Installation

Prerequisites

The following software is required:

• Boost Libraries
• Armadillo Library (Numerical linear algebra in c++)
• SWIG (Python Interface)
• Doxygen (Documentation for the C++ code)
• Sphinx (HTML Manual)
  • The breathe module that bridges sphinx and doxygen should be installed (e.g., "pip install breathe")
  • The bibtex module should be installed (e.g., "pip install sphinxcontrib-bibtex")
• MPI (Estimation with parallel Markov chains)

Generate makefiles with CMake

Out-of-source is the suggested build modality. To do this, first create a build folder (for example "tulipBin") as a sibling of the main source code folder (probably "gcode")

mkdir tulipBin

Cd into tulipBin

cd tulipBin

Now you can use the ccmake (command line) or cmake-gui (Qt-based CMake GUI) to create the make files. For example, using ccmake from the tulipBin folder type

ccmake ../tulip

After running a first configuration step (by typing "c" on ccmake), four options will be shown that enable the creation of the Python interface and documentation. These are

buildPythonInterface (default ON)
buildDocumentation   (default ON)
USE_SYSTEM_DOXYGEN   (default OFF)
USE_SYSTEM_SWIG      (default OFF)

If you only want to compile the C++ code then the options "buildPythonInterface" and "buildDocumentation" should be switched off. If you want to build the C++ code and Python wrapper but not the Doxygen+Sphinx documentation then set

buildPythonInterface ON
buildDocumentation   OFF

The options "USE_SYSTEM_DOXYGEN" "USE_SYSTEM_SWIG" tell CMake to look for local installations of these two applications, or to download them and install from a remote source. We suggest you to first install SWIG, DOXYGEN and SPHINX and to set these options as

USE_SYSTEM_SWIG    ON
USE_SYSTEM_DOXYGEN ON

Configure the code again, until CMake will let you generate the makefiles. Press "g" (ccmake) to generate the makefiles.

To build the code run (within "tulipBin")

make -j n

where n is the number of processors you want to use to build.

Generate the documentation

The sphinx documentation requires that doxygen is run first to generate the XML database.

To build the doxygen documentation type

make doxydoc

To build the sphinx documentation type (within "tulipBin")

make docs

You should be able to see the generated documentation by opening with a we browser the file

tulipBin/docs/sphinx/html/index.html

Location of executables and python wrappers

After the build process has finished you should find:

• all the C++ executables in the "tulipBin/bin" folder.
• all the python modules in the "tulipBin/py" folder.