Test: Check for missing coordinates in LAMMPS DumpReader

[IAyaanHere]

Fixes #5127

Changes made in this Pull Request:

• Added a new test case test_missing_coords_error in test_lammps.py.
• Verified that LAMMPS.DumpReader correctly raises a ValueError when the input file lacks coordinate columns (x, y, z).
• Uses tmpdir to generate a temporary dummy file for the test execution.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

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!)
• LLM/AI disclosure was updated.

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--5206.org.readthedocs.build/en/5206/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.72%. Comparing base (9cbc8ea) to head (e1348ca).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5206   +/-   ##
========================================
  Coverage    92.72%   92.72%           
========================================
  Files          180      180           
  Lines        22475    22475           
  Branches      3190     3190           
========================================
  Hits         20841    20841           
  Misses        1177     1177           
  Partials       457      457           

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[BradyAJohnston]

This seems OK - can you please run Black formatting to get the linting test to pass?

[IAyaanHere]

This seems OK - can you please run Black formatting to get the linting test to pass?

Thanks! @BradyAJohnston I've downgraded Black to the required version (v24) and applied the formatting fixes. Everything should be clean now.

[RMeli]

This only tests the "No coordinate information", while according to #5127 and https://github.com/MDAnalysis/mdanalysis/pull/5053/changes#r2427645640 the original issue was not having a test catching the wrong f-string. Could you please update the match to check that?

[IAyaanHere]

Thanks @RMeli , You were absolutely right.

I realized that while I was writing the test, the actual source code in LAMMPS.py was still raising the generic error message, which is why the strict regex check would have failed.

I have pushed a new commit that covers everything:

Source Code: Updated MDAnalysis/coordinates/LAMMPS.py to correctly include the filename in the ValueError (this ensures the f-string logic is actually active).

New Test: Updated test_missing_coords_error to use the strict regex match=r"No coordinate information found in .*bad_lammps.dump", verifying the filename is present.

Legacy Test: Updated the existing test_no_coordinate_info to match this new error message format so that the test suite remains green.

Verified locally, and all 157 tests passed.

[IAyaanHere]

@RMeli I updated the test to use regex so it catches the specific error message now. Ran it locally and it passes.