GitLab

Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.

Updated build script to require CMake 2.8, since CMAKE_OSX_DEPLOYMENT_TARGET is not supported on 2.6.

Moved SFMT into libraries folder, and restructured it to allow multiple independent random number generators

Unify FindOpenCL.cmake files to one location, under cmake_modules.
Other changes to permit building with nvidia opencl on Windows.

Including installing Test<Platform>HarmonicBondForce tests.

Added modern findpackagehandlestandardargs technique to FindCUDA.cmake, to permit configuration on machine
with no cuda installed.

Changed link line for gpu sniffing program so it works on Windows with new single FindCuda location.

FindCUDA.cmake.

based on the FindCUDA.cmake that was in the platforms/cuda/cuda-make directory.
Setting of CUDA_NVCC_FLAGS is now in top-level CMakeLists.txt, in case I ever figure out how
to get this working with the cmake 2.8 installed system version of FindCUDA.cmake.
Before this change, there were three separate FindCUDA.cmake areas.  Now there is just one.

Downgraded recent cmake changes to ghastly compliance with cmake 2.4, for the benefit of the simtk dart server.

Modified Cuda FreeEnergy plugin to use a different windows export macro than main openmm library and cuda library.
Modified CUDA_NVCC_FLAGS to be consistent with Peter's latest version in all three locations they are defined.
Added "-Xcompiler '/MD'" to CUDA_NVCC_FLAGS on Windows to avoid link error in Cuda FreeEnergy plugin.

move the plugin to its own project.
This change might also simplify pyopenmm nightly test issues.

day when we try it on Windows.
Added "-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5" to Mac compile flags,
to possibly help run on Leopard.