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DART-Pipeline

Python 3.12+ Tests Documentation status Ruff

Data analysis pipeline for the Dengue Advanced Readiness Tools (DART) project.

The aim of this project is to develop a scalable and reproducible pipeline for the joint analysis of epidemiological, climate, and behavioural data to anticipate and predict dengue outbreaks.

Documentation | Contributing Guide

Setup

We use uv to setup and manage Python versions and dependencies. uv can be installed using the following method:

curl -LsSf https://astral.sh/uv/install.sh | sh

If you do not have curl installed, then use brew install curl on macOS or sudo apt install curl on Debian/Ubuntu or sudo dnf install curl on Fedora/RHEL.

If you have an existing virtual environment for DART pipeline, it should be removed as uv manages the .venv folder itself. Once installed, you can run dart-pipeline as follows

git clone https://github.com/kraemer-lab/DART-Pipeline
uv sync
uv run dart-pipeline

Development

Development requires the dev packages to be installed:

uv sync --all-extras
uv run pytest

The project uses pre-commit hooks, use pre-commit install to install hooks.

Authors and Acknowledgments

  • OxRSE
    • John Brittain
    • Abhishek Dasgupta
    • Rowan Nicholls
  • Kraemer Group, Department of Biology
    • Moritz Kraemer
    • Prathyush Sambaturu
  • Oxford e-Research Centre, Engineering Science
    • Sarah Sparrow

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Data analysis pipeline for the Dengue Advanced Readiness Tools (DART) project

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