Simulation Generator

Project setup

The whole project's library can be installed via with the help of setuptools. The project requires Python 3 to run in order for all the functionalities to work, on a Linux based operating system.

Prerequisites

• Singularity 3 or greater
  • The singularity image for voXSim can be pulled with singularity pull library://avcaron/default/voxsim_singularity
• MPI libraries
  • On Ubuntu, install openmpi-bin
• A good multi-core CPU
• RAM sized to the number of fibers simulated
  • ~90ko per fiber at 100 interpolation samples

Documentation

The project is partially documented; the documentation is generated using sphinx, as well as the autodoc module. To build the documentation, run the build_documentation.sh script at the base of the project.

Installation

• Create a python virtual environment (virtualenv, pyenv, etc.) and activate it

• Install required packages with

  pip install -r requirements.txt

• Install the project inside the virtual environment with

  python setup.py install

• To install the project as developper, use

  pip install -e . or python setup.py develop