2023_09_2 (Q3 2023) Release

[greglandrum]

Release_2023.09.2

(Changes relative to Release_2023.09.1)

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)

Tad Hurst, Gareth Jones, Dan Nealschneider, Ricardo Rodriguez-Schmidt, Paolo
Tosco, Rachel Walker, Meng Wu, vslashg

New Features and Enhancements:

• add maxRecursiveMatches to SubstructMatchParameters
  (github issue add maxRecursiveMatches to SubstructMatchParameters #6017 from greglandrum)
• Removed some code duplication between Depictor.cpp and common.h
  (github pull Removed some code duplication between Depictor.cpp and common.h #6799 from greglandrum)
• Add support for writing chirality and stereo in MaeWriter
  (github pull Add support for writing chirality and stereo in MaeWriter #6810 from rachelnwalker)
• Implement MinimalLib get_mcs() version that returns JSON
  (github pull Implement MinimalLib get_mcs() version that returns JSON #6812 from ptosco)
• support generalized substructure search in the SubstructLibrary
  (github pull support generalized substructure search in the SubstructLibrary #6835 from greglandrum)
• Support copying of GeneralizeQueryMolecules
  (github issue Support copying of GeneralizeQueryMolecules  #6851 from greglandrum)

Bug Fixes:

• CXSMILES: atom with labels should not also have dummyLabel property set
  (github issue CXSMILES: atom with labels should not also have dummyLabel property set #6309 from greglandrum)
• Fixes for canonicalization, and stereochemistry
  (github pull Fixes for canonicalization, and stereochemistry #6743 from tadhurst-cdd)
• MCS query incorrect when ringCompare=RingCompare.StrictRingFusion
  (github issue MCS query incorrect when ringCompare=RingCompare.StrictRingFusion #6773 from d-b-w)
• Fixes bug in get_sss_json()
  (github pull Fixes bug in get_sss_json() #6806 from ptosco)
• SWIG builds failing on Windows
  (github pull SWIG builds failing on Windows #6808 from jones-gareth)
• We should be able to run the tests without boost::iostreams
  (github issue We should be able to run the tests without boost::iostreams #6818 from greglandrum)
• Fix stereo bond corruption on RGD.
  (github pull Fix stereo bond corruption on RGD. #6832 from jones-gareth)
• Fix unclosed resource in BuildFuncGroupHierarchy
  (github pull Fix unclosed resource in BuildFuncGroupHierarchy #6846 from ricrogz)
• RGD: Fix doEnumeration true for cores that are not bundles
  (github pull RGD: Fix doEnumeration true for cores that are not bundles #6857 from jones-gareth)
• Fix build error when serialization is off.
  (github pull Fix build error when serialization is off. #6867 from vslashg)

Cleanup work:

• Switch over to using pytest to run the python tests
  (github pull Switch over to using pytest to run the python tests #5916 from greglandrum)
• Redundant variablehasCoreDummies in R-group decomposition code
  (github issue Redundant variablehasCoreDummies in R-group decomposition code #6779 from MarioAndWario)
• remove the deprecated python implementation of MolStandardize
  (github pull remove the deprecated python implementation of MolStandardize #6819 from greglandrum)
• Update CI, remove some warnings
  (github pull Update CI, remove some warnings #6882 from greglandrum)

---

This discussion was created from the release 2023_09_2 (Q3 2023) Release.

[greglandrum]

Note that this minor release includes new features. This is a change from our previous policy of only including bug fixes in minor releases and releasing new features twice a year. As with past release cycles, there should be nothing here which changes the fundamental behavior or API of the code (though bug fixes can always result in changed results).