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raven-toolbox (Python)

raven-toolbox is the Python implementation of RAVEN, built on cobrapy. It is distributed on PyPI.

Requirements

  • Python ≥ 3.11
  • cobrapy — installed automatically as a dependency
  • A solver: GLPK (bundled with cobrapy) works for small and medium models; Gurobi is recommended for genome-scale work. See Choosing a solver.

Use a virtual environment

python -m venv .venv
source .venv/bin/activate      # Windows: .venv\Scripts\activate

Install

pip install raven-toolbox

For the latest unreleased code or to contribute:

git clone https://github.com/SysBioChalmers/raven-toolbox.git
cd raven-toolbox
pip install -e .

Verify

import raven_toolbox
print(raven_toolbox.__version__)

Note

The import package is raven_toolbox (underscore); the PyPI distribution name is raven-toolbox (hyphen).

Upgrade

pip install --upgrade raven-toolbox

git pull origin develop

Remove

pip uninstall raven-toolbox

Solver configuration

raven-toolbox uses cobrapy's solver interface:

import cobra
cobra.Configuration().solver = "gurobi"   # or "glpk"