Installation

Stable Release

With uv (recommended):

uv add neurodags
# Or with TUI support
uv add neurodags[tui]

With pip:

pip install neurodags
# Or with TUI support
pip install neurodags[tui]

The core install provides the neurodags CLI, including run, dry-run, dataframe, dag, view, and validate. The tui subcommand requires the optional [tui] extra.

Development Install

git clone https://github.com/yjmantilla/neurodags
cd neurodags
uv sync --all-extras    # creates .venv and installs all deps incl. dev/test/docs
uv run pre-commit install

No uv? pip install uv or curl -Ls https://astral.sh/uv/install.sh | sh. Without uv: python -m venv .venv && source .venv/bin/activate && pip install -e .[dev,test,docs] && pre-commit install

Running Commands

All development commands use uv run so you never need to activate the environment:

uv run ruff check src/              # lint
uv run ruff check src/ --fix        # lint + autofix
uv run black --check .              # format check
uv run black .                      # format
uv run pytest -q                    # run tests
uv run pytest -s -q --no-cov --pdb  # debug a test

uv run sphinx-build -b html docs docs/_build/html -W --keep-going  # build docs
rm -rf docs/_build                                                   # clean docs

HDF5 / NetCDF Note

If you encounter RuntimeError: NetCDF: HDF error when writing .nc files:

uv run pip install --no-binary=h5py h5py

Requirements

• Python >= 3.10

• Core dependencies: mne, xarray, netCDF4, pydantic, networkx, joblib, plotly, dash, structlog, pyyaml, fooof, antropy, neurokit2