Installation¶

biosigIO uses UV for Python environment and package management. There are several ways to install biosigIO depending on your needs.

From PyPI (Recommended)¶

The easiest way to install biosigIO is from PyPI:

uv pip install biosigio

If your own project is uv-managed, use uv add biosigio instead to track it as a dependency.

From GitHub Repository¶

To install the latest development version directly from GitHub:

uv pip install "git+https://github.com/neuromechanist/biosigio.git"

Or clone and install:

git clone https://github.com/neuromechanist/biosigio.git
cd biosigio
uv pip install .

Development Installation¶

For development purposes, install biosigIO in editable mode with dev dependencies:

git clone https://github.com/neuromechanist/biosigio.git
cd biosigio
uv sync --extra dev

This allows you to modify the source code and see the changes without reinstalling.

Optional Dependencies¶

biosigIO provides optional dependency groups. For an existing install use uv pip install (this is a UV-only project):

# Development tools (pytest, pytest-cov, ruff, ty)
uv pip install "biosigio[dev]"

# Documentation tools (mkdocs, mkdocs-material, mkdocstrings)
uv pip install "biosigio[docs]"

# MEG (.fif / CTF .ds) and BrainVision (.vhdr) import via MNE
uv pip install "biosigio[meg]"

# Parquet / Arrow / Feather serialization via pyarrow
uv pip install "biosigio[arrow]"

# Proprietary electrophysiology formats (Intan, Blackrock, Spike2, Plexon,
# Micromed, Neuralynx, ...) via python-neo
uv pip install "biosigio[neo]"

# Sharded Zarr v3 serving store via zarr v3
uv pip install "biosigio[zarr]"

# All optional dependencies
uv pip install "biosigio[all]"

Dependencies¶

biosigIO has the following core dependencies:

Dependency	Purpose	Minimum Version
numpy	Array operations	>=1.20.0
pandas	Data manipulation	>=1.3.0
scipy	Signal processing	>=1.7.0
matplotlib	Visualization	>=3.4.0
pyedflib	EDF/BDF file handling	>=0.1.30
wfdb	WFDB format support	>=4.0.0
pyxdf	XDF/LSL format support	>=1.16.0

These dependencies are automatically installed when you install biosigIO.

Python Version¶

biosigIO requires Python 3.11 or later. We test on Python 3.11, 3.12, 3.13, and 3.14.

Testing¶

To run the tests:

uv sync --extra dev
uv run pytest

Verifying Installation¶

Verify that biosigIO is correctly installed:

import biosigio
print(biosigio.__version__)

You should see the version number (e.g., 1.0.1 or later) without any errors.