installation.md

Installation

Biotope 0.10 supports Python 3.10–3.12. The graph extra installs BioCypher and Pyright for typed graph checking and export. The base package supports the metadata workflow without those graph dependencies.

Install the published package

The examples below use uv and a POSIX shell on Linux or macOS:

uv venv --python 3.12 .venv
uv pip install --python .venv/bin/python 'biotope[graph]>=0.10,<0.11'
source .venv/bin/activate
biotope --version

croissant-baker is installed from PyPI as a dependency. A sibling checkout or editable croissant-baker installation is unnecessary.

Pyright needs Node.js on PATH. To let the Pyright package supply its runtime instead:

uv pip install --python .venv/bin/python 'pyright[nodejs]'
python -m pyright --version

The first invocation may download Node.js. Prepare this runtime before using an environment without network access.

Existing uv project

Add Biotope to the project's dependencies and run commands through its environment:

uv add 'biotope[graph]>=0.10,<0.11'
uv run biotope --version

The same Node.js requirement applies. Install the libraries your own loaders import in this environment too, and declare them in graph/pyproject.toml; biotope graph check warns about an undeclared import.

Standard Python environment

With Python 3.10–3.12 selected:

python -m venv .venv
source .venv/bin/activate
python -m pip install 'biotope[graph]>=0.10,<0.11'

On Windows, activate with .venv\Scripts\Activate.ps1 in PowerShell and use .venv\Scripts\python.exe where these examples use .venv/bin/python.

For metadata-only work, install biotope in place of biotope[graph]. A one-off scaffold can also be created with uvx biotope init my-kg; subsequent graph work needs a project environment with the graph extra.

Create a project

biotope init my-kg
cd my-kg
biotope graph scaffold

init creates metadata configuration and purpose files. graph scaffold adds the Python graph workspace, including a dependency declaration in graph/. Neither command installs dependencies or completes a pipeline. Adapt the scaffold using the typed graph guide, or run the completed tutorial.

Develop Biotope itself

From a repository checkout:

uv sync --locked --extra dev --extra graph
uv run python -m pyright --version
uv run pytest

This uses the published croissant-baker version in uv.lock. See the contributor guide for the full checks and documentation build.