EpiBenchmark

EpiBench is a work-in-progress benchmarking tool for evaluating performance of infectious disease forecasting models. The package is still in development.

Choose the installation guide that matches your environment:

• Personal computer or standard Linux workstation (Windows/macOS/Linux): Continue with the instructions below.
• High-performance computing (HPC) cluster: See installation_longleaf.

Requirements

• Python 3.10 or later
• Git
• R and the scoringutils package for the epibench score command

Quick Start

git clone https://github.com/ACCIDDA/EpiBenchmark.git
cd EpiBenchmark
uv sync
uv run epibench --help

Installation

Clone the repository:

git clone https://github.com/ACCIDDA/EpiBenchmark.git

cd EpiBenchmark

EpiBenchmark supports installation using either uv (recommended) or pip.

Option 1: Install with uv

This is the fastet installation method.

uv sync

Activate the virtual environment

Windows

.venv\Scripts\activate

macOS/Linux

source .venv/bin/activate

Alternatively, users can run commands without activating the virtual environment when using uv:

uv run epibench --help

Option 2: Install with pip

Create a virtual environment.

Windows

python -m venv .venv
.venv\Scripts\activate

macOS/Linux

python -m venv .venv
source .venv/bin/activate

Upgrade pip:

python -m pip install --upgrade pip

Install EpiBenchmark in editable mode:

python -m pip install -e .

Verify the Installation

After installation, verify that the command-line interface is available:

epibench
epibench --help

Users can also verify the available subcommands:

epibench setup --help
epibench score --help
epibench plot --help

R Requirements for Scoring

The Python virtual environment only manages EpiBenchmark's Python dependencies. The epibench score command also calls Rscript, so scoring has two external requirements:

• Rscript must be available on users' PATH
• the CRAN package scoringutils must be installed in the R library used by that Rscript

Check that R is available with:

Rscript --version

Install scoringutils with:

Rscript -e 'install.packages("scoringutils")'

Verify that the package is available with:

Rscript -e 'library(scoringutils)'

If epibench score reports that Rscript or scoringutils is missing, make sure they are installed in the same R environment used by Rscript command.

Remove the virtual environment

Deletes the local .venv directory, allowing users to create a fresh virtual environment.

Windows

If Command Prompt:

rmdir /s /q .venv 

If PowerShell:

Remove-Item -Recurse -Force .venv (PowerShell)

macOS/Linux

rm -rf .venv