* remove no-op macros and dead code (pt 2)
* test failures due to whitespace changes?
* actually run the testFeatures tests
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* fixes a copy constructor issue:
In copy constructor ‘boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]’,
inlined from ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14:
/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: warning: ‘*(const boost::shared_ptr<RDKit::ROMol>*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)).boost::shared_ptr<RDKit::ROMol>::px’ may be used uninitialized [-Wmaybe-uninitialized]
416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn )
| ~~^~
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’:
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: ‘<anonymous>’ declared here
129 | ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17:
In copy constructor ‘boost::detail::shared_count::shared_count(const boost::detail::shared_count&)’,
inlined from ‘boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]’ at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72,
inlined from ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14:
/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: ‘((const boost::detail::shared_count*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)))[1].boost::detail::shared_count::pi_’ may be used uninitialized [-Wmaybe-uninitialized]
438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_)
| ~~^~~
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’:
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: ‘<anonymous>’ declared here
129 | ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Fixes a (weird) allocation warning in GCC 12
In file included from /usr/include/c++/12/bits/alloc_traits.h:33,
from /usr/include/c++/12/ext/alloc_traits.h:34,
from /usr/include/c++/12/bits/basic_string.h:39,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/streambuf:41,
from /usr/include/c++/12/bits/streambuf_iterator.h:35,
from /usr/include/c++/12/iterator:66,
from /usr/include/boost/iterator/iterator_traits.hpp:10,
from /usr/include/boost/range/iterator_range_core.hpp:26,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/detail/call_traits.hpp:15,
from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22,
from /usr/include/boost/iostreams/tee.hpp:18,
from /tmp/rdkit_builder/rdkit/Code/RDGeneral/RDLog.h:17,
from /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:11:
In function ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = pair<int, int>; _Args = {const pair<int, int>&}]’,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const std::pair<int, int>*; _ForwardIterator = std::pair<int, int>*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*; _Tp = pair<int, int>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const std::pair<int, int>*; _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/vector.tcc:808:38,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1409:17,
inlined from ‘void testReplaceCoreMatchVectMultipleMappingToCore()’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:974:17:
/usr/include/c++/12/bits/stl_construct.h:119:7: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 56 bytes into a region of size 48 overflows the destination [-Wstringop-overflow=]
119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33,
from /usr/include/c++/12/bits/allocator.h:46,
from /usr/include/c++/12/string:41:
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = std::pair<int, int>]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_CharT> >::allocate(allocator_type&, size_type) [with _Tp = std::pair<int, int>]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:378:33,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const std::pair<int, int>*; _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/vector.tcc:799:40,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1409:17,
inlined from ‘void testReplaceCoreMatchVectMultipleMappingToCore()’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:974:17:
/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset [8, 56] into destination object of size 56 allocated by ‘operator new’
137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
* finalForce maybe uninitialized in inlined copy constructor
* failure is being used uninitialized
* MaeWriter::write overrides a method of the base class without being marked 'override'
This one is annoying because it happens in an exported header, so it propagates
to any code using the header!
* otq is never used
* fix implicitly declared assignment operator warning
* variables in catch statements that are never used
* fix type (sign) mismatch warning
* drop duplicate export macro
* Most tests working
* All tests working
* Fixed tests after merge with master
* Create header and implementations for RCore
* Updated comments
* Removed old code
* DLL export for MolMatchFinalCheckFunctor
* Information line for failing Mac test
* Log replace core behaviour
* Ordering fix for OSX
* Possible fuzzer fix
* Removed debug output
* Fix unmatched user R group bug
* Code review changes
* Bug fix and ChemTransforms test
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* unused vars in bison parser cleanup
* initialization order in TopologicalTorsionGenerator
* unused params in SLN bison
* sln flex unused params
* throwing destructor in TDTWriter
* signed comparison in substructmethods
* unused input param in smiles/smarts bison
* unused ms param in sln bison
* signed comparison in FingerprintGenerator
* store return of fscanf in StructCheckerOptions
* unreferenced var in catch
* uninitialized value in FileParserUtils
* avoid override overload warning in MolDraw2DSVG
* non-final overrides in Validate.h
* unused static var in Avalon
* unused vars in catch blocks
* make AvalonTools avalonSimilarityBits & avalonSSSBits const int
* assert fscanf result in StructCheckerOptions
* 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
* Adds replaceCore function that takes a matchVect
* Fixes error reporting, adds tests
* Switches PRECONDITION to ValueError exceptions
* Fixes MatchVectType annoyance in swig. Don't know why this is necessary.
* Silences warnings
* Adds working doctests and better explanations.
* Adds useChirality to replaceCore, fixes atom ordering
n.b. when replaceDummies==False and labelByIndex==True
the indices used are the indices of the dummy atom,
previously they were the atoms the dummy was connected
to.
* Adds useChirality to the remaining functions in ChemTransforms
* Adds a mess o tests
* Fixes labelByIndex=false ordering for dummies
* Removes debugging statements
