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