Install From Command Line

This page describes how to install SanPy from the command-line.

If you want to download and run SanPy as a pre-built desktop application, please see our easy to follow download SanPy page.

Install from the command line

SanPy currently uses Python 3.13 and a pinned scientific stack. We recommend uv to create and manage the environment.

Install uv and Git.

1) Clone the repository

git clone https://github.com/cudmore/SanPy.git

2) Install the environment

cd SanPy

Core library:

    uv sync

Desktop app and GUI tests:

    uv sync --extra gui

Matplotlib plots, including `sanpy.analysisPlot`:

    uv sync --extra plot

With pip, those are `pip install .`, `pip install ".[gui]"`, and
`pip install ".[plot]"`.

3) Install NicePool for local development

NicePool is a sibling package. It is not part of `sanpy-ephys[gui]`.
From the SanPy repository root, after the GUI sync:

    (cd ../mapmanager-web-components && npm run build --workspace @mapmanager/nicepool-pyqt5-frontend)

    uv pip install --python .venv/bin/python --editable \
      ../mapmanager-web-components/integrations/nicepool-pyqt5

`uv sync` removes that editable install. Run the `uv pip install` command
again after every sync.

4) Run SanPy

uv run sanpy

The first time you run from the command line will take some time. Please be patient.

5) Run the tests

uv run pytest

That command includes the NicePool browser test when `nicepool_pyqt5` is
installed. The test is skipped when that package is not installed.