* Speed up boost vector iterators by 300x
* Add vector testing code
* Update test
* Remove GetPosition notebook
* Move all wrapped int vectors to top level
* Grab MatchTypeVect from rdBase
* Actually wrap the vectors
* - 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>
* make sure that we can build without boost iostreams or seralization
adds some "private" variables on the python side to check for these compilation flags
* get out minimal cmake version correct
* get minimallib js building
installs an up-to-date cmake
also updates the version of boost being used for the minimallib
adds extra argument to allow the repo to be specified
* add test
* fix LogStateSetter
* fix BlockLogs() usage in Draw module
* allow BlockLogs() as a contestmgr
* move test to more suitable location
* guarantee log restoration on __exit__
* skip test if logs cannot be grabbed before block
* disable the info and debug logs by default
* adjust tests to the newly disabled logs
* add LogStateSetter
* namespace reorg
* add some tests
* remove vestigial code
* switch to using std::vector
* Support for logging via Python's logging module.
* Avoid the Python 3.9+ PyObject_CallOneArg function.
* Move logging functions to RDBase; Python logger by default; clean up tests.
* See if removing NOGIL fixes the Windows stall.
* get tests running on windows
* Reset to using C++ logging; whiespace tweaks.
* Longer timestamp grace period; try tempfile vs Windows logging stall.
* Clean up commented code; get details for log count bug.
* SubstructLibrary: Fix c++ threads calling into python
* FilterCatalog: Fix c++ threads calling into python
* Release notes; make sure Jupyter still logs to sys.stderr.
* Always use thread-local log buffers.
* de-verbosify a test
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
- switched to using std::vector<int> instead of std::list<int> for _ErGAtomTypes property
- added RegisterListConverter<std::vector<unsigned int>>
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* Fix issues with rendering fragments/smarts patterns in MolsToGridImage
* Add LogStatus and BlockLogs functionality to temporarily block logging
* Move BlockLogs to C++
* Fix kekulization errors in reactions
* Reenable tests
* Use using over typedef
* Fix comment placement
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* add overrides for what()
* translation fot KeyErrorException; update tests
* Switch all exceptions to `const char *` as a return type from message() (#4)
* switch return type of message() from std::string to const char *
* adjust one test to the new return type from message()
remove unnecessary verbosity from some tests
* fix cartridge build: update call to message().c_str()
* rebase agains master; fix another issue in cartridge build
* add deprecation note for message() and getMessage()
* amend Release notes
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* - made Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp and Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
more robust against very small coordinate variations which may induce UFF energy variations in the 1-kcal/mol range.
This was observed in a single case using the MinGW 32-bit g++ compiler. The check for identity of conformations
between single- and multi-threaded runs is now complemented by a 3D coordinate MSD check
* - lowered the energy tolerance to 1.0 kcal/mol
* - added rdkitBuild string with compile-time information
- added runtime check in Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
and Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
to use more lenient tolerances with MinGW compilers
This "lookalike" implementation is much cruder than the real thing and does not really support
enabling and disabling logs, or associating them with files, but those components were not being
particularly used in the RDKit anyway.
