Python module for use as user-space front-end for doing research easily with EMOD (MALARIA_SIM) via idmtools.
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.
The emodpy-malaria package (and its supporting packages) is currently hosted on IDM's Python package repository.
python3 -m pip install emodpy-malaria --index-url=https://packages.idmod.org/api/pypi/pypi-production/simpleNote: you may need to only use python on Windows machines rather than python3.
Documentation available at https://docs.idmod.org/projects/emodpy-malaria/en/latest/.
To build the documentation locally, do the following:
-
Create and activate a venv.
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Navigate to the root directory of the repo and enter the following:
pip install -r requirements.txt cd docs pip install -r requirements.txt cd .. pip install -e . cd docs 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.
Frequently asked questions are answered in https://docs.idmod.org/projects/emodpy-malaria/en/latest/faq.html.
##Community
The EMOD Community is made up of researchers and software developers, primarily focused on malaria and HIV research. We value mutual respect, openness, and a collaborative spirit. If these values resonate with you, we invite you to join our EMOD Slack Community by completing this form:
https://forms.office.com/r/sjncGvBjvZ
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 https://github.com/InstituteforDiseaseModeling/emodpy-malaria/blob/main/CONTRIBUTING.rst' page for how to provide your feedback.
There are several options if you are modifying the code locally.
Option 1:
install in the emodpy-malaria directory:
pip install -e .
Option 2: Each time you make a change you want to use:
python setup.py bdist_wheel
pip install dist\emodpy_malaria-XXX.whl
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.