Installation

Recommended: uv

At the repository root:

uv sync
source .venv/bin/activate
which python

After activation, which python should resolve to .venv/bin/python.

Optional extras are declared in pyproject.toml. The most relevant ones are:

• docs for the Sphinx documentation toolchain

• asksage for AskSage-backed model access

• aps_mic for APS microscopy integrations

• postgresql_vector_store for external PostgreSQL/pgvector client dependencies

Install an extra set with:

uv sync --extra docs

Editable install with pip

python -m venv .venv
source .venv/bin/activate
pip install -e .

With extras:

pip install -e .[docs]

Documentation build

uv sync --extra docs
source .venv/bin/activate
cd docs
make html

The built HTML site is written to docs/_build/html/.

Read the Docs

This repository includes .readthedocs.yaml and docs/requirements.txt. Read the Docs builds the Sphinx site from docs/conf.py and installs the documentation dependencies declared in docs/requirements.txt.

Status note on memory dependencies

The project defines a postgresql_vector_store extra, but the built-in MemoryManager path in the current repository creates a Chroma-backed store. Use the PostgreSQL extra only if you are extending the memory stack yourself or maintaining local integrations around it.