Installation

Prerequisite: LaTeX

The visualisation of particular representations of models requires that you have a LaTeX distribution installed.

You can now install MuMoT within a conda environment or within a Python virtualenv.

Installing MuMoT within a Conda environment

  1. Clone this repository.

  2. Install the conda package manager by installing a version of Miniconda appropriate to your operating system.

  3. Open a terminal within which conda is available; you can check this with

    conda --version

  4. Create a new conda environment containing just Python >=3.6 e.g.:

    conda update conda
conda create -n mumot-env python=3.7

  5. Check that conda environment has been created:

    conda env list

    mumot-env should appear in the output.

  6. Activate the environment:

    source activate mumot-env    # on macOS/Linux with older versions of conda
conda activate mumot-env    # on macOS/Linux with newer versions of conda
activate mumot-env           # on Windows

  7. Install MuMoT and dependencies into this conda environment:

    conda install graphviz
python -m pip install path/to/clone/of/MuMoT/repository

    NB if your clone of the MuMot repository is a subdirectory of the current directory, make sure you run python3 -m pip install ./MuMoT instead of python3 -m pip install MuMoT (to ensure MuMoT is installed from your Git clone and not from PyPI).

Installing MuMoT within a VirtualEnv

  1. Clone this repository.

  2. Ensure you have the following installed:

    • Python >= 3.6
    • the pip package manager (usually comes with Python 3.x but might not for certain flavours of Linux)
    • the virtualenv tool for managing Python virtual environments
    • graphviz

    You can check this by opening a terminal and running:

    python3 --version
python3 -m pip --version
python3 -m virtualenv --version
dot -V

  3. Create a Python virtualenv in your home directory:

    cd
python3 -m virtualenv mumot-env

  4. Activate this Python virtualenv:

    source mumot-env/bin/activate    # on macOS/Linux
mumot-env/bin/activate           # on Windows

  5. Install MuMoT and dependencies into this Python virtualenv, then enable interactive Notebook widgets:

    python3 -m pip install path/to/clone/of/MuMoT/repository
jupyter nbextension enable --py widgetsnbextension --sys-prefix

    NB if your clone of the MuMot repository is a subdirectory of the current directory, make sure you run python3 -m pip install ./MuMoT instead of python3 -m pip install MuMoT (to ensure MuMoT is installed from your Git clone and not from PyPI).

Installing MuMoT from PyPI

Follow the instructions as above for ‘Installing MuMoT within a VirtualEnv’, but at stage 5 replace

python3 -m pip install path/to/clone/of/MuMoT/repository

with

python3 -m pip install mumot

(Optional) Enable tables of contents for individual Notebooks

Hyperlinked tables of contents can be userful when viewing longer Notebooks such as the MuMoT User Manual.

Tables of contents can be displayed if you enable the TOC2 Jupyter Extension as follows:

  1. Ensure the jupyter_contrib_nbextensions package is installed. This is “a collection of extensions that add functionality to the Jupyter notebook”. If you installed MuMoT into a virtualenv using pip then you need to ensure that virtualenv is activated before running:

    pip install jupyter_contrib_nbextensions

  2. Enable jupyter_contrib_nbextensions:

    jupyter contrib nbextension install --sys-prefix

  3. Enable the TOC2 (‘table of contents’) extension that is provided by jupyter_contrib_nbextensions:

    jupyter nbextension enable toc2/main

  4. Enable a graphical interface for enabling/disabling TOC2 and other Jupyter extensions. If using conda:

    conda install -c conda-forge jupyter_nbextensions_configurator

    Or if using a virtualenv instead:

    pip install jupyter_nbextensions_configurator  # AND
jupyter nbextensions_configurator enable --sys-prefix

The next time you start Jupyter from your conda environment or virtualenv then open a Notebook you should see a table of contents displayed down the left-hand-side of the Notebook.

If you subsequently want to disable the TOC2 extension and/or enable other Notebook extensions then click Nbextensions in the Jupyter file browser tab.