raven-toolbox requires Python ≥ 3.11.
git clone https://github.com/SysBioChalmers/raven-toolbox
cd raven-toolbox
pip install -e ".[dev]"The core install pulls in cobra, numpy, pandas, scipy, ruamel.yaml, requests and tqdm. Some features need extra packages, exposed as optional extras:
| Extra | Pulls in | Needed for |
|---|---|---|
excel |
openpyxl |
{func}raven_toolbox.io.excel.export_to_excel |
dev |
pytest, pytest-cov, ruff |
running the test-suite / linting |
pip install -e ".[excel,dev]"Linear and most MILP work runs on the open-source GLPK that ships with cobra. Genome-scale (f)tINIT MILPs currently require Gurobi for tractable solve times — see the solver benchmark for the Gurobi vs HiGHS vs GLPK comparison and portability notes.
Homology and KEGG-HMM reconstruction shell out to BLAST+ / DIAMOND / HMMER. These are
not Python packages; raven-toolbox resolves them from a version-pinned, SHA256-verified
release registry (see {mod}raven_toolbox.binaries). The
binary maintenance guide covers building and
publishing those release ZIPs.