Installation Extras

NeuRodent provides optional dependency groups for different use cases. Install any extra with:

pip install neurodent[extra_name]
# or with uv:
uv add neurodent[extra_name]

Note

Using conda? Conda does not support pip-style extras. To use optional dependency groups, install NeuRodent via pip or uv instead of conda.

Available Extras

Extra	Description
[pipeline]	Snakemake and dependencies for running automated analysis workflows
[readers]	Readers for EDF and NWB files (edfio, pyedflib, pynwb)
[dev]	Development tools plus the pipeline and readers extras (for contributors)
[all]	Installs all optional runtime dependencies

[pipeline] Extra

The pipeline extra includes Snakemake and related dependencies for running the automated analysis workflow on single machines or HPC clusters.

pip install neurodent[pipeline]

See Pipeline & Cluster Setup for SLURM cluster configuration.

[readers] Extra

Readers for formats not covered by the core dependencies. .edf and .nwb files need this extra; the documentation tutorials use it for their single-file loading example.

pip install neurodent[readers]

[dev] Extra

The development extra includes everything needed to contribute to NeuRodent:

pip install neurodent[dev]

See the canonical CONTRIBUTING.md guide for development setup instructions.

[all] Extra

Installs [pipeline] and [readers] together.

pip install neurodent[all]