Extend unit test suite to >90% coverage

[Copilot]

Coverage was at 82% (204 uncovered statements). This adds 55 new tests across 4 files to reach 91% (108 uncovered).

New test files

• tests/test_compatibility_calculate.py — Direct unit tests for compatibility/calculate.py:

  • Deprecated delta_temp/delta_press parameter warnings
  • Error cases: zero/negative temperature in NVT/NPT, too many temperatures, pressure list >6 elements, all-None pressure
  • NPT with array-valued pressure (covers the per-axis pressure string-building branch)
  • tloop parameter, NVE+Langevin warning, NVT/NPT Langevin paths
  • Helpers: _set_initial_velocity (all flag combinations), _pressure_to_lammps (rotation applied/skipped, error paths), _is_isotropic_hydrostatic, _get_rotation_matrix (no-structure warning), _modify_structure_to_allow_requested_deformation (non-diagonal, already-skewed, AttributeError path)

• tests/test_compatibility_structure.py — Tests for LammpsStructureCompatibility:

  • Init, structure getter, setter with atom_type='atomic' and 'charge'
  • structure_full with empty bond dict via a patched subclass that provides default molecule_ids (the base implementation sets it to None then subscripts it without computing it)
  • get_bonds error tolerance for incompatible structuretoolkit API

Extended test files

• tests/test_structure.py — UnfoldingPrism with scalar pbc=True/False (covers the isinstance(pbc, bool) branch) and a skewed cell that triggers the prism folding edge-case branches

• tests/test_output.py — Four new cases:

  • Dump with c_* computes column → populates hdf_generic (line 95)
  • Log with non-generic column (e.g. KinEng) → routes to hdf_lammps (line 114)
  • H5MD dump + non-ortho prism → RuntimeError (line 135)
  • mean_pressure[*] log + ortho prism → rotation applied to mean pressures (lines 311–312)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.76%. Comparing base (64de756) to head (6d3beca).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #329      +/-   ##
==========================================
+ Coverage   82.36%   88.76%   +6.39%     
==========================================
  Files          11       11              
  Lines        1157     1157              
==========================================
+ Hits          953     1027      +74     
+ Misses        204      130      -74     

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