2023_09_4 (Q3 2023) Release

Release_2023.09.4

(Changes relative to Release_2023.09.3)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to
see your contribution acknowledged with your name, please set your name in
GitHub)

Jason Biggs, David Cosgrove, Tad Hurst, Gareth Jones, Axel Pahl, Paolo Tosco,
Riccardo Vianello, Nicola Zonta, skystreet8, dhibbit

New Features and Enhancements:

• Add Python modules to generate stubs and automatically patch docstrings
  (github pull #6919 from ptosco)
• Update molecular templates headers and drop bond-length tests
  (github pull #6960 from ricrogz)
• Add in place and multithread support for more of the MolStandardize code
  (github pull #6970 from greglandrum)
• Enable in-tree builds and improve overloaded constructor docstrings
  (github pull #6980 from ptosco)
• Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers
  (github pull #6991 from jones-gareth)

Bug Fixes:

• SpacialScore ignores undefined bond stereo
  (github issue #6957 from jasondbiggs)
• DetermineBonds() for PH3 yields no bonding
  (github issue #6961 from dhibbit)
• Highlights of triple bonds come out wrong
  (github issue #6968 from DavidACosgrove)
• MaeMolSupplier cannot read dummy atoms from Maestro files
  (github issue #6973 from ricrogz)
• Chem.FindMolChiralCenters function should not be sensitive to atom-map numbers
  (github issue #6975 from skystreet8)
• Parsing a Mol leaks the "_needsDetectBondStereo" property
  (github issue #6981 from ricrogz)
• SubstructMatch maxRecursiveMatches is not being honored
  (github issue #6983 from ricrogz)
• HierarchicalClusterPicker::pick() randomly fails with Invariant Violation
  (github issue #7001 from ricrogz)
• rdkit.Dbase doesn't work correctly with Python 3.12
  (github issue #7009 from rvianello)

Cleanup work:

• Drop unrequired zlib include which may break the windows build
  (github pull #6966 from ricrogz)