diff --git a/CMakeLists.txt b/CMakeLists.txt index a870caf81f..cb79b16e81 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -137,7 +137,7 @@ set(RDK_PYTHON_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/rdkit") # Config variables: set(RDKit_Year "2023") set(RDKit_Month "09") -set(RDKit_Revision "2") +set(RDKit_Revision "3") set(RDKit_RevisionModifier "") set(RDKit_ABI "1") diff --git a/Docs/Book/conf.py b/Docs/Book/conf.py index 760c933ca9..9604083eba 100644 --- a/Docs/Book/conf.py +++ b/Docs/Book/conf.py @@ -54,7 +54,7 @@ # The short X.Y version. version = '2023.09' # The full version, including alpha/beta/rc tags. -release = '2023.09.2' +release = '2023.09.3' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/ReleaseNotes.md b/ReleaseNotes.md index 4e42d5f1b2..616a58ff9d 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -6,12 +6,72 @@ see your contribution acknowledged with your name, please set your name in GitHub) +Jason Biggs, Hussein Faara, Brian Kelley, Yoshinobu Ogura, Yakov Pechersky, +Ricardo Rodriguez-Schmidt, Leonid Stolbov, Paolo Tosco, Ivan Tubert-Brohman, +dehaenw ## New Features and Enhancements: + - Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism + (github issue #5819 from greglandrum) + - Support copying of GeneralizeQueryMolecules + (github issue #6851 from greglandrum) + - Enable chemist-friendly depiction of R-groups + (github pull #6866 from ptosco) + - Allow building DetermineBonds without YAeHMOP support + (github pull #6885 from greglandrum) + - Add multithreading to getBestRMS and new getAllConformerBestRMS + (github pull #6896 from greglandrum) + - switch to catch2 v3 + (github pull #6898 from greglandrum) + - minilib functions exposure: mmpa + (github pull #6902 from StLeonidas) + - Add multi-threaded versions of some MolStandardize operations + (github pull #6909 from greglandrum) + - Add (multithreaded) functions to the fingerprint generators for calculating multiple fingeprints in one call + (github pull #6910 from greglandrum) + - Add Python modules to generate stubs and automatically patch docstrings + (github pull #6919 from ptosco) ## Bug Fixes: + - MolEnumerator: use repeat counts for SRUs when present + (github issue #6429 from greglandrum) + - Double bonds should not be depicted as crossed bonds in the presence of wavy bonds + (github issue #6816 from ptosco) + - MurckoScaffold.MakeScaffoldGeneric() has issues with isotopes + (github issue #6836 from dehaenw) + - Wavy bonds in mol blocks can't be stereo enumerated + (github issue #6876 from bp-kelley) + - CDXML read of AND1 group (specifying racemic center) gets associated into an OR1 group + (github issue #6887 from pechersky) + - Segfault in JSONToMols when "commonchem" is an int + (github issue #6890 from i-tub) + - reapplyMolBlockWedging() should retain ENDDOWNRIGHT, ENDUPRIGHT dirs + (github issue #6893 from ptosco) + - MMPA FragmentMol segfaults when new stereo perception is turned on + (github issue #6900 from jasondbiggs) + - Obtaining descriptors via Descriptors.descList results in duplication of SPS. + (github issue #6928 from wsuzume) + - Some Clang-specific build instructions skip some clang compilers on mac + (github issue #6941 from whosayn) + - With new stereo, removing H from an Imine double bond does not remove bond stereo + (github issue #6944 from ricrogz) + - FindMolChiralCenters should honor RDK_USE_LEGACY_STEREO_PERCEPTION + (github issue #6945 from ricrogz) + - generateDepictionMatching2DStructure does not optimally align when refPatt!=None, allowRGroups=False, alignOnly=True + (github issue #6952 from ptosco) + - GetAtomPairFingerprint yields different rooted FP from generator + (github issue #6958 from ptosco) ## Cleanup work: + - cmake cleanup + (github pull #6814 from greglandrum) + - Deprecate some of the ancient python-based ML code + (github pull #6891 from greglandrum) + - Remove boost::regex support #6817 + (github pull #6913 from whosayn) + - Fix minimal build, allow building without boost::serialization + (github pull #6932 from greglandrum) + ## Deprecated code (to be removed in a future release): - The RDKit implementation of standard machine learning algorithms are