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cpockrandtcpockrandt
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PhyloCSF++ initial version (squashed commits)
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‎.gitignore

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.idea
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external
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build
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cmake-build-*

‎.travis.yml

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sudo: true
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language: cpp
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matrix:
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include:
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##########################################################################
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# GCC on Linux
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##########################################################################
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# Debug builds on linux (gcc) with sanitizer, TODO: add coverage
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- os: linux
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dist: bionic
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compiler: gcc-9
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addons:
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apt:
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sources: ['ubuntu-toolchain-r-test']
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packages: ['cmake', 'g++-9', 'libgsl0-dev']
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# ubuntu toolchain does not contain the latest bugfixes for /usr/bin/ld
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env: CXX=g++-9 CMAKE_ARGS="-DCMAKE_BUILD_TYPE=Debug" CMAKE_CXX_FLAGS="-fsanitize=address -fno-omit-frame-pointer" THREADS=1 # -fuse-ld=gold
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- os: linux
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dist: xenial
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compiler: gcc-4.9
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addons:
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apt:
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sources: ['ubuntu-toolchain-r-test']
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packages: ['cmake', 'g++-4.9', 'libgsl0-dev']
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env: CXX=g++-4.9 THREADS=1
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- os: linux
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dist: bionic
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compiler: gcc-5
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addons:
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apt:
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sources: ['ubuntu-toolchain-r-test']
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packages: ['cmake', 'g++-5', 'libgsl0-dev']
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env: CXX=g++-5 THREADS=2
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- os: linux
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dist: bionic
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compiler: gcc-6
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addons:
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apt:
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sources: ['ubuntu-toolchain-r-test']
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packages: ['cmake', 'g++-6', 'libgsl0-dev']
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env: CXX=g++-6 THREADS=3
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- os: linux
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dist: bionic
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compiler: gcc-7
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addons:
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apt:
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sources: ['ubuntu-toolchain-r-test']
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packages: ['cmake', 'g++-7', 'libgsl0-dev']
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env: CXX=g++-7 THREADS=4
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- os: linux
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dist: bionic
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compiler: gcc-8
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addons:
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apt:
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sources: ['ubuntu-toolchain-r-test']
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packages: ['cmake', 'g++-8', 'libgsl0-dev']
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env: CXX=g++-8 THREADS=5
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- os: linux
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dist: bionic
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compiler: gcc-9
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addons:
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apt:
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sources: [ 'ubuntu-toolchain-r-test' ]
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packages: [ 'cmake', 'g++-9', 'libgsl0-dev' ]
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env: CXX=g++-9 THREADS=6
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- os: linux
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dist: bionic
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compiler: gcc-10
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addons:
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apt:
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sources: [ 'ubuntu-toolchain-r-test' ]
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packages: [ 'cmake', 'g++-10', 'libgsl0-dev' ]
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env: CXX=g++-10 THREADS=7
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##########################################################################
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# Clang on Linux
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##########################################################################
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# - os: linux
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# dist: xenial
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# compiler: clang-3.8
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# addons:
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# apt:
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# packages: ['cmake', 'make', 'libc++-dev', 'libomp-dev', 'clang-3.8', 'libgsl0-dev']
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# env: CXX=clang++-3.8 THREADS=8
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#
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# - os: linux
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# dist: xenial
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# compiler: clang-4.0
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# addons:
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# apt:
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# packages: ['cmake', 'make', 'libc++-dev', 'libomp-dev', 'clang-4.0', 'libgsl0-dev']
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# env: CXX=clang++-4.0 THREADS=1
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#
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# - os: linux
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# dist: bionic
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# compiler: clang-5.0
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# addons:
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# apt:
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# packages: [ 'cmake', 'make', 'libc++-dev', 'libomp-dev', 'clang-5.0', 'libgsl0-dev' ]
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# env: CXX=clang++-5.0 THREADS=2
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#
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# - os: linux
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# dist: bionic
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# compiler: clang-6.0
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# addons:
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# apt:
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# packages: [ 'cmake', 'make', 'libc++-dev', 'libomp-dev', 'clang-6.0', 'libgsl0-dev' ]
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# env: CXX=clang++-6.0 THREADS=3
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#
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# - os: linux
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# dist: bionic
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# compiler: clang-7.0
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# addons:
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# apt:
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# packages: [ 'cmake', 'make', 'libc++-dev', 'libomp-dev', 'clang-7', 'libgsl0-dev' ]
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# env: CXX=clang++-7 THREADS=4
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#
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# - os: linux
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# dist: bionic
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# compiler: clang-8.0
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# addons:
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# apt:
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# packages: [ 'cmake', 'make', 'libc++-dev', 'libomp-dev', 'clang-8', 'libgsl0-dev' ]
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# env: CXX=clang++-8 THREADS=5
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##########################################################################
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# Clang on OSX (with Xcode)
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##########################################################################
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# - os: osx
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# osx_image: xcode7.3
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# compiler: clang
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# addons:
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# homebrew:
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# packages:
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# - gsl
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# update: true
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#
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# - os: osx
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# osx_image: xcode8.3
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# compiler: clang
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# addons:
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# homebrew:
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# packages:
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# - gsl
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# update: true
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#
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# - os: osx
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# osx_image: xcode9.4
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# compiler: clang
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# addons:
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# homebrew:
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# packages:
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# - gsl
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# update: true
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#
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# - os: osx
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# osx_image: xcode10.1
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# compiler: clang
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# addons:
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# homebrew:
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# packages:
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# - gsl
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# update: true
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##########################################################################
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# GCC on OSX
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##########################################################################
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# Homebrew seems not to have the latest bugfixes :(
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# https://github.com/nest/nest-simulator/issues/486
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# - os: osx
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# osx_image: xcode8.3
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# compiler: gcc-4.9
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# before_install:
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# - brew update
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# - brew install [email protected]
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# - sudo xcode-select --switch /Applications/Xcode.app/Contents/Developer/
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# - sudo xcode-select -s /Library/Developer/CommandLineTools
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# install: export CXX="g++-4.9"
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#
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# - os: osx
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# osx_image: xcode8.3
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# compiler: gcc-5
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# before_install:
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# - brew update
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# - travis_wait 60 brew install gcc@5
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# - sudo xcode-select --switch /Applications/Xcode.app/Contents/Developer/
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# - sudo xcode-select -s /Library/Developer/CommandLineTools
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# install: export CXX="g++-5"
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# - os: osx
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# osx_image: xcode8.3
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# compiler: gcc-6
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# before_install:
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# - brew update
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# - travis_wait 60 brew install gcc@6
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# install: export CXX="g++-6"
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#
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# - os: osx
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# osx_image: xcode8.3
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# compiler: gcc-7
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# before_install:
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# - brew update
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# - travis_wait 60 brew install gcc@7
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# install: export CXX="g++-7"
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#
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# - os: osx
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# osx_image: xcode8.3
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# compiler: gcc-8
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# before_install:
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# - brew update
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# - travis_wait 60 brew install gcc@8
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# install: export CXX="g++-8"
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script:
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- mkdir -p build && cd build
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- cmake .. ${CMAKE_ARGS} -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -Werror"
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- make VERBOSE=1
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- cd ..
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- ./build/phylocsf++
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- test/tests.sh ${THREADS}

‎CMakeLists.txt

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cmake_minimum_required(VERSION 3.2)
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string(ASCII 27 Esc)
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set(ColourBold "${Esc}[1m")
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set(ColourReset "${Esc}[m")
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set(ColourRed "${Esc}[31m")
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include(ExternalProject)
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message("${ColourBold}Compiler Detection${ColourReset}") # This needs to go before "project ()".
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project(PhyloCSF++ CXX)
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# ----------------------------------------------------------------------------
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# Compiler detection
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# ----------------------------------------------------------------------------
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# TODO: check whether older compilers work as well
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if (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
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if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9.1)
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message(FATAL_ERROR "Your GCC version is too old. Minimum version is GCC-4.9.1!")
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return()
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endif ()
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elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
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if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.6)
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message(FATAL_ERROR "Your Clang version seems too old. Please upgrade to 3.8.0 or use GCC.")
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return()
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elseif (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.8)
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message(WARNING "Your Clang version is too old, you will not have parallelism! Upgrade to 3.8.0 or newer.")
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endif ()
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elseif (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
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if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 17)
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message(WARNING "Your Intel Compiler version is too old. Please upgrade to 17.0.0 or newer!")
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endif ()
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else ()
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message(WARNING "Unknown compiler, you are on your own!")
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endif ()
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message(STATUS "Compiling with ${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILER_VERSION}.")
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message(STATUS "The requirements were met.")
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# ----------------------------------------------------------------------------
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# Dependency detection
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# ----------------------------------------------------------------------------
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message("\n${ColourBold}Dependency detection${ColourReset}")
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find_package(OpenMP QUIET)
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find_package(Git)
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find_package(GSL REQUIRED)
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# TODO: don't build in source in case we have multiple build folders with different compiler flags
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ExternalProject_Add(libBigWig
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GIT_REPOSITORY "https://github.com/cpockrandt/libBigWig"
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UPDATE_COMMAND ""
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DOWNLOAD_DIR "${CMAKE_SOURCE_DIR}/external/"
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SOURCE_DIR "${CMAKE_BINARY_DIR}/libBigWig"
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BUILD_IN_SOURCE 1
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CONFIGURE_COMMAND ""
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BUILD_COMMAND ${MAKE}
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INSTALL_COMMAND ""
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)
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# Pass git hash and git date to C++ compiler as macros to include them into the help string.
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# Source: https://stackoverflow.com/a/21028226 (by Drew Noakes)
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if (GIT_FOUND)
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execute_process(COMMAND
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"${GIT_EXECUTABLE}" describe --match=NeVeRmAtCh --always --abbrev=8 --dirty
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WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
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OUTPUT_VARIABLE GIT_HASH
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ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
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execute_process(COMMAND
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"${GIT_EXECUTABLE}" log -1 --date=short --format=%cd
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WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
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OUTPUT_VARIABLE GIT_DATE
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ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DGIT_HASH=\"${GIT_HASH}\" -DGIT_DATE=\"${GIT_DATE}\"")
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endif()
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message(STATUS "These dependencies where found:")
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message( " GSL ${GSL_FOUND} ${GSL_VERSION}")
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message( " OPENMP ${OPENMP_FOUND} ${OpenMP_CXX_FLAGS}")
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message( " GIT ${GIT_FOUND} (optional)")
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if (OPENMP_FOUND)
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add_definitions(-DENABLE_OPENMP)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
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else ()
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message(WARNING "WARNING WARNING WARNING\nWARNING: OpenMP not found. PhyloCSF++ will be built without multi-threading! "
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"This is probably not what you want! Use GCC >= 4.9.1 or Clang >= 3.8.0\nWARNING WARNING WARNING")
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endif ()
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include_directories(${GSL_INCLUDE_DIRS})
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message(STATUS "The requirements were met.")
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# ----------------------------------------------------------------------------
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# Build configuration
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# ----------------------------------------------------------------------------
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message("\n${ColourBold}Build configuration${ColourReset}")
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# ----------------------------------------------------------------------------
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# Make "Release" the default cmake build type
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# ----------------------------------------------------------------------------
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if (NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE Release CACHE STRING
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"Choose the type of build, options are: Debug Release RelWithDebInfo"
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FORCE)
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endif ()
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# ----------------------------------------------------------------------------
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# Warn if cmake build type is not "Release"
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# ----------------------------------------------------------------------------
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if (NOT CMAKE_BUILD_TYPE STREQUAL Release)
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message(STATUS "${ColourRed}CMAKE_BUILD_TYPE is not \"Release\", your binaries will be slow.${ColourReset}")
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endif ()
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option(PHYLOCSFPP_NATIVE_BUILD "Architecture-specific optimizations, i.e., g++ -march=native." ON)
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if (PHYLOCSFPP_NATIVE_BUILD)
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add_definitions(-DPHYLOCSFPP_NATIVE_BUILD=1)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
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if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHOST -ipo -no-prec-div -fp-model fast=2")
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endif ()
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endif ()
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include_directories(SYSTEM ${CMAKE_BINARY_DIR}/libBigWig)
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link_directories(${CMAKE_BINARY_DIR}/libBigWig)
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message(STATUS "The following options are selected for the build:")
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message( " PHYLOCSFPP_NATIVE_BUILD ${PHYLOCSFPP_NATIVE_BUILD}")
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message(STATUS "Run 'cmake -LH' to get a comment on each option.")
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message(STATUS "Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option.")
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# ----------------------------------------------------------------------------
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# Build Setup
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# ----------------------------------------------------------------------------
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add_definitions(-DCMAKE_BUILD_TYPE="${CMAKE_BUILD_TYPE}")
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# TODO: -Wconversion
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic -DNOCURL -std=c++11 -fpermissive -DHAVE_INLINE")
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add_executable(phylocsf++ src/phylocsf++.cpp)
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add_dependencies(phylocsf++ libBigWig)
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target_link_libraries(phylocsf++ z)
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target_link_libraries(phylocsf++ gsl)
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target_link_libraries(phylocsf++ gslcblas)
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target_link_libraries(phylocsf++ BigWig)
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install(TARGETS phylocsf++ DESTINATION bin)
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message("\n${ColourBold}Finishing up${ColourReset}")

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