v0.3.1
Changed
• Migrated to MorganGenerator API: replaced deprecated GetMorganFingerprintAsBitVect / GetHashedMorganFingerprint with rdFingerprintGenerator.GetMorganGenerator across fingerprints, similarity, diversity, and sascorer modules. Also migrated AtomPair and TopologicalTorsion fingerprints.
• Smart parallelism defaults: global default changed from all cores (-1) to single-threaded (1), avoiding IPC overhead on fast commands. Heavy workloads (descriptors --all, descriptors --category) auto-scale to all cores. Users can always override with -n -1.
• Optimized README: replaced verbose per-command docs with compact help-style reference and benchmark table. Full command docs moved to docs/commands.md.
Removed
• Dead _fgs reference in fragment module (unused GetMorganFingerprint assignment)