emodpy 3.0.0

Core tools for modeling using EMOD

emodpy

Documentation available at https://emod-hub.github.io/emodpy/

Table of Contents

• User Installation
  • Pre-requisites
• Development Environment Setup
  • First Time Setup
  • Development Tips
  • To run examples or tests
  • Building docs
• Community
• Disclaimer

User Installation

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

Pre-requisites

• Python 3.9 x64

Development Environment Setup

When setting up your environment for the first time, you can use the following instructions

First Time Setup

1. Clone the repository:

   > git clone https://github.com/EMOD-Hub/emodpy.git
   

2. Create a virtualenv. On Windows, please use venv to create the environment python -m venv idmtools On Unix(Mac/Linux) you can use venv or virtualenv
3. Activate the virtualenv
4. If you are on windows, run pip install py-make --upgrade --force-reinstall
5. Then run python ./.dev_scripts/bootstrap.py. This will install all the tools.

Development Tips

There is a Makefile file available for most common development tasks. Here is a list of commands

clean       -   Clean up temproary files
lint        -   Lint package and tests
test        -   Run All tests
coverage    -   Run tests and generate coverage report that is shown in browser

On Windows, you can use pymake instead of make

To run examples or tests

First, install idmtools packages including emodpy package from idm artifactory

staging artifactory with nightly build packages:

pip install idmtools[idm] --index-url=https://email:[e-mail]/api/pypi/pypi-staging/simple
OR
pip install idmtools[full] --index-url=https://email:[e-mail]/api/pypi/pypi-staging/simple

[idm] option will install all idmtools packages except idmtools_platform_local package

[full] option will install all idmtools packages including idmtools_platform_local package

email:password is your company login credentials. password should be encoded for specially characters

production artifactory with latest release packages:

pip install idmtools[idm] --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
OR
pip install idmtools[full] --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

To run integration tests or examples, you also need to install idmtools-test package

pip install idmtools-test --extra-index-url=https://email:[e-mail]/api/pypi/pypi-staging/simple
OR
pip install idmtools-test --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

Building docs

Install all necessary documentation tools using pip install .[docs] --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple and run the command mkdocs build. After changing docstrings, reinstall emodpy to pick up the latest changes in the documentation build.

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

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.