* Speed up GetProp Python keyerrors
A common pattern _in Python_ for checking for the presence or
absence of a key is:
try:
return mol.GetProp('mykey')
except KeyError:
return None
Shockingly, this is really slow with boost python objects! I was
recently profiling a workflow and 90% of the time or more was
spent in failed GetProp calls (mostly on bonds, some on atoms
or mols).
I sped up the workflow by protecting the calls using HasProp. But
I think this is a silly trap we've set for our users.
The problem comes because boost::python uses a C++ exception to
indicate that there is already a Python exception set. In C++,
exceptions are slow - they require unrolling a stack. In Python,
exceptions are about the same speed as any other control flow!
This commit speeds up GetProp failures by circumventing the
boost throw_exception_already_set() mechanism.
In my testing, this speeds up failed GetProp substantially:
* Factor of 1000x on Mac
* Factor of 40x on Linux
* Update typed GetXXXProp to bypass boost exceptions
Based on PR #8372
Updates the typed GetIntProp, GetDoubleProp, etc to bypass C++
exceptions in access. This speeds up missing key errors
significantly - for instance, calling mol. GetIntProp with a
missing prop 100,000 times:
Before: 28s
After: 0.05s
* - 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>
* Optimize GetPropsFromDict, use tags for conversion, not the try and fail technique
* Autoconvert strings to ints and bools if possible
* Add autoConvert option to GetPropsAsDict default=true
* Update Code/GraphMol/Wrap/props.hpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* change autoConvert to autoConvertStrings, add failed datatype conversion notices
* Fix Invariant usage
* Fix namespace for string
* Add GetProp(key, autoConvert) to allow for converting only what you want
* Make TestSetProps private
* Get _TestSetProps from rdmolops
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* do not throw in desctructor
* remove unused var; reserve
* provide operator= for DiscreteValueVect
* provide operator= for SparseIntVect
* remove unknown 'omp' #pragmas; refactor loop
* remove unused var
* remove unused variables
* give EmbeddedAtom a default constructor & early exit on self assignç
* handle unused vars/args
* catch exception by ref
* address unused args
* fix signed type comparison; refactor extra checks
* remove unused variable
* suppress switch fallthtough warning
* handle signed type comparison
* handle signed type comparison
* potentially uninitialized vars
* fix abs() of bool
* unused vars in catch statements
* remove unused variables
* python::list returns will be copied
* give ValidationMethod constructor & virtual destructor
* remove extra semicolon
* 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
* first steps towards StructureGroups being editable in Python
* typo fix
* Add initial features to allow editing SGroups from Python.
* update test
* typo
