adjusting to rdkit fp generator changes #54
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…ing and pickling.
- nBits->fpSize - remove properties / overwrite setattr - adapt tests.
- moving code around for easier oversight - adding nicer dpecrecation warnings.
- add new generator functions to transformer test
- add DeprecationWarnings to not harmonized fpSize bits.
…r_changes adapting to new rdkit fingerprint generators.
…roper deprecation warnings. Only implemented in the MorganFP so far
… most flexible testing setup tbh
…, and only warnings from dependencies
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Maintenance update, with a transition from soon deprecated RDKit fingerprint calls to the newer generator based calls for Morgan, AtomPair, TopologicalTorsion and RDKitFP.
Deprecation warnings and transparent handling of deprecated keywords has been put in place, and will easen the transition for users. Most notably is the change of the nBits to fpSize keyword throughout the library. e.g.
MorganFingerprintTransformer(nBits=256)will work for now but give a warning, and should be changed toMorganFingerprintTransformer(fpSize=256)The abstract class FpsTransformer is now sharing a base class BaseFpsTransformer with the new abstract class FpsGeneratorTransformer that supports creation, pickling and automatic update of an internal generator object.
fingerprints.py has for better overview been changed to a module with single files for related fingerprints. All fingerprints can still be imported from scikit_mol,fingerprints.