[jkalayan]

Summary

This pull request focuses on improving robustness and clarity in schema path resolution and trajectory metadata extraction, as well as cleaning up debugging code.

Schema path resolution improvements:

• Updated resolve_schema_inputs to prefer args.mappingschema/args.biosimschema, but fall back to args.mapping_path/args.biosim_path if the former are not set, allowing for more flexible argument handling.
• In main, if schema arguments are missing, now sets args.mapping_path and args.biosim_path instead of local variables, ensuring downstream functions receive the correct paths.

Trajectory metadata extraction robustness:

• Refactored box property extraction in toptraj.py to always use the first trajectory frame's dimensions, with improved checks for trajectory existence and non-null dimensions, making the logic more reliable and faster.

Testing updates:

• Updated test cases to include the new mapping_path and biosim_path arguments, ensuring tests accurately reflect the new input handling logic. [1] [2]

Code cleanup:

• Removed commented-out debug print statements from both toptraj.py and populatemetadata.py for cleaner code. [1] [2]

Dependency cleanup:

• Removed an unused import of numpy from toptraj.py.

Impact

• Extracting dimension information by checking only the first frame of the trajectory contains dimension information (rather than iterating over frames until a dimension is found), ensures extraction completes in a timely manner (<1 minute for a 14 GB trajectory)

[coveralls]

Coverage Report for CI Build 38268906850

Coverage decreased (-0.01%) to 90.661%

Details

• Coverage decreased (-0.01%) from the base build.
• Patch coverage: 2 uncovered changes across 1 file (2 of 4 lines covered, 50.0%).
• No coverage regressions found.

Uncovered Changes

File	Changed	Covered	%
biosim_extractor/metadata/populatemetadata.py	4	2	50.0%

Coverage Regressions

No coverage regressions found.

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Coverage Stats

Relevant Lines:	1028
Covered Lines:	932
Line Coverage:	90.66%
Coverage Strength:	8.16 hits per line

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💛 - Coveralls