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.travis.yml
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.travis.yml
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# vim ft=yaml
# travis-ci.org definition for CoSMoMVPA build (based on PyMVPA, which is
# based on nipype configuration, which in turn was based on nipy)
#
# We pretend to be java because we need GNU Octave which is not
# available (as of June 2019)
language: java
dist: xenial
cache:
- apt
env:
global:
- COVERALLS_PARALLEL=true
matrix:
- TRAVIS_WITH_EXTERNALS=false TRAVIS_WITH_COVERAGE=false COVERALLS_PARALLEL=false
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=false COVERALLS_PARALLEL=false
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=1 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=2 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=3 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=4 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=5 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=6 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=7 PARTITION_COUNT=8 COVERALLS_PARALLEL=false NO_DOC_TEST=true
# - TRAVIS_WITH_EXTERNALS=true TRAVIS_WITH_COVERAGE=true PARTITION_INDEX=8 PARTITION_COUNT=8 TRAVIS_AFTER_ALL_ARGS='--is_master' COVERALLS_PARALLEL=true NO_DOC_TEST=true
before_install:
# to prevent IPv6 being used for APT
- sudo bash -c "echo 'Acquire::ForceIPv4 \"true\";' > /etc/apt/apt.conf.d/99force-ipv4"
# ensure up-to-date prior to software-properties-common
- travis_retry sudo apt-get -y -qq update
# get Octave 4.0
- travis_retry sudo apt-get install -y -qq software-properties-common python-software-properties libtool autoconf automake m4
- travis_retry sudo apt-add-repository -y ppa:octave/stable
- travis_retry sudo apt-get -y -qq update
- travis_retry sudo apt-get -y install octave
- travis_retry sudo apt-get -y install liboctave-dev
- travis_retry sudo apt-get -y -qq install octave
- octave --version
- which make
# when installing externals, get recent GCC for Octave parallel toolbox
- if [[ "${TRAVIS_WITH_EXTERNALS}" == "trueDISABLED" ]]; then
travis_retry sudo add-apt-repository 'ppa:ubuntu-toolchain-r/test' -y;
travis_retry sudo apt-get update -y -q;
travis_retry sudo apt-get install gcc-4.8 g++-4.8 -y -q;
travis_retry sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 20;
travis_retry sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 20;
travis_retry sudo update-alternatives --config gcc;
travis_retry sudo update-alternatives --config g++;
travis_retry sudo apt-get install gcc-multilib;
travis_retry sudo apt-get install libgomp1;
c++ --version;
g++ --version;
NAME=automake;
VERSION=1.6;
FULL=${NAME}-${VERSION};
wget https://ftp.gnu.org/gnu/${NAME}/${FULL}.tar.gz;
tar -xzf ${FULL}.tar.gz;
cd ${FULL};
./configure && make && sudo make install;
cd ..;
NAME=autoconf;
VERSION=2.69;
FULL=${NAME}-${VERSION};
wget https://ftp.gnu.org/gnu/${NAME}/${FULL}.tar.gz;
tar -xzf ${FULL}.tar.gz;
cd ${FULL};
./configure && make && sudo make install;
cd ..;
fi
# go up one level
- cd ..
# retrieve MOxUnit
- rm -rf MOxUnit
- travis_retry git clone -v git://github.com/MOxUnit/MOxUnit.git
- make -C MOxUnit install
# retrieve MOdox
- rm -rf MOdox
- travis_retry git clone -v git://github.com/MOdox/MOdox.git
- make -C MOdox install
# optionally retrieve MOcov
- if [[ "$TRAVIS_WITH_COVERAGE" == "true" ]]; then
rm -rf MOcov;
git clone git://github.com/MOcov/MOcov.git;
make -C MOcov install;
fi
# Show package info
- autoconf --version
- automake --version
- m4 --version
install:
- PTH=`pwd`
- OCTAVERC=~/.octaverc
- OCTAVEPTH=`pwd`/CoSMoMVPA/mvpa
- CHECKEXTCMD=""
- OCTAVE_DISABLE_WARNINGS=" Octave:array-to-scalar
Octave:imag-to-real
Octave:language-extension
Octave:missing-semicolon
Octave:resize-on-range-error
Octave:separator-insert
Octave:single-quote-string
Octave:str-to-num
Octave:mixed-string-concat
Octave:variable-switch-label"
- OCTAVE=octave
- if [[ "$TRAVIS_WITH_EXTERNALS" == "true" ]]; then
EXTERNALS="
afni
surfing
fieldtrip
libsvm
gifti
octave_pkg_struct
octave_pkg_parallel
octave_pkg_statistics
octave_pkg_miscellaneous
";
fi
# ensure Octave rc file exists
- echo "" >> $OCTAVERC;
# use travis-retry
- RETRY=travis_retry
# load Octave io package
- $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','io');";
# optionally enable Octave struct package
- if [[ " $EXTERNALS " = *" octave_pkg_struct "* ]]; then
$RETRY $OCTAVE --eval "pkg('install','-auto','-forge','struct');";
fi
# optionally enable Octave statistics package
# $RETRY $OCTAVE --eval "pkg('install','-forge','statistics');";
- if [[ " $EXTERNALS " = *" octave_pkg_statistics "* ]]; then
$RETRY sudo apt-get -y -qq octave-statistics;
fi
# optionally enable Octave miscellaneous package
# (the "general" package is required for the "miscellaneous" package)
# (the "miscellaneous" package also requires "units")
- if [[ " $EXTERNALS " = *" octave_pkg_miscellaneous "* ]]; then
$RETRY $OCTAVE --eval "pkg('install','-auto','-forge','general');";
$RETRY sudo apt-get -y -qq install units;
$RETRY $OCTAVE --eval "pkg('install','-auto','-forge','miscellaneous');";
fi
# As of Aug 2017, the parallel package is disabled because it made Octave crash
# when using travis
#
# For example see https://travis-ci.org/CoSMoMVPA/CoSMoMVPA/jobs/264122792
#
# Relevant command & travis output
#
# if [[ " $EXTERNALS " = *" octave_pkg_parallel "* ]]; then $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','parallel');"; fi
# octave: X11 DISPLAY environment variable not set
# octave: disabling GUI features
# warning: pkg: autoload is no longer supported. Add a 'pkg load ...' command to octaverc instead.
# warning: called from
# pkg at line 316 column 9
# warning: doc_cache_create: unusable help text found in file 'parallel_interface'
# For information about changes from previous versions of the parallel package, run 'news parallel'.
# *** Error in `/usr/bin/octave-cli': double free or corruption (fasttop): 0x0000000001669e00 ***
# panic: Aborted -- stopping myself...
# attempting to save variables to 'octave-workspace'...
# panic: attempted clean up failed -- aborting...
# /home/travis/.travis/job_stages: line 229: 15780 Aborted (core dumped) "$@"
# The command "octave --eval pkg('install','-auto','-forge','parallel');" failed. Retrying, 2 of 3.
#
## - if [[ " $EXTERNALS " = *" octave_pkg_parallel "* ]]; then
## $RETRY $OCTAVE --eval "pkg('install','-auto','-forge','parallel');";
## fi
# optionally install surfing toolbox
- if [[ " $EXTERNALS " = *" surfing "* ]]; then
rm -rf surfing;
git clone git://github.com/nno/surfing.git --depth 1;
make -C surfing install;
fi
# optionally install afni
- if [[ " $EXTERNALS " = *" afni "* ]]; then
rm -rf afni;
git clone git://github.com/afni/afni.git --depth 1;
$OCTAVE --eval "addpath('${PTH}/afni/src/matlab');savepath();";
fi
# optionally install FieldTrip, using one of the branches below
# If FieldTrip temporarily breaks the build, we can switch to another
# custum branch that fixes the issue. The official branch is the
# last entry in the list below.
#
# git clone git://github.com/nno/fieldtrip.git --depth 1 -b _fix/octave_fixname_empty_input
# git clone git://github.com/fieldtrip/fieldtrip.git --depth 1;
- if [[ " $EXTERNALS " = *" fieldtrip "* ]]; then
rm -rf fieldtrip;
git clone git://github.com/fieldtrip/fieldtrip.git --depth 1;
$OCTAVE --eval "cd('${PTH}/fieldtrip');
ft_defaults();
savepath();";
fi
# optionally install libsvm
- if [[ " $EXTERNALS " = *" libsvm "* ]]; then
rm -rf libsvm;
git clone git://github.com/cjlin1/libsvm.git;
$OCTAVE --eval "cd('${PTH}/libsvm/matlab');
make;
addpath(pwd);
savepath();";
fi
# optionally install gifti library
- if [[ " $EXTERNALS " = *" gifti "* ]]; then
GIFTI_VERSION=1.6;
GIFTI_NAME=gifti-${GIFTI_VERSION};
rm -rf ${GIFTI_NAME}.zip;
wget http://www.artefact.tk/software/matlab/gifti/${GIFTI_NAME}.zip;
unzip ${GIFTI_NAME}.zip;
$OCTAVE --eval "cd('${PTH}/${GIFTI_NAME}/@gifti/private');
mex('zstream.c');
addpath('${PTH}/${GIFTI_NAME}');
savepath();";
fi
# disable "more"
- echo "more('off');" >> $OCTAVERC
# prevent shippable from re-using old test results
- if [[ "$SHIPPABLE" == "true" ]]; then
rm -f shippable/testresults/*.xml;
fi
before_script:
# (note: Shippable.com does not work properly if the
# Octave pacakges are installed in the "install" section)
# Shippable.com seems to puke on travis_retry with quoted arguments,
# so only use travis_retry on travis
- if [[ "$SHIPPABLE" != "true" ]] && [[ "$TRAVIS" == "true" ]]; then
RETRY=travis_retry;
fi
# show Octave-rc
- echo "Octave-rc:"; cat $OCTAVERC
# show which packages are installed
- $OCTAVE --eval "pkg('list')"
# show WTF
- $OCTAVE --eval "addpath('${PTH}/CoSMoMVPA/mvpa');cosmo_wtf()"
script:
- cd CoSMoMVPA
- ls
- if [[ "$TRAVIS_WITH_COVERAGE" == "true" ]]; then
TEST_ARGS=WITH_COVERAGE=true;
COVER_ARGS=COVER=`pwd`/mvpa;
if [[ "$SHIPPABLE" == "true" ]]; then
OUTPUT_ARGS=COVER_XML_FILE=shippable/codecoverage/coverage.xml;
elif [[ "$TRAVIS" == "true" ]]; then
OUTPUT_ARGS=COVER_JSON_FILE=`pwd`/coveralls.json;
AFTER_SCRIPT="curl --verbose -F json_file=@`pwd`/coveralls.json https://coveralls.io/api/v1/jobs";
if [ ! -z "$PARTITION_INDEX" ]; then
PARTITION_ARGS="TEST_PARTITION_INDEX=${PARTITION_INDEX} TEST_PARTITION_COUNT=${PARTITION_COUNT}";
fi
fi;
elif [[ "$SHIPPABLE" == "true" ]]; then
RESULT_ARGS=JUNIT_XML_FILE=shippable/testresults/test_results.xml;
fi
- make test $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS $PARTITION_ARGS
after_script:
- echo "After script"
- tools/travis_after_all.py $TRAVIS_AFTER_ALL_ARGS
- cat .to_export_back
- export $(cat .to_export_back)
- if [[ "$TRAVIS_WITH_COVERAGE" == "true" ]]; then
if [[ "$TRAVIS" == "true" ]]; then
echo "Sending json";
cat `pwd`/coveralls.json;
fi;
fi
- $AFTER_SCRIPT