Installation¶

EpiBenchmark uses a standard Python installation flow with one extra runtime requirement for scoring: epibench score calls Rscript and needs the CRAN packages scoringutils and purrr.

Requirements¶

Python 3.10 or later
Git
R and the scoringutils and purrr packages 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 create --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 packages scoringutils and purrr must be installed in the R library used by that Rscript

Check that R is available with:

Rscript --version

Install the required R packages with:

Rscript -e 'install.packages(c("scoringutils", "purrr"))'

Verify that the packages are available with:

Rscript -e 'library(scoringutils); library(purrr)'

If epibench score reports that Rscript, scoringutils, or purrr 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