.travis.yml

# Note: with `language: cpp`, `cache: ccache` works
# but `cache: pip` and `python:` is ignored
language: cpp
dist: bionic  # Ubuntu 18.04 LTS
cache:  # cache C/C++/pip (shared between builds)
- ccache
- pip
# No need for sudo
sudo: false

# Currently commented out as set with environment flags
# Both clang and gcc can be tested. More is the better.
#compiler:
# - clang
# - gcc

# Compilation dependencies
addons:
 apt:
  sources:
  - ubuntu-toolchain-r-test
  packages: &addons_apt_packages
  - git-core
  - build-essential
  - libhdf5-serial-dev
  - libfftw3-dev
  - python3-dev
  - python3-tk
  - libopenblas-dev
  - libatlas-base-dev
  - liblapack-dev
  - libxml2-dev
  - libarmadillo-dev
  - libgtest-dev
  - libplplot-dev
  - swig
  - ccache
  # not in whitelist
  - libxslt-dev
  - libace-dev
  # - root-system-bin

# Environment variables
# Note: On trusty we need to build Armadillo and boost ourselves (the system versions are too old)
# Note: On OSX we can't test SYSTEM_Boost=OFF due to excessive log size (https://github.com/CCPPETMR/SIRF-SuperBuild/issues/167)
# Note: currently ACE is not building correctly, so ACE is not built on any configuration https://github.com/CCPPETMR/SIRF-SuperBuild/issues/#174
# Note: on Trusty, g++-7 causes errors with the system ACE, so cannot use g++-7 or later https://github.com/CCPPETMR/SIRF-SuperBuild/issues/169
# Note: altering the matrix here will cause re-building of caches,
# so try to keep this concise to avoid need to update
# Note: the line above each `env` contains a resume of the parameters passed to cmake.
#       + or - refer to the value of the parameter affecting the specific package is passed to cmake:
#       i.e. -boost == -DUSE_SYSTEM_Boost=OFF, which means that Boost will be built.
env:
 global:
 - #STIR_BRANCH="-DSTIR_URL:STRING=https://github.com/KrisThielemans/STIR-1 -DSTIR_TAG=scatter_improvements_2"
 - BUILD_FLAGS="-DCMAKE_BUILD_TYPE=Release ${STIR_BRANCH}"
 # don't use too many threads - may crash
 - MAKEFLAGS="-j 2"
matrix:
 include:
 # linux g{cc,++}-{6,7,8}
 - os: linux
   dist: focal
   python: 3
   addons:
    apt:
     packages:
     - *addons_apt_packages
     - [g++-8, libinsighttoolkit4-dev]
   name: focal gcc8 -boost +itk +fftw3 +hdf5 +ace
   env: EXTRA_BUILD_FLAGS="-DUSE_ITK:BOOL=ON -DUSE_SYSTEM_ITK:BOOL=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON" MATRIX_EVAL="CC=gcc-8 CXX=g++-8" PYMVER=3
 - os: linux
   dist: focal
   python: 3
   addons:
     apt:
       packages:
       - *addons_apt_packages
       - [g++-8, libboost-all-dev, libinsighttoolkit4-dev]
   name: focal gcc8 +boost +itk +fftw3 +hdf5 +siemens_to_ismrmrd +swig +ace
   env: EXTRA_BUILD_FLAGS="-DUSE_ITK:BOOL=ON -DUSE_SYSTEM_ITK:BOOL=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DUSE_SYSTEM_ACE=ON" MATRIX_EVAL="CC=gcc-8 CXX=g++-8" PYMVER=3
 - os: linux
   python: 3
   addons:
    apt:
     packages:
     - *addons_apt_packages
     - [g++-6, libboost-all-dev]
   name: bionic gcc6 +DEVEL -boost -hdf5 -fftw3 +ace +siemens_to_ismrmrd
   env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_ACE=ON -DBUILD_siemens_to_ismrmrd=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
 - os: linux
   python: 3
   addons:
    apt:
     packages:
     - *addons_apt_packages
     - [g++-7, libinsighttoolkit4-dev]
   name: bionic gcc7 +DEVEL -boost -fftw3 -hdf5 -swig +ace
   env: EXTRA_BUILD_FLAGS="-DUSE_ITK:BOOL=ON -DUSE_SYSTEM_ITK:BOOL=ON -DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc-7 CXX=g++-7" PYMVER=3
 ## osx g{cc,++} py{27,36}
 #- os: osx
 #  osx_image: xcode11.2
 #  python: 3
 #  # +boost -hdf5 -swig
 #  env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3
 #- os: osx
 #  # +boost +fftw3 -hdf5 -swig
 #  osx_image: xcode11.2
 #  python: 3
 #  env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3
 #- os: osx
 #  python: 3
 #  # +DEVEL +boost -hdf5 +swig
 #  osx_image: xcode11.2
 #  env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3
 #- os: osx
 #  python: 3
 #  # +DEVEL +boost -fftw3 -hdf5 +swig +itk
 #  osx_image: xcode11.2
 #  env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON -DUSE_ITK=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3
 - os: linux
   python: 3
   addons:
    apt:
     packages:
     - *addons_apt_packages
     - [g++-6, libboost-all-dev]
   name: bionic gcc6 +boost +itk +fftw3 +hdf5 +vtk
   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
 #- os: osx
 #  python: 3
 #  # +boost +itk -hdf5 +swig +vtk
 #  osx_image: xcode11.2
 #  env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON -DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3

before_install:
# Set C and C++ compiler etc using trick from
# https://docs.travis-ci.com/user/languages/cpp/#c11c11-and-beyond-and-toolchain-versioning
- eval "${MATRIX_EVAL}"
- export CC="${CC:-gcc}"
- export CXX="${CXX:-g++}"
- $CC --version
- $CXX --version
- mkdir -p ~/.local/bin
- pushd ~/.local/bin
# Note: use ( set -ev; ... ) to echo commands and exit immediately on failure
# in compounds statements (note that export/cd etc won't persist).
- |
   if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
     # Update and upgrade brew
     brew update
     brew upgrade

     BUILD_FLAGS="$BUILD_FLAGS -DSHARED_LIBS_ABS_PATH=ON"
     brew install openblas
     # Let CMake find this blas version (note: we use /usr/local/opt/openblas symlink to get the most recent brew version)
     EXTRA_BUILD_FLAGS="$EXTRA_BUILD_FLAGS -DCBLAS_INCLUDE_DIR=/usr/local/opt/openblas/include -DCBLAS_LIBRARY=/usr/local/opt/openblas/lib/libblas.dylib"
     PY_EXE=$(which python${PYMVER})
     if [[ $EXTRA_BUILD_FLAGS == *"-DUSE_VTK=ON"* ]] && [[ $EXTRA_BUILD_FLAGS == *"-DUSE_SYSTEM_VTK=ON"* ]]; then
       brew install vtk
     fi
     BUILD_FLAGS="$BUILD_FLAGS -DPYTHON_EXECUTABLE=$PY_EXE"
     ( set -ev
       # boost is already installed but 1.65 doesn't work so update
       brew reinstall boost
       # we currently need boost-python
       # brew install boost-python
       brew install ace
       brew install swig
       brew install ccache
       if [[ $EXTRA_BUILD_FLAGS == *"SYSTEM_FFTW3=ON"* ]]; then
           brew install fftw
       else
           echo "Not installing FFTW as we are building it"
       fi
       # need curl to get pip and more recent cmake
       brew install curl
       #brew install cmake # already present
       # alternative: get our own
       #curl -L -O https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Darwin-x86_64.tar.gz
       #tar xzf cmake-*.tar.gz
       #mv cmake-*/CMake.app/Contents/* cmake
       #export PATH="$PWD/cmake/bin:$PATH"
     )
   elif [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
     PY_EXE=python$PYMVER
     #curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Linux-x86_64.tar.gz
     #tar xzf cmake.tgz && rm cmake.tgz
     #ln -s cmake-*x86_64 cmake
     #export PATH="$PWD/cmake/bin:$PATH"
     if [[ $EXTRA_BUILD_FLAGS == *"-DUSE_VTK=ON"* ]] && [[ $EXTRA_BUILD_FLAGS == *"-DUSE_SYSTEM_VTK=ON"* ]]; then
       sudo apt install libvtk7-dev
     fi
   fi
# for counting clones, excluding ours
- |
   if [[ -n "$GITHUB_API_TOKEN" ]]; then
     git clone https://$GITHUB_API_TOKEN@github.com/ccp-petmr-codebot/github-stats --branch CCPPETMR/SIRF-SuperBuild
     # update with last fortnight's clones from GitHub API
     TRAVIS_REPO_SLUG=CCPPETMR/SIRF-SuperBuild source github-stats/setup.sh
     # count unique clones, excluding travis, and print total
     TRAVIS_REPO_SLUG=CCPPETMR/SIRF-SuperBuild gh_stats_count -k uniques
   fi
- $PY_EXE --version
# ccache compiler override
- ln -s "$(which ccache)" g++
- ln -s "$(which ccache)" g++-6
- ln -s "$(which ccache)" g++-7
- ln -s "$(which ccache)" gcc
- ln -s "$(which ccache)" gcc-6
- ln -s "$(which ccache)" gcc-7
- export PATH="$PWD:$PATH"
- popd
# get pip
- curl -0 https://bootstrap.pypa.io/get-pip.py -o get-pip.py
- $PY_EXE get-pip.py --user
- echo "Using Python executable $PY_EXE"
- $PY_EXE --version
- $PY_EXE -m pip --version
# setuptools may be out of date on osx
- $PY_EXE -m pip install --user -U pip setuptools wheel
- $PY_EXE -m pip freeze
- $PY_EXE -m pip install --user -r requirements.txt
- $PY_EXE -m pip install --user -r ci-requirements.txt
# no point re-downloading SIRF - just use local version
# N.B.: don't put into build matrix to allow caching.
- BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER -DSIRF_SOURCE_DIR:PATH=$PWD -DDISABLE_GIT_CHECKOUT_SIRF=ON"
# get SuperBuild
- cd ..
- git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master
- cd SIRF-SuperBuild
- cmake --version
- echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS"

install:
- cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
# Job may timeout (>50min) if no ccache, otherwise should be <1min:
- make
- |
   if [[ -f INSTALL/share/gadgetron/config/gadgetron.xml.example ]]; then
     mv INSTALL/share/gadgetron/config/gadgetron.xml.example INSTALL/share/gadgetron/config/gadgetron.xml
   fi
- source $PWD/INSTALL/bin/env_ccppetmr.sh

script:
- ./INSTALL/bin/gadgetron >& gadgetron.log&
# print for debugging
- cat builds/SIRF/build/CMakeCache.txt
- |
   cd builds/SIRF/build && ctest --verbose ; test_fail=$?
   # echo "----------- Killing gadgetron server"
   # killall gadgetron
   if [[ $test_fail -ne 0 ]]; then
     #echo "----------- Test output"
     # cat builds/SIRF/build/Testing/Temporary/LastTest.log
     echo "----------- Last 70 lines of gadgetron.log"
     tail -n 70 gadgetron.log
     travis_terminate $test_fail
   fi

after_success:
- pushd ../SIRF
- sed -r 's/SIRF-SuperBuild\/INSTALL\/python\/sirf\/(\w*)\.py/SIRF\/src\/x\1\/p\1\/\1.py/g' ../SIRF-SuperBuild/sources/SIRF/.coverage > .coverage
- codecov
- coveralls
- popd