* set export.h and test.h to go to the correct places in RDKitUtils
* use cmake_source_dir so cmake files are picked up in list
* use cmake_current_source_dir in MolInterchange
* use rdkit variables to place rapidjson and headers in correct places
* - avoid a large number of warnings when building MinimalLib with emscripten, which does not support SHARED
- fix indentation in CoordGen CMakeLists.txt
* disable RDK_USE_BOOST_STACKTRACE on emscripten platform
* revert change done by mistake
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* export the targets with a python dependency to a different config file
* add the forgotten file
* improve the dependency from boost components
* fix management of dependencies for RDKitPython
* fix install location for RdkitPython cmake config file
* fix finding boost components
* put libraries that depend on rdkit_py_base in the python component
* cmake modernization
- get rid of some warnings
- switch to what I hope is the correct way of doing things
- bump min cmake version to 3.16
- bump min boost version to 1.70
This builds on linux
* remove some usages of PYTHON_EXECUTABLE
* remove old-school python usage from coverage tests
* remove unused CI file
* bump boost version for windows builds to 1.84
* still trying to get the ci builds working
* typo
* eventually the CI will work
* robustify some tests
* Update CMake modules for finding flex and bison(#7590)
This will improve the executable finding procedures and allow us to
require minimum release versions. The current modules have been around
for about 15 years, and currently limits us from using newer flex
features.
* remove modules
Updated compiler id comparisons to do a regex comparison against "Clang"
instead of doing a direct string comparison. This allows us to match
compiler ids like "AppleClang"
Made the following changes
* removed RDK_USE_BOOST_REGEX cmake option and its references
* removed usage of RDKIT_USE_BOOST_REGEX macro
* removed install instructions related to boost regex
* misc adaptations/modernizations
plus a few changes to allow pytest discovery
* get the recap unittests running
* pytest config updates
* all tests pass
* integrate the pytest stuff into ctest
* integrate Projects dir
better cmake integration
* ci build env updates
* ignore more files
* remove six.py
* cleanup UnitTestPandasTools
* cleanup pytest
* remove obsolete use of rdkit.six from doctests
* update release notes
* mysterious CI fix
* add conftest to remove some tests
* remove the old python-based testing infrastructure
---------
Co-authored-by: Ric <ricrogz@gmail.com>
* fixes#4681
* fixes a few Windows build problems
* added comments to adapter.cpp to explain the changes
* get PostgreSQL to build on Windows with both MSVC and MinGW compilers
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - fixes MinGW build
- make sure that supplier istream is opened in binary mode or istream::tellg() will
report wrong offsets on MinGW builds (MSVC will make no difference)
- avoid that in MSVC conda DLL builds the libboost_*.lib static
libraries are picked by cmake instead of the boost_*.lib import libraries
by defining BOOST_ALL_DYN_LINK
* - make sure that C# wrappers build with MinGW compilers
- make sure that static builds work under Windows with both MSVC and
MinGW
* - disable building static libraries on Windows also when using MinGW compilers
- fix the C# wrapper build on Windows under both MSVC and MinGW
* reverted -DSWIGWORDSIZE64 as it was originally
* reverted -DSWIGWORDSIZE64 definition
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
- make sure that supplier istream is opened in binary mode or istream::tellg() will
report wrong offsets on MinGW builds (MSVC will make no difference)
- avoid that in MSVC conda DLL builds the libboost_*.lib static
libraries are picked by cmake instead of the boost_*.lib import libraries
by defining BOOST_ALL_DYN_LINK
* set all source code files to have native line endings
* normalized all source code line endings
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* start to add some human-readable regression-test like examples for RGD
* small examples from JMedChem
* add helper viewer
* make that generate actual JSON
* use JSON of full output for tests
move JSON generation to RGroupUtils.h
* switch to using JSON from files
* add test notebook
* add jupyter testing to the code
* add nbval to linux test env
* add notebook tests to mac and windows too
* add toJSON for columns too
* - allow defining a specific path to Cairo libraries and headers
- link against Xau library if needed
* changes in response to review
* removed the libXau bit as it is not needed
* avoid that if CMAKE_BINARY_DIR==CMAKE_SOURCE_DIR (e.g., conda builds)
export.h is overwritten at each incremental build causing the whole
RDKit to be rebult every time
* use existing CMake function so we don't have to maintain our own
with cmake 3.17.2 the original code produced the following warning:
"The package name passed to `find_package_handle_standard_args` (INCHI) does
not match the name of the calling package (Inchi). This can lead to
problems in calling code that expects `find_package` result variables
(e.g., `_FOUND`) to follow a certain pattern."
* clean up in testDatastructs
* avoid jump on unassigned mem in rxns
* set valgrind error exit code
* update suppressions
* clean up RDValue in testDict
* don't leak mol if parsing Maestro file fails
* don't leak mol if parsing PDB block fails
* cleanup leftover rxns in testReaction
* cleanup mol if CX extensions cannot be parsed
* cleanup leftover mols in smiTest1
* cleanup leftover mols in moldraw2DTest1
* cleanup leftover mols in testSubstructMatch
* make testEnumeration go easier on valgrind
* reduce R counts
* 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>
* 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
* 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
The curl file download fallback option was not saving files as
the correct filename. Instead, it used the -O option, which
saved the files using the remote's name for the file! This
was problematic for files downloaded using specification of git
sha.
