Installation

Pre-build binaries

The Python package can be installed with Pypi:

pip install higra

Supported systems:

  • Python 3

  • Linux 64 bits, macOS, Windows 64 bits

Manual build

Higra can be build from source directly with cmake or through a wrapper setuptools setup.py script. The latter is especially useful to create wheels (pip installable packages).

Building Higra from source requires:

  • a c++ 14 compiler (tested with GCC, Clang, Visual Studio 2019)

  • cmake

  • Python 3 with Numpy

With cmake

The following commands will download and build Higra from source. The python package will be in the directory build/higra/. Note that the python package must be findable by Python in order to be used (e.g. by setting your PYTHONPATH environment variable).

git clone https://github.com/higra/Higra.git
mkdir build
cd build
cmake  -DDO_AUTO_TEST=ON -DHG_USE_TBB=OFF ../Higra/
make

Sometimes, cmake gets confused when several Python versions are installed on the system. You can specify which version to use with -DPython_EXECUTABLE:FILEPATH=/PATH-TO-PYTHON/python, e.g.

cmake -DDO_AUTO_TEST=ON -DHG_USE_TBB=OFF -DPython_EXECUTABLE=/anaconda3/bin/python ../Higra/

Cmake options:

  • USE_SIMD (boolean, default ON): Use SIMD instructions

  • DO_CPP_TEST (boolean, default ON): Build the c++ test suit

  • DO_AUTO_TEST (boolean, default OFF): Execute test suit automatically at the end of the build

  • HG_USE_TBB (boolean, default OFF): Use Intel Threading Building Blocks (TBB)

If HG_USE_TBB is equal to ON, cmake will try to locate TBB automatically. TBB path can however be specified manually with the following parameters:

  • TBB_INCLUDE_DIR (path): path to TBB include (path containing a folder called tbb that contains TBB header files)

  • TBB_LIBRARY (path): path to TBB library (path containing tbb.so on Unix or tbb.lib on Windows)

With setuptools

The file setup.py is a thin wrapper around the cmake script. The following commands will download the library, create a binary wheel and install it with pip.

git clone https://github.com/higra/Higra.git
cd Higra
python setup.py bdist_wheel
cd dist
pip install higra*.whl

In order to activate TBB, one must define the following environment variable before calling setup.py

  • HG_USE_TBB (any value): will activate use of TBB

  • TBB_INCLUDE_DIR (optional, path): path to TBB include (path containing a folder called tbb that contains TBB header files)

  • TBB_LIBRARY (optional, path): path to TBB library (path containing tbb.so on Unix or tbb.lib on Windows)

  • TBB_DLL (mandatory on Windows, filepath): path to TBB DLL