Installation Extras
===================

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

.. code-block:: bash

   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
----------------

.. list-table::
   :header-rows: 1
   :widths: 20 80

   * - 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

``[pipeline]`` Extra
^^^^^^^^^^^^^^^^^^^^

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

.. code-block:: bash

   pip install neurodent[pipeline]

See :doc:`pipeline` for SLURM cluster configuration.

``[dev]`` Extra
^^^^^^^^^^^^^^^

The development extra includes everything needed to contribute to NeuRodent:

.. code-block:: bash

   pip install neurodent[dev]

See the :doc:`../contributing/index` for development setup instructions.

``[all]`` Extra
^^^^^^^^^^^^^^^

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

.. code-block:: bash

   pip install neurodent[all]