2023_09_5 (Q3 2023) Release

Release_2023.09.5

(Changes relative to Release_2023.09.4)

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)

Christopher Von Bargen, Jonathan Bisson, James Davidson, Hussein Faara,
Christoph Hillisch, Gareth Jones, Kevin Keating, Brian Kelley, Joos Kiener,
Marta Pasquini, Patrick Penner, Ricardo Rodriguez-Schmidt, Nate Russell,
Riccardo Vianello

New Features and Enhancements:

• add more error checking to substance groups
  (github issue #5923 from greglandrum)
• Allow sanitization to be disabled in PandasTools.LoadSDF
  (github issue #7019 from christophhillisch)
• Add Atom::hasValenceViolation (Take 2)
  (github pull #7030 from cdvonbargen)
• Please consider exposing maxBondMatchPairs param in rdRascalMCES.RascalOptions()
  (github issue #7054 from nate-russell)
• expose EmbedParameters::coordMap to Python
  (github pull #7086 from greglandrum)
• Add a 'force' option to MolStandardizer::Uncharger
  (github pull #7088 from rvianello)
• support sanitization of reaction product templates
  (github pull #7095 from greglandrum)
• Compatibility with pathlib.Path
  (github pull #7100 from PatrickPenner)
• Add option to sanitize reaction components like molecules
  (github issue #7108 from MartaPasquini)

Bug Fixes:

• Query Features: Different input format leads to a different molecule
  (github issue #6349 from kienerj)
• Unexpected non-matching ElementGraph hashes
  (github issue #6472 from jepdavidson)
• PositionVariationOp::getVariationCounts() does unnecessary copies of vectors
  (github issue #6906 from whosayn)
• "Inconsistent state" when manually sanitizing and assigning stereo when using the new stereo algorithm
  (github issue #7023 from ricrogz)
• Spacing bug in compute2DCoordsForReaction
  (github issue #7028 from KevKeating)
• Middle line in triple bond drawn to incorrect point when a wedged bond is present
  (github issue #7036 from greglandrum)
• CSharp Wrapper ExtendedQueryMol Read Access Violation
  (github issue #7069 from jones-gareth)
• Sanitizing and assigning stereo twice can change bond stereo with new stereo
  (github issue #7076 from ricrogz)
• testConrec.cpp:130 fails on ARM64
  (github issue #7083 from bjonnh-work)
• Quaternary nitrogens with hydrogens are not a candidate for stereo
  (github issue #7115 from bp-kelley)
• ReplaceBond may cause valence issues in specific edge cases
  (github issue #7128 from ricrogz)

Cleanup work:

• fix GCC 13.2 warnings about redundant move in return statement
  (github pull #7029 from rvianello)
• fix check of python version when updating Filters.cpp
  (github pull #7035 from rvianello)
• fix several warnings originating from the swig wrappers
  (github pull #7063 from rvianello)
• lock the versions of a bunch of stuff used in the CI builds
  (github pull #7082 from greglandrum)