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
`[dev]`	Development tools plus all pipeline dependencies (for contributors)
`[all]`	Installs all optional runtime dependencies

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.

The development extra includes everything needed to contribute to NeuRodent:

pip install neurodent[dev]

See the Contributing for development setup instructions.

Installs all optional runtime dependencies (currently equivalent to [pipeline]).

pip install neurodent[all]