* fix aliasing bug in MultithreadedSDMolSupplier
* update GeneralFileReader to v2 API
* add backwards incompatibility note
* v1 of this
* The helper function needs to be inline
* forgot the tests
* allow non-threadsafe builds
* MultithreadedMolSuppliers can now be destroyed without being used.
This was previously not possible
* add callbacks to the multithreaded readers
* document the new functions
* switch to storing the queues in unique_ptrs
* does not work
* only do those tests when in MT mode
* more generalfilereader cleanup
* tests pass
* passes tests
* extremely basic python wrapper
* better wrapper
* does not work
* tests pass
* test data
* fix failing test on ARM macs
we need to followup on why the wedging is different here
* move some stuff to the cpp file
the idea is to have the windows DLL builds not break
* fix(?) win64 linkage problems
* remove a warning in non-multi-threaded builds
* fix non-multi-threaded work
* well, at least local windows builds work
* remove duplicated code
* refactoring
simplification?
* simplify mutext handling
* review suggestions
* make sure that a full build and test can work even if boost::iostreams is not being used
Hopefully nobody every actually needs this, but as long as we supply the option, the tests should actually work
* update doctests for that change
* 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
- 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
* Fixes#3648
Code now builds without either MAEParser or coordgen integration enabled.
* add CI build with minimal dependencies
* remove doctests from the new CI build
they need the cairo support
* fixed issue #2965
* added test case for issue #2965
* fixed formatting and added comment.
* update
* General Reader files
* removed dependency on boost filesystems
* removed class
* clang-format
* added-comments
* further-cleanup
* added clang-formatting
* braces-for-if-else
* changed error messages, added option for windows file path
* fixed getFileName function
* cleanup
* option for filename without path
* further-cleanup
* added tests for determineFileFormat
* cleanup, const arguments for validate function
* init
* cleanup
* cleanup
* clang-format does not work for CMake
* added RDK_TEST_MULTITHREADED option
* add-flag
* cleanup
* Delete ConcurrentQueue.h
This PR deals with the Generalized File Reader.
* Delete testConcurrentQueue.cpp
This PR deals with the Generalized File Reader.
* no change
* concurrent queue
* print values
* Single Producer Multiple Consumer works
* cleanup
* Producer Consumer Example
* update queue methods and tests
* cleanup
* test
* fixed tests
* cleanup, updated tests
* Delete ProducerConsumer.h
* Delete testProducerConsumer.cpp
* cleanup
* futher cleanup
* changes based on feedback
* make queue non copyable
* psuedocode
* possible implementation
* untested implementation
* change class to typename
* basic-setup
* need to fix segfault
* need to fix blocking
* need to fix blocking
* need to fix blocking
* fix indentation
* one possibility
* without lambda function
* possible fix with some test cases
* performance tests
* added support for record id and item text
* cleanup
* cleanup
* fixed memory leak and added methods with tests for getting last id and item text
* cleanup
* added more test cases with different smi files
* cleanup
* SD mol supplier
* modified the parsing for SDMolSupplier
* cleanup
* cleanup
* new file for testing
* added support for reading molecule properties with tests
* thread-safe logging and exception handling
* cleanup
* without thread safe logging
* cleanup
* cleanup, modified MultithreadedSmilesMolSupplier
* cleanup, made reader and writer functions private
* move O2.sdf
* basic python wrapper with tests
* cleanup, added new methods for python wrappers
* made changes suggested by Andrew
* file and compression formats are case-insensitive
* cannot open files with gzstream
* cleanup
* possible fix for opening compressed streams (SMILES)
* removed seekg() and tellg() methods from multithreadeded suppliers
* cleanup
* test cases for python wrappers
* some wrapper cleanup
* cleanup, removed unused functions
* update the MT tests so that they actually do some work
also includes some cleanup here
* cleanup
* remove iterator_next header include
* added support for multithreaded readers
* use getNumThreadsToUse for multithreaded suppliers
* fixed documentation for multithreaded python wrappers
* commented performance test
* first draft of final evaluation report
* removed inline variables
* first draft getting started in python
* fixed typos in getting started in python
* fixed typos
* fix documentation tests
* fixed documentation tests
* added links to important files and PR
* added perfomance results
* first version of wrappers with compressed streams
* getting rid of streambuf stream method
* modified General File Reader
* make this work when building in non-threads mode
* rename a test
* rename a function in the python API
* rearrange the python test a bit
* disable the stream-based constructors in Python
* mark the multithreaded classes as experimental
Co-authored-by: greg landrum <greg.landrum@gmail.com>
