This repository holds a Python package for the simulation of the spread of trachoma over a population of individuals. This is an individuals-based model, meaning that the spread of trachoma is simulated by tracking the state of every single individuals in a finite population, over time. For a description of the underlying mathematical model and transmission rules, see Pinsent A, Hollingsworth TD (2018).
The package is currently in early development. No official package distribution is available on either PyPI or Anaconda cloud yet, but it shouldn't be too hard to install the package from source.
git clone https://github.com:NTDMC-Modelling-consortium/trachoma
In addition to Python (3.9+), you'll need a C compiler, for instance
gcc or clang. You can then install the model package using pip
$ cd trachoma
$ python -m pip install .The package only depends on NumPy, but it is still recommended to use a virtual environment to isolate this verion on NumPy from others you might have installed on your machine.
The package is currently changing on a daily basis. To update, your local copy of the repository, run
git pull origin main
from the repo root directory.
In you installed the package in editable mode (see next section), then no more actions are required. If not, you'll need to reinstall the Python package into your environment:
$ python -m pip install .
Start by install the package in editable mode:
$ python -m pip install -e .Currently there are only tests covering the C core functions in
tests/C. You can run these tests using
pytest:
$ python -m pip install pytest
$ pytest tests/C
You'll need Sphinx and Hawkmoth. The latter is used to automatically populate the documentation source with documentation comments written directly in the C source files. it uses the Clang python interface to parse C source code and extract documentaion comments.
$ python -m pip install sphinx hawkmoth libclang
To build the documentation website:
make -C docs html
The built website is generated under docs/build/html. Open
docs/build/html/index.html with a web browser to view it.