INSTALL.md

Installing the workshop environment

Overview

This workshop is delivered mainly through a series of Jupyter notebooks that allow for interactive Python programming.

To use these, several Python packages must be installed. A full list of these can be found in environment.yml. Should you want to install MDAnalysis under a separate environment, you can find the installation instructions here: https://www.mdanalysis.org/pages/installation_quick_start/. See below for instructions on how to set up a local copy of the Python environment.

Installing the Python environment

Due to the complexity of the workshop environment, we strongly recommend the use of the Anaconda Python distribution. The instructions provided here assume the use of conda.

1. Creating a workshop environment

To create an environment named mda_workshop with all the necessary Python dependencies:

conda env create --file=environment.yml

See the conda documentation for more information on how to access and manage conda environments.

To then activate this environment:

conda activate mda_workshop

2. Activating the Jupyter extensions

The workshop leverages the extended utility of several Jupyter nbextensions.

To install these, the followed should be run once (after having activated the conda environment):

jupyter contrib nbextension install --user
jupyter nbextension enable splitcell/splitcell
jupyter nbextension enable rubberband/main
jupyter nbextension enable exercise2/main
jupyter nbextension enable autosavetime/main
jupyter nbextension enable collapsible_headings/main
jupyter nbextension enable codefolding/main
jupyter nbextension enable limit_output/main
jupyter nbextension enable toc2/main