.travis.yml

language: cpp
cache: ccache
matrix:
  include:
# list of configurations to be attempted:
# MPI + doc
# this is the "master" one, it is going to update the manual every time
# Variable PLUMED_ALL_TESTS=yes ensures that all the regtests can be run.
# If some of them is not enabled, the whole suite will fail.
  - name: Run all tests and build doc on ubuntu 18. All features enabled (system blas and lapack + asmjit)
    os: linux
    dist: bionic
    sudo: required
    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++ MAKEDOC=yes PLUMED_ALL_TESTS=yes LAPACK=yes ASMJIT=yes
  - name: Run all tests and scan coverage
    os: linux
    dist: trusty
    sudo: required
    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++ MAKECOVERAGE=yes PLUMED_ALL_TESTS=yes
  - name: Debug flags, no MPI
    os: linux
    dist: trusty
    sudo: required
    env: PLUMED_CC=gcc   PLUMED_CXX=g++    CONFIG_FLAGS="--enable-debug --enable-debug-glibcxx"
  - name: Debug flags, MPI
    os: linux
    dist: trusty
    sudo: required
    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++ CONFIG_FLAGS="--enable-debug --enable-debug-glibcxx"
  - name: Cppcheck and codecheck
    os: linux
    dist: trusty
    sudo: required
    env: CPPCHECK=yes CPPCHECK_VERSION=1.90
  - name: External blas with internal lapack, including asmjit
    os: linux
    if: branch =~ ^test- OR type IN(pull_request)
    dist: trusty
    sudo: required
    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3 LAPACK=yes CONFIG_FLAGS="--disable-external-lapack" ASMJIT=yes
  - name: Docker image (ubuntu 17, with gcc6)
    sudo: required
    if: branch =~ ^test- OR type IN(pull_request)
    services: docker
    env: PLUMED_DOCKER=yes
  - name: MacOS, serial build
    os: osx
    if: branch =~ ^test- OR type IN(pull_request)
    osx_image: xcode8.3
    env: PLUMED_CC=clang PLUMED_CXX=clang++ PLUMED_CXXFLAGS=-O3
# this should not be required. I add it since it looks like with OSX it does not work otherwise
    cache:
      directories:
      - $HOME/.ccache
  - name: MacOS, MPI build
    os: osx
    if: branch =~ ^test- OR type IN(pull_request)
    osx_image: xcode8.3
    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3
# this should not be required. I add it since it looks like with OSX it does not work otherwise
    cache:
      directories:
      - $HOME/.ccache
  - name: MacPorts, default modules
    os: osx
    if: branch =~ ^test- OR type IN(pull_request)
    osx_image: xcode8.3
    env: PLUMED_MACPORTS="plumed" PLUMED_PYTHON="3.6 3.7"
    cache:
      directories:
      - $HOME/.macports-ci-ccache
  - name: MacPorts, all modules
    os: osx
    if: branch =~ ^test- OR type IN(pull_request)
    osx_image: xcode8.3
    env: PLUMED_MACPORTS="plumed +allmodules" PLUMED_PYTHON="3.6 3.7"
    cache:
      directories:
      - $HOME/.macports-ci-ccache
  - name: MacPorts, Xcode 9.4, all modules
    os: osx
    osx_image: xcode9.4
    env: PLUMED_MACPORTS="plumed +allmodules" PLUMED_PYTHON="3.6 3.7"
    cache:
      directories:
      - $HOME/.macports-ci-ccache
# linux conda package
  - name: Conda build, linux
    os: linux
    if: branch =~ ^test- OR tag IS present OR type IN(pull_request) OR type IN(cron)
    dist: trusty
    sudo: required
    env: PLUMED_CONDA=yes
# osx conda package
  - name: Conda build, MacOS
    os: osx
    if: branch =~ ^test- OR tag IS present OR type IN(pull_request) OR type IN(cron)
    osx_image: xcode9.4
    env: PLUMED_CONDA=yes
# I don't put any mpi variant with macports since it takes too long to compile
## This command can be used to allow failures:
  allow_failures:
# I allow this to fail temporarily
  - env: PLUMED_DOCKER=yes
# this is failing due to problems in installing MPI, should be allowed to fail until we fix it.
  - env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3
## Possible additional variables:
#   VALGRIND=yes to make valgrind tests, only when log contains string [valgrind]
install:
# setup environment to allow install on the home directory
  - export PATH="$HOME/opt/bin:$PATH"
  - export CPATH="$HOME/opt/include:$HOME/opt/arrayfire/include:$CPATH"
  - export INCLUDE="$HOME/opt/include:$HOME/opt/arrayfire/include:$INCLUDE"
  - export LIBRARY_PATH="$HOME/opt/lib:$HOME/opt/arrayfire/lib:$LIBRARY_PATH"
  - export LD_LIBRARY_PATH="$HOME/opt/lib:$HOME/opt/arrayfire/lib:$LD_LIBRARY_PATH"
  - export PYTHONPATH="$HOME/opt/lib/plumed/python:$PYTHONPATH"
# Setting the TMPDIR in this way allegedly prevents problems with the compilation of 
# PLUMED + Python on macos
  - export TMPDIR="/tmp" 
# on travis, better dump stack trace in case there is an error
  - export PLUMED_STACK_TRACE=yes
  - export PLUMED_NUM_THREADS=2
  - ./.travis/check.log valgrind || VALGRIND=no
# update packages
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && test -n "$PLUMED_CXX" ; then
      brew update > /dev/null ;
      brew install ccache ;
      brew install gawk ;
      export PLUMED_MPIRUN="mpirun --oversubscribe" ;
    fi
  - if [[ "$TRAVIS_DIST" == xenial ]] || [[ "$TRAVIS_DIST" == bionic ]] ; then
      export PLUMED_MPIRUN="mpirun.openmpi" ;
    fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update -qq ; fi
# install some package - these are fast, we install them anyway
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y libfftw3-dev gsl-bin libgsl0-dev ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      if [[ "$CONFIG_FLAGS" == *debug* ]] ; then 
        .travis/install.boost ;
      else
        sudo apt-get install -y libboost-serialization-dev ;
      fi
    fi
  - if test "$PLUMED_CXX" ; then ./.travis/install.xdrfile ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      ./.travis/install.ccache v3.5 ;
    fi
# cppcheck:
# I use 1.71 since 1.72 seems to report a lot of false positive
  - if test "$CPPCHECK" == yes ; then  ./.travis/install.cppcheck $CPPCHECK_VERSION ; fi
# for plumedcheck I need latest gawk
  - if test "$CPPCHECK" == yes ; then  ./.travis/install.gawk 5.0.1 ; fi
# for plumedcheck I need astyle
  - if test "$CPPCHECK" == yes ; then make -j 4 -C astyle ; fi
# installation of these packages takes a lot of time
# we do it only when needed
  - if test "$PLUMED_CXX" == "mpic++" -a "$TRAVIS_OS_NAME" == "linux" ; then sudo apt-get install -y libopenmpi-dev openmpi-bin ; fi
  - if test "$PLUMED_CXX" == "mpic++" -a "$TRAVIS_OS_NAME" == "osx" ;   then brew install openmpi ; fi
  - export OMPI_MCA_btl="^openib"
  - if test "$MAKEDOC" == yes ; then sudo apt-get install -y graphviz            ; fi
# install doxygen-latex
  - if test "$MAKEDOC" == yes ; then sudo apt-get install -y doxygen-latex ; fi
# install aspell
  - if test "$MAKEDOC" == yes ; then sudo apt-get install -y aspell aspell-en  ; fi
# install lcov
  - if test "$MAKECOVERAGE" == yes ; then ./.travis/install.lcov v1.14 ; fi
# install cython for python interface
# nose and other packages are needed for running tests
# only for linux
# with homebrew I currently have problem in installing python 3 so I leave it out
# pandas: needed by mdtraj and by plumed
  - if test "$PLUMED_CXX" ; then
      if test "$TRAVIS_OS_NAME" == "linux" ; then
        pyenv global 3.6;
        pip install --user Cython ;
        pip install --user nose ;
        pip install --user numpy ;
        pip install --user six ;
        pip install --user pandas ;
        pip install --user mdtraj ;
        pip install --user MDAnalysis ;
        python -c "import MDAnalysis" ;
        python -c "import mdtraj" ;
      fi ;
    fi
# then replace doxygen with the desided version
# I use 1.8.10 instead of 1.8.11 since it looks like 1.8.11 have troubles with
# non case sensitive files (it writes capitalized filenames)
  - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_14 ; fi
  - if test "$VALGRIND" == yes ; then sudo apt-get install -y valgrind           ; fi
  - if test "$LAPACK" == yes ; then sudo apt-get -y install libatlas-base-dev      ; fi
# moreover, we hardcode path to dynamic library, required for xdrfile to link properly
# I do it only when LD_LIBRARY_PATH is non blank, since otherwise clang gives problems
  - if test -n "$LD_LIBRARY_PATH" ; then PLUMED_LDFLAGS="-Wl,-rpath,$LD_LIBRARY_PATH" ; fi
# arrayfire
  - if test "$ARRAYFIRE" == yes; then ./.travis/install.arrayfire ; fi 
# macports related stuff
# configure macports
  - if test -n "$PLUMED_MACPORTS" ; then
      export COLUMNS=80 ;
      wget https://raw.githubusercontent.com/GiovanniBussi/macports-ci/master/macports-ci ;
      chmod +x ./macports-ci ;
      ./macports-ci install ;
      PATH="/opt/local/bin:$PATH" ;
      make macports ;
      ./macports-ci localports macports ;
      ./macports-ci ccache ;
    fi
script:
# make sure all modules are enabled
  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=all"
# disable tracking dependencies, to build faster
  - CONFIG_FLAGS="$CONFIG_FLAGS --disable-dependency-tracking"
# we enable fftw, which is off by default
  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-fftw"
# enable boost_serialization to test drr module
  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-boost_serialization"
  - if test "$MAKEDOC" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-pdfdoc" ; fi
  - if test "$MAKECOVERAGE" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-gcov" ; fi
  - if test "$ARRAYFIRE" == yes; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-af_cpu"; fi
# when running lcov plumed use moderate optimization
  - if test "$MAKECOVERAGE" == yes ; then PLUMED_CXXFLAGS=-O ; fi
  - if test "$ASMJIT" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-asmjit" ; fi

# BUILD:
# this is done only if PLUMED_CXX is defined
  - if test "$PLUMED_CXX" ; then
      ccache -s ;
      ./configure CXX="ccache $(which $PLUMED_CXX)" CC=$(which $PLUMED_CC) CXXFLAGS="$PLUMED_CXXFLAGS" LDFLAGS="$PLUMED_LDFLAGS" CPPFLAGS="$PLUMED_CPPFLAGS" $CONFIG_FLAGS --prefix="$HOME/opt" ;
      make -j 4 ;
      make install ;
      ccache -s ;
    fi

# build using macports
  - if test -n "$PLUMED_MACPORTS" ; then
      travis_wait sudo port -N -k install $PLUMED_MACPORTS ;
      plumed config show ;
      ./macports-ci ccache --save ;
      for p in $PLUMED_PYTHON ; do
        travis_wait sudo port -N install py${p//./}-plumed ;
      done
    fi

  - CONDA_VERSION=none
  - export CONDA_LABEL=
# set CONDA_VERSION to TRAVIS_TAG, if available
  - if test -n "${TRAVIS_TAG}" ; then
       CONDA_VERSION="${TRAVIS_TAG//-/_}" ;
       CONDA_VERSION="${CONDA_VERSION#v}" ;
       CONDA_LABEL=tags ;
    fi
# set CONDA_VERSION to branch + date when on nightly build
  - if test "$TRAVIS_EVENT_TYPE" = cron ; then
       if test "$TRAVIS_BRANCH" = master ; then CONDA_VERSION=2.99.$(date +%y%m%d) ; fi ;
       if [[ "$TRAVIS_BRANCH" =~ ^v2.[0-9]+$ ]] ; then CONDA_VERSION=${TRAVIS_BRANCH#v}.$(date +%y%m%d) ; fi ;
       CONDA_LABEL=nightly ;
    fi
# build conda package
  - if test -n "$PLUMED_CONDA" ; then VERSION="$CONDA_VERSION" make -C conda ; fi

# build docker container
  - if test "$PLUMED_DOCKER" = yes ; then make -C docker ; fi

# TEST:
  - if test "$VALGRIND" == yes ; then OPT=valgrind ; else OPT="" ; fi
# --no-print-directory make it more silent
  - if test "$PLUMED_CXX" ; then make --no-print-directory -C regtest $OPT ; fi

# test with gcc6
  - if test "$PLUMED_DOCKER" = yes ; then docker run -v "$PWD/regtest":/home/plumed/regtest -it plumed /bin/bash -c "make -C regtest" ; fi
# currently, gcc6 fails for numerical reasons. Once this is fixed we can add the "make -C regtest checkfail" command below

  - if test "$MAKEDOC" == yes ; then make -C regtest copytodoc ; fi
  - if test "$MAKECOVERAGE" == yes ; then make -C developer-doc coverage ; fi
  - if test "$MAKEDOC" == yes ; then make doc >/dev/null ; fi
  - if test "$MAKEDOC" == yes ; then make -C user-doc spelling ; fi
  - if test "$PLUMED_CXX" ; then make -C regtest checkfail ; fi
# OpenBLAS is needed for numpy, I install it separately since it takes a long time
  - if test -n "$PLUMED_MACPORTS" ; then
      travis_wait sudo port -N -d test $PLUMED_MACPORTS ;
      travis_wait sudo port -N install OpenBLAS ;
      for p in $PLUMED_PYTHON ; do
        travis_wait sudo port test py${p//./}-plumed ;
      done
    fi
  - if test "$PLUMED_CXX" ; then
      if test "$TRAVIS_OS_NAME" == "linux" ; then
        nosetests -v -w python ;
      fi ;
    fi

# CPPCHECK:
# this is required so as to have all the include files inplace:
# notice that this is done automatically in build
  - if test "$CPPCHECK" == yes ; then make -C src/lib/ dirslinks ; fi
# then we do cppcheck
# notice that with make codecheck we also run the maketools/plumedcheck
# script which check if coding policies are satisfied
  - if test "$CPPCHECK" == yes ; then make codecheck ; fi
after_success:
  - if test "$MAKEDOC" == yes ; then ./.travis/push doc ; fi 
  - if test "$MAKECOVERAGE" == yes ; then ./.travis/push coverage ; fi 
  - if test "$MAKECOVERAGE" == yes ; then bash <(curl -s https://codecov.io/bash) > /dev/null ; fi
# upload conda package
  - if test -n "$PLUMED_CONDA" && test -n "$CONDA_LABEL" ; then make -C conda upload ; fi