emodpy-malaria 5.0.3

IDM's malaria-specific EMOD-API binding code

emodpy-malaria

Python module for use as user-space front-end for doing research easily with EMOD (MALARIA_SIM) via idmtools.

Description

This package provides a Python scriptable interface for configuring EMOD for malaria modeling. This Python interface abstracts the process of creating JSON formatted files for parameter specification, demographics specification and intervention specification along as well as abstracting the process of creating binary climate and migration files.

Getting started

Before installing emodpy_malaria, please see the Getting Started page. It can guide you through trying EMOD before you try it on your own machine.

Get emodpy-malaria

The emodpy-malaria package (and its supporting packages) is currently hosted on IDM's Python package repository.

python3 -m pip install emodpy-malaria --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

Note: you may need to only use python on Windows machines rather than python3.

Documentation

Documentation available at https://docs.idmod.org/projects/emodpy-malaria/en/latest/.

To build the documentation locally, do the following:

1. Create and activate a venv.

2. Navigate to the root directory of the repo and enter the following:

   pip install -e . --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
   cd docs
   pip install -r requirements.txt
   make html
   

You may need to open a new command prompt before running make html. The HTML documentation will be output to the docs/_build/html directory.

FAQ

Frequently asked questions are answered in https://docs.idmod.org/projects/emodpy-malaria/en/latest/faq.html.

Community

Have a question or a comment? Check out our Discussions space.

Support and Contributions

The code in this repository was developed by IDM to support our research in disease transmission and managing epidemics. We’ve made it publicly available under the MIT License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as contemplated under the MIT License.

If you have feature requests, issues, or new code, please see our CONTRIBUTING page for how to provide your feedback.

Developer Installation

There are several options if you are modifying the code locally.

Option 1: install in the emodpy-malaria directory:

pip install -e . --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

Option 2: Each time you make a change you want to install 'build':

pip install build 

..and then run the following commands to build the package with latest code and install it:

python -m build --wheel
pip install dist\emodpy_malaria-XXX.whl 

Disclaimer

The code in this repository was developed by IDM and other collaborators to support our joint research on flexible agent-based modeling. We've made it publicly available under the MIT License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as permitted under the MIT License.