AMR Hub ABM

An agent-based model (ABM) for simulating the spread of Antimicrobial Resistant (AMR) infections in hospital settings.

This project is developed in collaboration with the Centre for Advanced Research Computing, University College London.

Overview

amr-hub-abm is a Python package that provides a framework for modeling and analyzing the transmission dynamics of antimicrobial-resistant pathogens within healthcare facilities. The simulation incorporates spatial modeling, agent behavior, and task management to provide realistic representations of hospital environments and infection spread patterns.

Key Features

Spatial modeling: Representation of hospital buildings, floors, and room layouts
Agent-based simulation: Model individual agents (patients, healthcare workers) with distinct behaviors
Task management: Simulate realistic workflow patterns with priority-based task assignment
Flexible architecture: Extensible design for incorporating custom behaviors and scenarios

Installation

Prerequisites

amr-hub-abm requires Python 3.13 or higher.

We recommend using a virtual environment manager such as Conda or venv to create an isolated environment for the package.

Install from GitHub

To install the latest development version directly from GitHub:

pip install git+https://github.com/UCL-ARC/amr-hub.git

Install from Source (Development)

For development or to make local modifications:

Clone the repository:

git clone https://github.com/UCL-ARC/amr-hub.git
cd amr-hub/python-code

Install in editable mode:

pip install -e .

Optional Dependencies

Install additional dependencies for development and documentations:

# For development tools (testing, linting, etc.)
pip install -e ".[dev]"

# For building documentation
pip install -e ".[docs]"

# For running tests
pip install -e ".[test]"

Usage

Basic example of using the package:

from amr_hub_abm import __version__
from amr_hub_abm.space import Location, Building
from amr_hub_abm.agent import Agent
from amr_hub_abm.task import Task, TaskType, TaskPriority

# Create a location
location = Location(x=10.0, y=20.0, floor=1)

# Additional usage examples coming soon...

For more detailed examples and API documentation, please refer to the documentation.

Development

Running Tests

Tests can be run across all compatible Python versions in isolated environments using tox:

tox

To run tests manually with pytest:

pytest tests

To run tests with coverage reporting:

pytest --cov --cov-report=xml

Building Documentation

Build the MkDocs HTML documentation locally:

tox -e docs

The built documentation will be written to the site/ directory.

Alternatively, to build and preview the documentation with live reloading:

mkdocs serve

Then open your browser to http://localhost:8000.

Code Quality

This project uses several tools to maintain code quality:

pre-commit: Git hooks for automatic code formatting and linting
ruff: Fast Python linter and formatter
mypy: Static type checker

To set up pre-commit hooks:

pre-commit install

To manually run all pre-commit hooks:

pre-commit run --all-files

Contributing

Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to:

Update tests as appropriate
Follow the existing code style
Run the test suite before submitting

Contributors

_{Arindam Saha} 💻 📖 ⚠️ 🚧 🔬 🐛 👀	_Dependabot 🛡️	_{Ed Manley} 🔍 🤔 🧑‍🏫	_{George Svarovsky} 🚇	_{James Hetherington} 🤔 🧑‍🏫 🔍	_{Keiran Suchak} 💻 📖 ⚠️ 🔌 🔬 👀	_{Lauren Sheridan} 🚇
_Marlon 🚇	_MonikaSvata 📆	_{Paul Smith} 🔣 🚇	_{Sarah Keating} 🚇	_{Sarah Wise} 🤔 🧑‍🏫	_yidilozdemir 📖 🔬 💻