The BRAINSTools is a harness to assist in building the many of the BRAINSTools under development.

Developers should run the ./Utilities/SetupForDevelopment.sh script to get started.

If developing on Mac OS X, make sure the xcode command line tools are installed with the command: xcode-select --install

For more information on the individual BRAINSTools, please see the following link: https://github.com/BRAINSia/BRAINSTools/wiki

Building

Mac OSX and Linux RedHat 6

Example session for a clean build:

mkdir ~/src/mytester
cd ~/src/mytester
git clone git://github.com/BRAINSia/BRAINSTools.git

cd BRAINSTools/
bash ./Utilities/SetupForDevelopment.sh

mkdir -p ../BRAINSTools-build
cd ../BRAINSTools-build/
CC=/usr/bin/gcc-4.2 CXX=/usr/bin/g++-4.2 ccmake ../BRAINSTools \
    -DUSE_BRAINSConstellationDetector:BOOL=ON \
    -DUSE_BRAINSABC:BOOL=ON
## NOTE: If you are using a version of Python different from the system default, CMake will ignore your
##       environment variables.  To ensure CMake points to the right version, you need to set the
##       following variables as well:
## -DPYTHON_LIBRARY:PATH=/path/to/python/lib \
## -DPYTHON_INCLUDE_DIR:PATH=/path/to/python/include

make -j${NUMOFTHREADS} -k

## NOTE: The fetching of data still has problems with parallel builds, so we need to restart it at least
#        once
make

Linux Debian (Ubuntu)

Building BRAINSTools on a fresh install has the additional dependency of building CMake on your system. You cannot use the version from apt-get as that does some unnatural things with Python resources to be backwards compatible (see http://public.kitware.com/Bug/view.php?id=14156).

1. Install the necessary dependencies:

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install git python2.7
python2.7-dev g++ freeglut3-dev

2. Get the CMake binaries:

# You can find the URL of the latest CMake binary by
# * Go to www.cmake.org/download in a browser
# * Hover over the desired 'Binary distribution' for your operating
#     system
# * Right-click and select 'Copy Link Address' for the file ending in
#     "tar.gz"
URL=http://www.cmake.org/files/v3.2/cmake-3.2.1-Linux-x86_64.tar.gz
wget ${URL}
# Decompress the file
tar -xzvf cmake-3.2.1-Linux-x86_64.tar.gz
# Add the binary to your PATH environment variable
export PATH=${PWD}/cmake-3.2.1-Linux-x86_64/bin:${PATH}

2. Clone the repository and build:

git clone https://github.com/BRAINSia/BRAINSTools.git
mkdir build
cd build
CC=/usr/bin/gcc-4.8 \
CXX=/usr/bin/g++-4.8 \
cmake ../BRAINSTools \
-DPYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 \
-DPYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 \
-DPYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so
make -j${NUMOFTHREADS} -k

⚠️ You can find the number of threads on your system in Ubuntu with lscpu

Testing

BRAINSTools_MAX_TEST_LEVEL adjusts how agressive the test suite is so that long running tests or incomplete tests can easily be silenced

1 - Run the absolute minimum very fast tests (These should always pass before any code commit)
3 - Run fast tests on continous builds (These need immediate attention if they begin to fail)
5 - Run moderate nightly tests (These need immediate attention if they begin to fail)
7 - Run long running extensive test that are a burden to normal development (perhaps test 1x per week)
8 - Run tests that fail due to incomplete test building, these are good ideas for test that we don't have time to make robust)
9 - Run silly tests that don't have much untility
set(BRAINSTools_MAX_TEST_LEVEL 3 CACHE STRING "Testing level for managing test burden")