* c++20 builds working
* get MolStandardize building with clang19
* get FMCS building with clang-19
* set cxx version to c++20
* remove a few more compiler warnings
* bump min boost version, CI cleanup
* boost 1.81 is not available from conda-forge
* remove unused constants
* bump linux version for CI
* remove another unused variable
* fix (hopefully) cartridge CI builds
* simplify cartridge environment
* try postgresql14 in CI
* start the postgresql service
* change the columns used in the pandastools nbtest
* remove missed merge conflict artifact
* get github4823 test to pass with numpy 2.2
* remove a compiler warning/error with g++13
* refactor the code to determine whether or not an atom is in brackets
* move the definition of isMetal to QueryOps
* atoms bound to metals in SMILES should always be in square brackets
Implementation and some test updates
needs confirmation that all of tests run
* basic tests pass
* java tests pass
* update js tests
* doc updates
* Update Code/GraphMol/catch_graphmol.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Update Code/GraphMol/SmilesParse/test.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* finish fixing tests
* bump yaehmop version to allow compilation to work
---------
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* - 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>
* switch to basic cmake from external project
the external project stuff in cmake is overly opaque
* enable yaehmop builds in CI
* disable building of the yaehmop binary
* Update External/YAeHMOP/CMakeLists.txt
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* revert duplicate chunk in release notes
* replace deprecated ifdefs
This one gets rid of USE_BUILTIN_POPCNT and RDK_THREADSAFE_SS
use RDK_OPTIMIZE_POPCNT or RDK_BUILD_THREADSAFE_SSS instead
* get rid of BUILD_COORDGEN_SUPPORT from ROMol.i
* fix a stupid typo
* update release notes
* slow steps towards a string_view experiment
* Move first set of file-handling code to use string_view
This is about 12% faster on my machine
* oops, yaehmop had not been updated to C++17
* start moving v3000 over
* disable storing string_views in Dicts.
* a bit more optimization
* get windows builds working
* fix a couple leaks in the test code
* changes in response to review
* changes suggested in review
+ more refactoring
* fix an oversight
* remove another one
* remove debugging numbers
* - fix non-threaded *nix builds that currently fail because
boost flyweight introduces a dependency on pthreads
- make sure that mutexes and futures are only used when
RDK_BUILD_THREADSAFE_SSS is ON
- fix SubstructMatch failing test when RDK_BUILD_THREADSAFE_SSS is OFF
due to misplaced #ifdef's
- rename RDK_TEST_MULTITHREADED to RDK_THREADSAFE_SSS in inchi.cpp
(which is not a test)
* - the limitexternal Linux build is now single-threaded so we make
sure single-threaded builds do not break in the future
(suggestion from Greg)
* reverted unnecessary change to Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* fix leak in testConformerParser
* fix leaks in testMultithreadedMolSupplier
* fix leak in catch_graphmol
* pass build type to YAEHMOP
* cleanup fragments in CoordGen minimizeOnly
* fix leaking ConjElectrons stack in res mol supplier
* avoid double delete
* do not delete 'this'; clean ce not added to map
* delete mol if Multithreaded SD readMolProps throws
* fix typo
* fix typo in comment
* 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
* 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
