artrabbitstudio/epioncho-ibm

Modelling exposure heterogeneity and density dependence in onchocerciasis using a novel individual-based transmission model in python

Welcome to EPIONCHO-IBM

Requirements

Epioncho-IBM requires Python 3.10 or newer, as well as Poetry installed and internet connection with access to GitHub.

Installation

1. First, check if you have pip installed (pip3 --version). It's very likely that you do already. If you don't run: python3 -m ensurepip
2. If you don't have Poetry installed yet, you can either follow the official guidline or the following steps. The commands below will install poetry for your user only. It will be available in $HOME/.local/bin. It's often useful to add this path to $PATH so that it can be accessed just by typing poetry in the terminal.

   pip3 install poetry # installing in the user's home directory
   echo "export PATH=$HOME/.local/bin:$PATH" >> ~/.bashrc # Adding to $PATH

3. If you want to install poetry for all of the users instead, you should run sudo pip3 install poetry instead. You then don't need to worry about $PATH.
4. Now we are ready to checkout the project and install all of the dependencies

   git clone [email protected]:dreamingspires/EPIONCHO-IBM.git
   # optionally select a desired branch: git checkout <branch>
   cd EPIONCHO-IBM
   poetry install

5. If you are expecting to make code contribution, run the following to make sure the code conforms to the coding guidlines:

   poetry run pre-commit install

6. Check that everything works as expected:

   poetry run python examples/test_new.py
   cd tests
   poetry run pytest

Running simulations and testing

As per above, you can run tests by executing:

cd tests
poetry run pytest

You can run execute any python file by prefixing it with poetry run python. This ensures that the installed python environment is used. For example:

poetry run python examples/test.py

Profiling

Profiling is a way of finding out how the execution time of all of the functions in a program. You can run the following to see an execution graph of a given program:

poetry run python -m cProfile -o /tmp/program.prof examples/test_new.py; poetry run snakeviz /tmp/program.prof -s # opens a browser