.gitignore

# Standard
.svn/
*.tmp
*~
.DS_Store
src/ocl/opencl_kernels.h
*.cxx
tags
.ctags
*.plist
.vscode/

# CMake generated files
CMakeCache.txt
CMakeFiles
Makefile
cmake_install.cmake
install_manifest.txt
cmake_uninstall.cmake
CMakeScripts/
HyPhy.build/
HyPhy.xcodeproj


# HYPHY binaries
hyphy
HYPHYMP
HYPHYMPI
HyPhy.app
iHyPhyDebug.app
HYPHYDEBUG
HYPHYDEBUG.dSYM

# GTEST 
HYPHYGTEST
contrib/gtest-1.7.0/libgtest.a
contrib/gtest-1.7.0/CMakeScripts
contrib/gtest-1.7.0/HyPhy.build
contrib/gtest-1.7.0/gtest.xcodeproj/
gmon.out

#HyPhy generated files
**/*.log*
**/*.log*
**/data/*.samples*
messages.log
errors.log
tests/hbltests/libv3/data/CD2.nex.*.json
tests/hbltests/data/tempFileTesting*
tempOutput.txt
tests/hbltests/data/CD2*.json
testMethodOutput
tests/hbltests/data/CD2*.cache
test


#Utility function
remake_hyphy.sh
remake_hyphydebug.sh

docs.md