* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* add reference input/output files for yaehmop
* orbital energies, overlap matrix, and hamiltonian on the C++ side
* add the python wrappers for the new functions
* 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
* add the ring decomposer lib (temporarily?)
* simplify makefile
* very basics work
* backup
* basics working
* builds and basic tests pass
* get this building again
* expose the ring families
* add tests on the python side
* make the pywrapper for this optional
* remove some extra bits
* cleanup
* switch to using RDL as an external project
* make sure this still works if we do not use the URF code
* remove BUILD_ALWAYS
* fix linkage of Java wrapper and cartridge (hopefully)
* fix cmake for wrappers (hopefully)
* forgot a semicolon
* try to force URF lib to build first
* improve memory management and interface
* fix dependency specifier
* make pointer initialization explicit
This may not be necessary, but it feels safer.
* not pleasing and needs to be cleaned up
but it builds
* not pleasing and needs to be cleaned up
but it builds
* cleanup in preparation for merging
* cleanup in preparation for merging
* switch to rareylab repo
* fix updated copyright date
* Fix updated copyright date
* switch to a specific library tag
Co-Authored-By: Florian Flachsenberg <flachsenberg@zbh.uni-hamburg.de>
* change in response to review
* add linux_java build
* trigger azure pipelines builds on dev/ branches
* make sure boost::iostreams gets linked in the SWIG wrappers
* updates to get static boost builds working on mac
* update linux a bit and add mac build
* forgot to save the mac file
* install version of boost with -fPIC
* try to force use of the boost installed in /usr
* typo
* add library hint
* diagnosing a failing build
* be explicit about CXX version
* try to force use of the system compilers
instead of the ones from conda
* stop using conda
* typp
* re-enable full build
* disable the appveyor builds
* stub for YAeHMOP integration
* switch to using catch for the test
* first steps towards calling from rdkit
* switch to using some smart pointers
* runs, but has unpredictable seg faults. Needs valgrinding
* cleanup
* allow hacky linux builds too
* start using unique_ptrs for memory management
* don't find princ axes by default
Support probably isn't compiled in.
* save computed properties
* additional cleanup
* start working on a smarter way to get the code
* start making the cmake externalproject support work
* seems to work
* does not work yet
* this actually seems to build and work on linux
* theoretically more robust
* handle the parameter file
* first wrapper
* try to get mac builds working too
* initial pass at including reduced charge and overlap population matrices
* update docs
* backup commit
* switch to using cmake to handle the C++ spec
* switch to using a results object for the eHT calculations
* support fermi and total E
* change to make the SWig builds work on windows
* add the wrapper. Still needs tests
* first rgd java wrapper test, does not pass
* get static builds working 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
* remove all of the "from __future__" imports
* remove the first batch of rdkit.six imports/uses
* next step of rdkit.six removal
* removing xrange, range, and some maps
* next round of removals
* next round of cleanups
* fix inchi test
* last bits of "from rdkit.six" are gone
* and the last of the six stuff is gone
* strange importlib problem
* don't use a ctab as input for the computation of 2D coordinates
Fix GitHub issue 1062.
* make sure that the output 2D coordinates are ordered correctly
* 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
* switch the catch2 handling to a normal download
the externalproject thing was not actually working on windows
* fix the includes
* <sigh>
* try switching back to normal include_directories
* push the define up to the parent scope
* Adding the RDK_BUILD_RPATH_SUPPORT build flag to specify that RDKit
should link its shared libraries using -rpath. This allows the C++
shared libraries to be loaded from python without needing
LD_LIBRARY_PATH to be set.
This assumes the user has specified CMAKE_INSTALL_PREFIX to be the
place the RDKit will be installed to as this will use absolute paths
with -rpath. More work will need to be done by any user wishing to
make rpath work with relative paths from $ORIGIN.
* Allow the catch source code to be populated directly by un-taring the source code into the proper location.
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
