* fixleak in CIP labels catch test
* fix leak in Murtagh clustering
* do not leak writers in streambuf
* fix leaks in fingerprintgeneratorwrapper
* remove 'minor leak' comments
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)
* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest
* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods
* patched sources
* address residual few remarks
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* start MaeWriter class
* start Wrapping MaeWriter
* mol -> mae block conversion
* copy general properties, except stereo
* improve docstrings
* Fix property filtering
* fail if no atoms; do not write empty bond blocks
* update atom indexes in bond block
* Fixes in MaeMolSupplier: check for duplicate bond definitions, stip property prefixes.
* add some tests
* adjust access, make dp_writer unique_ptr
* make Mol Writers non copyable
* extract bond translation to mapBond
* add write overload with heavy atom color arg
* forward declare mae::Writer, reverse CMakeFile changes
* revert the property filtering "fix"
* add some Python tests
* fix the windows build
* implement getText() static method
* mark the close() method as override
* locally undefine RDK_BUILD_MAEPARSER_SUPPORT
* Add context managers for writers
Allow calling close() on already closed Writers
Fixes#2217
* add a close method to MolSuppliers
* modernize the way we handle presence/absence of MAEPARSER support
* add context managers to suppliers
* changes in response to review
* some cleanup
* more cleanup
* auto generate coords in mol block writer if includeChirality = True
* default to include chirality when writing mol blocks/files
* make isomeric smiles the default; note that not all tests are passing at the moment
* update a reaction test
* update expected cartridge search results
at this point all python, c++, and cartridge tests pass
* docs
* update incompatibility docs
* update doctests
* these now build
* minor example update
* update expected c++
* typo
* make allowCXSMILES=true the default
* add auto perception of chirality when reading 3D structures from mol blocks
* explain changes in release notes
* further doc update
