Build Heimdali in development mode

Development mode is usefull for developer. It consist in iterating in the cycle:

  • modify source code
  • build
  • run the test

without having to run the make install step.

Install dependencies

Create a conda enviromnent named heimdali-dev containing all dependencies:

conda config --add channels http://conda.binstar.org/dfroger
conda create -n heimdali-dev h5unixpipe itk-heimdali-dbg libinrimage tclap cmake pip pexpect

For the rest of the section, we need to activate the conda environment, and set the CONDA_ENV_PATH environment variable:

source activate heimdali-dev
hash -r
CONDA_ENV_PATH=$(conda info -e | grep '*' | tr -s ' ' | cut -d" " -f3)

Install lettuce:

pip install lettuce

Build Heimdali

Build heidmali, asking CMake to search dependances in the Conda environment:

variable meaning
CONDA_ENV_PATH For example, ~/miniconda/envs/heimdali-dev
CMAKE_PREFIX_PATH Where CMake will search for dependent libraries
.. Path to Heimdali main CMakeLists.txt

On Mac OS X your will need to install /Developer/SDKs/MacOSX10.5, and use it:

export MACOSX_DEPLOYMENT_TARGET=10.5

cd heimdali
mkdir build; cd build
cmake -DCMAKE_PREFIX_PATH=$CONDA_ENV_PATH ..
make

Configure examples

As before, the Conda environment is used. Moreover, because Heimdali has been built in heimdali/build and is not installed (development mode), we need to specified all paths to CMake.

cd heimdali
HEIMDALI_ROOT=$PWD
[ `uname` == 'Darwin' ] && EXT=dylib || EXT=so
cd example
mkdir build; cd build
cmake \
    -DCMAKE_PREFIX_PATH=$CONDA_ENV_PATH \
    -DHEIMDALI_INCLUDE=$HEIMDALI_ROOT/libheimdali \
    -DITKINRIMAGEIO_INCLUDE=$HEIMDALI_ROOT/itkINRimageIO/include \
    -DHEIMDALI_LIBRARY=$HEIMDALI_ROOT/build/libheimdali/libheimdali.$EXT \
    -DITKINRIMAGEIO_LIBRARY=$HEIMDALI_ROOT/build/itkINRimageIO/libitkINRImageIO.$EXT \
    ..

Run functional tests

Get Heimdali data files, and set HEIMDALI_DATA_DIR:

git clone https://github.com/dfroger/heimdali-data
export HEIMDALI_DATA_DIR=/path/to/heimdali-data

Add path to the built executables:

cd heimdali
export PATH=$PWD/build/cmd:$PATH

Run the functional tests:

cd tests
lettuce

Writting documentation

Install Sphinx and Doxygen:

sudo apt-get install doxygen
conda create -n heimdali-doc sphinx
source activate heimdali-doc

Build the documentation:

cd doc
make html

View the documentation:

cd doc
firefox _build/html/index.html

Note that breathe, a Sphinx extension, is already provided in heimdali/doc/ext/breathe.