* 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>
* Updated CMakeLists.txx
* Updated all examples, extended some.
* Added info about highlighting atoms.
* Added info about annotation to python getting started.
* Minor tweaks.
* Minor tweaks. Can only examine the rst in GitHub.
* Minor tweaks. Can only examine the rst in GitHub.
* get doctests working
* update an example image
* Include the GettingStartedInC++ doc in the standard docs build
* move the C++ docs after the python docs
* update backwards incompatible changes doc
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* 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
* boost::thread mostly gone... still need to get rid of once
everything compiles
* replace boost::call_once
* remove link-time dependency on boost::thread
* first pass at using async
* switch to using async everywhere
* auto generate coords in mol block writer if includeChirality = True
* default to include chirality when writing mol blocks/files
* make isomeric smiles the default; note that not all tests are passing at the moment
* update a reaction test
* update expected cartridge search results
at this point all python, c++, and cartridge tests pass
* docs
* update incompatibility docs
* update doctests
* these now build
* minor example update
* update expected c++
* typo
* make allowCXSMILES=true the default
* add auto perception of chirality when reading 3D structures from mol blocks
* explain changes in release notes
* further doc update
* New syntax to import Qt5 dependency in MolDraw2D
* In QTDemo, not necessary to import Qt explicitly because it is automatically imported through target MolDraw2D
* improve import of Cairo dependency
* Remove explicit linking of Cairo in C++ examples
* Use imported targets for Boost
* Using imported CMake targets for Eigen
* Use imported targets for Threads
* Simplify sample CMakeLists
* Remove duplication
* a couple small changes for travis
* typo
* update toolchain to trusty
* switch to requiring at least boost 1.56
* typo
* update boost dependency to pull in the build that has more libraries
* meaningless commit to trigger travis
* switch to ust libc++
* install libc++
* check abi
* try the other one; disable py27 for the moment to speed things up
* switch to c++11, that seems necessary with the conda boost builds at the moment
* re-enable python2.7
* Start of GettingStartedInC++ documentation.
* Changed GettingStartedInC++ from rst to markdown format. Added some more text.
* Added Working with Molecules to GettingStartedInC++
* Expanded on behaviour of Kekulize wrt clearing aromatic flags on atoms and bonds.
* Added section Modifying Molecules.
* More plodding progress.
* A load more documentation.
* Undid change to global CMakeLists.txt
* Minor editing of docs.
* Changed examples so they use RDBASE to find test data rather than relative
path.
* Fixed use of -std=c++ in CMakeLists.txt. Extra waffling about memory.
* Modifications to examples and documentation as requested.
* Couple of minor changes.
* Change to example11.cpp and associated text in docs.
