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.travis.yml
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# ==================================================================================================
# Header
# ==================================================================================================
# General settings
language: cpp
cache: apt
# Jobs are on linux/bionic unless specified otherwise
os: linux
dist: bionic
# We only want to run specific branches
branches:
only:
- master
- misc
# We split the jobs into stages to get a better overview
stages:
- "Default"
- "Latest"
- "Legacy"
# ==================================================================================================
# Job Matrix
# ==================================================================================================
jobs:
include:
# ==========================================================================
# trusty
# ==========================================================================
# Cannot use gcc 4.8 because of missing regex implementation.
# - name: "trusty / default / debug"
# stage: "Default"
# os: linux
# dist: trusty
# - name: "trusty / default / release"
# stage: "Default"
# os: linux
# dist: trusty
# env: BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# trusty / gcc
# --------------------------------------------------------------------------
# # Cannot use gcc 4.8 because of missing regex implementation.
# - name: "trusty / g++-4.8 / debug"
# stage: "Legacy"
# os: linux
# dist: trusty
# addons: { apt: { packages: ["g++-4.8"] } }
# env: COMPILER=g++-4.8
- name: "trusty / g++-4.9 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-4.9"] } }
env: COMPILER=g++-4.9
- name: "trusty / g++-5 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-5"] } }
env: COMPILER=g++-5
- name: "trusty / g++-6 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-6"] } }
env: COMPILER=g++-6
- name: "trusty / g++-7 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-7"] } }
env: COMPILER=g++-7
- name: "trusty / g++-8 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-8"] } }
env: COMPILER=g++-8
- name: "trusty / g++-9 / debug"
stage: "Latest"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-9"] } }
env: COMPILER=g++-9
- name: "trusty / g++-9 / release"
stage: "Latest"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-9"] } }
env: COMPILER=g++-9 BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# trusty / clang
# --------------------------------------------------------------------------
# # Cannot use clang++ 3.5 because exception_ptr is not yet implemented.
# - name: "trusty / clang++-3.5 / debug"
# stage: "Legacy"
# os: linux
# dist: trusty
# addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.5"] } }
# env: COMPILER=clang++-3.5 OPENMP=OFF
- name: "trusty / clang++-3.6 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.6"] } }
env: COMPILER=clang++-3.6 OPENMP=OFF
# # Somehow, this just does not work... leave it for now.
# - name: "trusty / clang++-3.7 / debug"
# stage: "Legacy"
# os: linux
# dist: trusty
# addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.7", "libiomp-dev"] } }
# env: COMPILER=clang++-3.7
- name: "trusty / clang++-3.8 / debug"
stage: "Legacy"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.8", "libiomp-dev"] } }
env: COMPILER=clang++-3.8
- name: "trusty / clang++-3.9 / debug"
stage: "Latest"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.9", "libiomp-dev"] } }
env: COMPILER=clang++-3.9
- name: "trusty / clang++-3.9 / release"
stage: "Latest"
os: linux
dist: trusty
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.9", "libiomp-dev"] } }
env: COMPILER=clang++-3.9 BUILD_TYPE=RELEASE
# ==========================================================================
# xenial
# ==========================================================================
- name: "xenial / default / debug"
stage: "Default"
os: linux
dist: xenial
- name: "xenial / default / release"
stage: "Default"
os: linux
dist: xenial
env: BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# xenial / gcc
# --------------------------------------------------------------------------
# # Cannot use gcc 4.8 because of missing regex implementation.
# - name: "xenial / g++-4.8 / debug"
# stage: "Legacy"
# os: linux
# dist: xenial
# addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-4.8"] } }
# env: COMPILER=g++-4.8
- name: "xenial / g++-4.9 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-4.9"] } }
env: COMPILER=g++-4.9
- name: "xenial / g++-5 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-5"] } }
env: COMPILER=g++-5
- name: "xenial / g++-6 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-6"] } }
env: COMPILER=g++-6
- name: "xenial / g++-7 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-7"] } }
env: COMPILER=g++-7
- name: "xenial / g++-8 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-8"] } }
env: COMPILER=g++-8
- name: "xenial / g++-9 / debug"
stage: "Latest"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-9"] } }
env: COMPILER=g++-9
- name: "xenial / g++-9 / release"
stage: "Latest"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-9"] } }
env: COMPILER=g++-9 BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# xenial / clang
# --------------------------------------------------------------------------
# # Cannot use clang++ 3.5 because exception_ptr is not yet implemented.
# - name: "xenial / clang++-3.5 / debug"
# stage: "Legacy"
# os: linux
# dist: xenial
# addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.5"] } }
# env: COMPILER=clang++-3.5 OPENMP=OFF
- name: "xenial / clang++-3.6 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.6"] } }
env: COMPILER=clang++-3.6 OPENMP=OFF
# In theory, clang++-3.7 is the first version that supports OpenMP. But there are still issues,
# so we have to deactivate OpenMP here.
- name: "xenial / clang++-3.7 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.7", "libiomp-dev"] } }
env: COMPILER=clang++-3.7 OPENMP=OFF
- name: "xenial / clang++-3.8 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.8", "libiomp-dev"] } }
env: COMPILER=clang++-3.8
- name: "xenial / clang++-3.9 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.9", "libiomp-dev"] } }
env: COMPILER=clang++-3.9
- name: "xenial / clang++-4.0 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-4.0", "libiomp-dev"] } }
env: COMPILER=clang++-4.0
- name: "xenial / clang++-5.0 / debug"
stage: "Legacy"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-5.0", "libiomp-dev"] } }
env: COMPILER=clang++-5.0
- name: "xenial / clang++-6.0 / debug"
stage: "Latest"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-6.0", "libiomp-dev"] } }
env: COMPILER=clang++-6.0
- name: "xenial / clang++-6.0 / release"
stage: "Latest"
os: linux
dist: xenial
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-6.0", "libiomp-dev"] } }
env: COMPILER=clang++-6.0 BUILD_TYPE=RELEASE
# ==========================================================================
# bionic
# ==========================================================================
- name: "bionic / default / debug"
stage: "Default"
os: linux
dist: bionic
- name: "bionic / default / release"
stage: "Default"
os: linux
dist: bionic
env: BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# bionic / gcc
# --------------------------------------------------------------------------
# # Cannot use gcc 4.8 because of missing regex implementation.
# - name: "bionic / g++-4.8 / debug"
# stage: "Legacy"
# os: linux
# dist: bionic
# addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-4.8"] } }
# env: COMPILER=g++-4.8
- name: "bionic / g++-5 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-5"] } }
env: COMPILER=g++-5
- name: "bionic / g++-6 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-6"] } }
env: COMPILER=g++-6
- name: "bionic / g++-7 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-7"] } }
env: COMPILER=g++-7
- name: "bionic / g++-8 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-8"] } }
env: COMPILER=g++-8
- name: "bionic / g++-9 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-9"] } }
env: COMPILER=g++-9
- name: "bionic / g++-10 / debug"
stage: "Latest"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-10"] } }
env: COMPILER=g++-10
- name: "bionic / g++-10 / release"
stage: "Latest"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["g++-10"] } }
env: COMPILER=g++-10 BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# bionic / clang
# --------------------------------------------------------------------------
- name: "bionic / clang++-3.9 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-3.9", "libiomp-dev"] } }
env: COMPILER=clang++-3.9
- name: "bionic / clang++-4.0 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-4.0", "libiomp-dev"] } }
env: COMPILER=clang++-4.0
- name: "bionic / clang++-5.0 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-5.0", "libiomp-dev"] } }
env: COMPILER=clang++-5.0
- name: "bionic / clang++-6.0 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-6.0", "libiomp-dev"] } }
env: COMPILER=clang++-6.0
- name: "bionic / clang++-7 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-7", "libiomp-dev"] } }
env: COMPILER=clang++-7
- name: "bionic / clang++-8 / debug"
stage: "Legacy"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-8", "libiomp-dev"] } }
env: COMPILER=clang++-8
- name: "bionic / clang++-9 / debug"
stage: "Latest"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-9", "libiomp-dev"] } }
env: COMPILER=clang++-9
- name: "bionic / clang++-9 / release"
stage: "Latest"
os: linux
dist: bionic
addons: { apt: { sources: ["ubuntu-toolchain-r-test"], packages: ["clang-9", "libiomp-dev"] } }
env: COMPILER=clang++-9 BUILD_TYPE=RELEASE
# ==========================================================================
# osx
# ==========================================================================
# Need to deactivate OpenMP for default build, as standard osx clang does not support it.
- name: "osx / default / debug"
stage: "Default"
os: osx
env: OPENMP=OFF
- name: "osx / default / release"
stage: "Default"
os: osx
env: OPENMP=OFF BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# osx versions / apple
# --------------------------------------------------------------------------
# Default apple clang does not support openmp, so deactivate it here.
- name: "osx / xcode6.4 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode6.4
env: OPENMP=OFF
- name: "osx / xcode7.3 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode7.3
env: OPENMP=OFF
- name: "osx / xcode8 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode8
env: OPENMP=OFF
- name: "osx / xcode8.3 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode8.3
env: OPENMP=OFF
- name: "osx / xcode9 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode9
env: OPENMP=OFF
- name: "osx / xcode9.2 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode9.2
env: OPENMP=OFF
- name: "osx / xcode9.3 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode9.3
env: OPENMP=OFF
- name: "osx / xcode9.4 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode9.4
env: OPENMP=OFF
- name: "osx / xcode10 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode10
env: OPENMP=OFF
- name: "osx / xcode10.1 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode10.1
env: OPENMP=OFF
- name: "osx / xcode10.2 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode10.2
env: OPENMP=OFF
- name: "osx / xcode10.3 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode10.3
env: OPENMP=OFF
- name: "osx / xcode11 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode11
env: OPENMP=OFF
- name: "osx / xcode11.1 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode11.1
env: OPENMP=OFF
- name: "osx / xcode11.2 / apple / debug"
stage: "Legacy"
os: osx
osx_image: xcode11.2
env: OPENMP=OFF
- name: "osx / xcode11.3 / apple / debug"
stage: "Latest"
os: osx
osx_image: xcode11.3
env: OPENMP=OFF
- name: "osx / xcode11.3 / apple / release"
stage: "Latest"
os: osx
osx_image: xcode11.3
env: OPENMP=OFF BUILD_TYPE=RELEASE
# --------------------------------------------------------------------------
# osx versions / clang
# --------------------------------------------------------------------------
# Here, we install llvm and openmp explicityly, to test that as well.
# As of now (April 2020), travis homebrew is broken and needs to run `update` before it is able
# to install anything. However, for the older versions of osx, the update takes longer than
# travis max job time, so we cannot do this. That means, we cannot install llvm and libomp to
# get OpenMP support. Without llvm, these runs are the same as the above apple clang runs,
# and hence, for now, we can deactivate all of them. See
# https://travis-ci.community/t/macos-build-fails-because-of-homebrew-bundle-unknown-command/7296/10
# - name: "osx / xcode6.4 / clang / debug"
# stage: "Legacy"
# os: osx
# osx_image: xcode6.4
# addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
#
# - name: "osx / xcode7.3 / clang / debug"
# stage: "Legacy"
# os: osx
# osx_image: xcode7.3
# addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
#
# - name: "osx / xcode8 / clang / debug"
# stage: "Legacy"
# os: osx
# osx_image: xcode8
# addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
#
# - name: "osx / xcode8.3 / clang / debug"
# stage: "Legacy"
# os: osx
# osx_image: xcode8.3
# addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
#
# - name: "osx / xcode9 / clang / debug"
# stage: "Legacy"
# os: osx
# osx_image: xcode9
# addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
#
# - name: "osx / xcode9.2 / clang / debug"
# stage: "Legacy"
# os: osx
# osx_image: xcode9.2
# addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode9.3 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode9.3
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode9.4 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode9.4
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode10 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode10
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode10.1 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode10.1
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode10.2 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode10.2
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode10.3 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode10.3
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode11 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode11
addons: { homebrew: { packages: ["llvm", "libomp"], update: true } }
- name: "osx / xcode11.1 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode11.1
addons: { homebrew: { packages: ["llvm", "libomp"] } }
- name: "osx / xcode11.2 / clang / debug"
stage: "Legacy"
os: osx
osx_image: xcode11.2
addons: { homebrew: { packages: ["llvm", "libomp"] } }
- name: "osx / xcode11.3 / clang / debug"
stage: "Latest"
os: osx
osx_image: xcode11.3
addons: { homebrew: { packages: ["llvm", "libomp"] } }
- name: "osx / xcode11.3 / clang / release"
stage: "Latest"
os: osx
osx_image: xcode11.3
addons: { homebrew: { packages: ["llvm", "libomp"] } }
env: BUILD_TYPE=RELEASE
# ==========================================================================
# windows
# ==========================================================================
# Too many errors for now. Maybe later.
# - name: "windows / default"
# stage: "Default"
# os: windows
# env: ZLIB=OFF OPENMP=OFF
# ==========================================================================
# Exclude
# ==========================================================================
exclude:
# Shortcuts to not have to comment out the whole matrix above for travis debugging.
# - os: windows
# - os: osx
# - os: linux
# - dist: trusty
# - dist: xenial
# - dist: bionic
# - stage: "Default"
# - stage: "Latest"
# - stage: "Legacy"
# ==================================================================================================
# Install
# ==================================================================================================
# htslib needs autotools for compiling. Unfortunately, travis and homebrew don't work well together
# when using a normal `brew` command (see commented lines below; homebrew tries to update itself
# before running the brew command first, and fails...), but luckily travis provides a mechanism
# to still install autotools on osx.
addons:
homebrew:
packages:
- autoconf
before_install:
# --------------------------------------------------------------------------
# Toolchain
# --------------------------------------------------------------------------
# List available gcc and clang versions
# - apt-cache pkgnames g++ | sort
# - apt-cache pkgnames clang | sort
# install ubuntu toolchain
- |
if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
echo "adding toolchain"
sudo apt-get install -y software-properties-common
sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
sudo apt-get update -qq
fi
# install htslib required build tools
- |
if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
# sudo apt-get install autoheader autoconf
# sudo apt-get install zlib1g zlib1g-dev libbz2 libbz2-dev liblzma liblzma-dev
sudo apt-get install autoconf
sudo apt-get install zlib1g zlib1g-dev bzip2 liblzma-dev
fi
# Tests for autotools on osx. Doesn't work, because of travis...
# - |
# if [ "$TRAVIS_OS_NAME" == "osx" ]; then
# # sudo brew update-reset
# # sudo brew update
# # brew update-reset
# brew update
# brew install autoconf
# # xcode-select --install
# # brew install automake libtool zlib-devel libbz2-devel liblzma-dev
# fi
# --------------------------------------------------------------------------
# Paths and Environment
# --------------------------------------------------------------------------
# The following homebrew packages are not on the path by default. We need to prepend them to the
# path explicitly, so that clang can find OpenMP.
# set llvm path
- |
if [ "$TRAVIS_OS_NAME" == "osx" ]; then
echo "exporting llvm path"
export PATH="$(brew --prefix llvm)/bin:$PATH";
# To use OpenMP on Mac, we need custom clang versions. So, we need to set custom paths here.
if [ "${OPENMP}" != "OFF" ]; then
export COMPILER=/usr/local/opt/llvm/bin/clang++
export CFLAGS="-I /usr/local/include -I/usr/local/opt/llvm/include"
export CXXFLAGS="-I /usr/local/include -I/usr/local/opt/llvm/include"
export LDFLAGS="-L /usr/local/lib -L/usr/local/opt/llvm/lib"
fi
# Bugfix for https://github.com/Homebrew/homebrew-core/issues/52461-mlinker-version=450
# Otherwise, we get "ld: unknown option: -platform_version"
if [[ "${TRAVIS_OSX_IMAGE}" == "xcode10.2" || "${TRAVIS_OSX_IMAGE}" == "xcode10.3" ]]; then
export CXXFLAGS="${CXXFLAGS} -mlinker-version=450"
export LDFLAGS="${LDFLAGS} -mlinker-version=450"
fi
fi
# We need a few backs and forths between the variables, in the following order:
# 1. For default builds, COMPILER is not set, so we use CXX instead.
# 2. We also need to set CXX, as travis is so nice as to override this otherwise.
- if [[ "${COMPILER}" == "" ]]; then COMPILER=${CXX}; fi
- export CXX=${COMPILER}
install:
# --------------------------------------------------------------------------
# Directories
# --------------------------------------------------------------------------
# Dependencies required by the CI are installed in ${TRAVIS_BUILD_DIR}/ci/
- DEPS_DIR="${TRAVIS_BUILD_DIR}/ci"
- mkdir -p "${DEPS_DIR}"
- cd "${DEPS_DIR}"
# --------------------------------------------------------------------------
# Clang libc++
# --------------------------------------------------------------------------
# clang install libc++
# based on https://github.com/ldionne/hana/blob/master/.travis.yml
- |
LLVM_INSTALL=${DEPS_DIR}/llvm/install
if [[ "${TRAVIS_OS_NAME}" == "linux" && "${CXX%%+*}" == "clang" ]]; then
if [[ "${CXX}" == "clang++-3.5" ]]; then LLVM_VERSION="3.5.1";
elif [[ "${CXX}" == "clang++-3.6" ]]; then LLVM_VERSION="3.6.2";
elif [[ "${CXX}" == "clang++-3.7" ]]; then LLVM_VERSION="3.7.1";
elif [[ "${CXX}" == "clang++-3.8" ]]; then LLVM_VERSION="3.8.1";
elif [[ "${CXX}" == "clang++-3.9" ]]; then LLVM_VERSION="3.9.1";
elif [[ "${CXX}" == "clang++-4.0" ]]; then LLVM_VERSION="4.0.1";
elif [[ "${CXX}" == "clang++-5.0" ]]; then LLVM_VERSION="5.0.2";
elif [[ "${CXX}" == "clang++-6.0" ]]; then LLVM_VERSION="6.0.1";
elif [[ "${CXX}" == "clang++-7" ]]; then LLVM_VERSION="7.0.1";
elif [[ "${CXX}" == "clang++-8" ]]; then LLVM_VERSION="8.0.0";
elif [[ "${CXX}" == "clang++-9" ]]; then LLVM_VERSION="9.0.0";
else
echo "Unknown clang version ${CXX}"
exit 1
fi
# bionic clang 3.9 and 4.0 miss a file in their libstdc++, hence linking fails
# solution from https://github.com/carla-simulator/carla/issues/503#issuecomment-397658790
if [[ "${TRAVIS_DIST}" == "bionic" ]] && [[ "${CXX}" == "clang++-3.9" || "${CXX}" == "clang++-4.0" ]]; then
sudo ln -s /usr/include/locale.h /usr/include/xlocale.h
fi
if [[ "${TRAVIS_DIST}" == "bionic" ]] ; then
# Tests to get clang to compile with libc++ instead of libstdc++ on bionic.
# Did not work after several tries, so for now, we just compile with the given standard
# library. After all, we are interested in whether our code compiles - the standard library
# implementation should not change that.
:
# export CXXFLAGS="-isystem /usr/local/include/c++/v1 -stdlib=libc++ -nostdinc++"
# export LDFLAGS="-L /usr/local/lib -L /usr/local/lib/c++/v1 -l c++ -l c++abi"
# export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib/c++/v1"
# export CXXFLAGS="-stdlib=libc++ -nostdinc++"
# export LDFLAGS="-l c++ -l c++abi"
else
LLVM_URL="http://llvm.org/releases/${LLVM_VERSION}/llvm-${LLVM_VERSION}.src.tar.xz"
LIBCXX_URL="http://llvm.org/releases/${LLVM_VERSION}/libcxx-${LLVM_VERSION}.src.tar.xz"
LIBCXXABI_URL="http://llvm.org/releases/${LLVM_VERSION}/libcxxabi-${LLVM_VERSION}.src.tar.xz"
mkdir -p llvm llvm/build llvm/projects/libcxx llvm/projects/libcxxabi
travis_retry wget -O - ${LLVM_URL} | tar --strip-components=1 -xJ -C llvm
travis_retry wget -O - ${LIBCXX_URL} | tar --strip-components=1 -xJ -C llvm/projects/libcxx
travis_retry wget -O - ${LIBCXXABI_URL} | tar --strip-components=1 -xJ -C llvm/projects/libcxxabi
(cd llvm/build && cmake .. -DCMAKE_INSTALL_PREFIX=${LLVM_INSTALL})
(cd llvm/build/projects/libcxx && make install -j2)
(cd llvm/build/projects/libcxxabi && make install -j2)
export CXXFLAGS="-isystem ${LLVM_INSTALL}/include/c++/v1"
export LDFLAGS="-L ${LLVM_INSTALL}/lib -l c++ -l c++abi"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${LLVM_INSTALL}/lib"
fi
fi
# --------------------------------------------------------------------------
# htslib
# --------------------------------------------------------------------------
# install htslib --> not needed any more, as we use a locally installed htslib now, see CMakeLists.txt
# - |
# HTSLIB_INSTALL=${DEPS_DIR}/htslib
# git clone --recursive https://github.com/samtools/htslib.git ${HTSLIB_INSTALL}
# cd ${HTSLIB_INSTALL}
# git checkout bd133acf51498431a5c7dfd8aa06ce17ec6d3b96
# autoheader
# autoconf
# ./configure
# make
# sudo make install
# if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
# sudo ldconfig
# # cd /usr/local/lib/
# # sudo ln -s libhts.so libhts.so.3
# fi
# ==================================================================================================
# Script
# ==================================================================================================
before_script:
# --------------------------------------------------------------------------
# Info Output
# --------------------------------------------------------------------------
# travis environment
- echo "PATH = $PATH"
- echo "HOME = $HOME"
- echo ${CXX}
- echo ${COMPILER}
- ${CXX} --version
- ${COMPILER} --version
- cmake --version
# export cmake variables
# in this CI environment, we default to building debug, so that we do not have to set that
# for the majority of the jobs in the build matrix, and only set to release if the env is set.
- export GENESIS_DEBUG=ON
- export GENESIS_USE_OPENMP=ON
- export GENESIS_USE_ZLIB=ON
- if [[ "${BUILD_TYPE}" == "RELEASE" ]]; then export GENESIS_DEBUG=OFF; fi
- if [[ "${OPENMP}" == "OFF" ]]; then export GENESIS_USE_OPENMP=OFF; fi
- if [[ "${ZLIB}" == "OFF" ]]; then export GENESIS_USE_ZLIB=OFF; fi
script:
# --------------------------------------------------------------------------
# Build Script
# --------------------------------------------------------------------------
# set up directories
- cd "${TRAVIS_BUILD_DIR}"
- mkdir build
- cd build
# build
- cmake -DCMAKE_CXX_COMPILER=${COMPILER} -DGENESIS_USE_OPENMP=${GENESIS_USE_OPENMP} -DGENESIS_USE_ZLIB=${GENESIS_USE_ZLIB} ..
- make -j 2
- cd ..
# run tests
- |
if [[ "${BUILD_TYPE}" != "RELEASE" ]]; then
./bin/test/genesis_tests
fi