Refactored the code

[kousuke-nakano]

• CIF reader backend update: Replaced CIF read path from pymatgen.io.cif to PyCifRW (CifFile) for CIF parsing.

• Refactored symmetry detection: Changed from pymatgen's internal SpacegroupAnalyzer to direct spglib calls for improved transparency and control over symmetry operations.

  • Added helper functions: structure_to_spglib_cell(), get_symmetry_operations_from_spglib(), and get_symmetrized_structure_from_spglib()
  • Removed dependency on PatchedSpacegroupAnalyzer class
  • Symmetry information is now obtained directly from spglib's dataset

• Parallel tree search: Tree search now supports dynamic parallel execution using Python multiprocessing.

  • Added n_jobs parameter to Substitutor and PatternMaker classes (default: -1, uses all CPU cores)
  • Parallelization is applied at subtree level for both _invarless_search and _invar_search
  • Adaptive depth expansion: subtree seeds are expanded until enough splits are prepared (target = max(n_cores * 8, 32)) or depth limit is reached (max_depth <= 10, and bounded by stop)
  • Dynamic load balancing: worker tasks are scheduled with multiprocessing.Pool(...).imap_unordered(..., chunksize=1)
  • Progress reporting: parallel mode reports subtree processing progress (Processing subtrees), while sequential mode reports pattern generation progress (Making patterns)
  • Logging includes expansion and mode details, e.g. Expanding to depth ... and Parallel search (dynamic): ...