Getting Started

Prequisites

We use Git LFS to store large and binary files. Before you clone the repository, install Git LFS and run the command git lfs install. On Windows, simply run the installer. On MacOS, extract the contents of the .tar.gz file using tar xvfz <filename>.tar.gz and then run ./install.sh. The TLOmodel repository can then be cloned as normal.

Installation

To get started quickly, we recommend using Anaconda Python, and installing within a fresh environment. Please use the Installation Guide or, if you prefer, you can carry out the setup using the command line:

conda create -n tlo python=3.8
conda activate tlo
pip install -r requirements/dev.txt
pip install -e .

This will install the software in ‘editable’ mode, so any changes you make to the source will immediately be reflected. After the initial install, each time you wish to use the model simply activate the environment:

conda activate tlo

To update dependencies, perform the following steps in the TLOmodel directory:

conda activate tlo
pip install -r requirements/dev.txt

Documentation

To build the documentation, activate your environment as above then run:

tox -e docs

The generated HTML documentation will appear in dist/docs.

Wiki

Please note that we have a Wiki which you may wish to refer to. It has information on setup, conventions, checklists and code examples.

Development

To run the Python code tests only:

pytest

To run all the tests:

tox

Note, to combine test coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox