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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

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