W293 blank line contains whitespace
Line 289:80: E501 line too long (84 > 79 characters)

Comment last updated at 2024-10-15 12:19:10 UTC

[github-actions]

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	✅ Passed

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/11345880851/job/31553733947

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

[laksh-krishna-sharma]

@orbeckst Sir please review the Pull Request

[orbeckst]

There are many changes in this PR, most of which have nothing to do with the original issue. Please only change what needs changing to address the issue. Otherwise it takes too much time to review. The fewer changes there are in the diff view the easier it is for reviewers.

If you think that this a file needs to be refactored, open an issue, please. Note that nuclinfo is slowly being transitioned to a more modern framework #3720 so we really only want minimal changes here.

Please also check the tests (click on any of the failing tests and read the output to see where they are failing): They fail from code that you changed so you can immediately see that your changes are not correct.

[orbeckst]

Do not remove docs, especially not versionadded.

[laksh-krishna-sharma]

ok @orbeckst thanks for your response , i will make sure to do minimal changes from now and to fix the issue as soon as posible.

[orbeckst]

Can you please create a PR that only fixes the issue and does not change any other code?

• make sure that the tests still pass
• demonstrate that before your changes you see the warning (e.g., just run the tests for nuclinfo: pytest -v MDAnalysisTests/analysis/test_nuclinfo.py)
• demonstrate that after your changes you don't see the warning anymore.

You can copy and paste the output that shows warnings.

[orbeckst]

Look at the test output (click on Details in failing tests ❌ ) and you see that tests related to nuclinfo are now failing:

FAILED testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_as[RNAA-1-359.5758] - AssertionError: 
Arrays are not almost equal to 3 decimals
 ACTUAL: 89.57579515609689
 DESIRED: 359.5758
FAILED testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_as[RNAA-11-171.71645] - AssertionError: 
Arrays are not almost equal to 3 decimals
 ACTUAL: 261.7164514291825
 DESIRED: 171.71645
= 2 failed, 20003 passed, 147 skipped, 12 xfailed, 2 xpassed, 99736 warnings in 1005.44s (0:16:45) =

This means that your code changes introduced errors. You need to fix your code.