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bugfix: a plain pip install pestifer (without the optional ligand-paramgen extra) crashed on every CLI invocation with ModuleNotFoundError: No module named 'dimorphite_dl'; the optional rdkit and dimorphite_dl dependencies were imported at module load time in charmmff.ligand_paramgen.protonation and charmmff.ligand_paramgen.mol2_writer, and since subcommands/__init__.py eagerly imports the make-ligand-mol2 subcommand at startup, those imports ran for every command. The imports are now lazy (deferred into the functions that use them) and raise a clear pip install pestifer[ligand-paramgen] hint when actually needed
bugfix: the dependencies array in pyproject.toml was missing its closing ]