Installation
============

Install Conda
-------------

Install `Anaconda <https://docs.anaconda.com/anaconda/install/index.html>`_ or `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_. Create and activate an environment called ``snub`` with python≥3.8::

   conda create -n snub python=3.8
   conda activate snub

.. note::
   Python version 3.8 is required for Linux. For Windows and MacOS, any version ≥3.8 should work.



Install SNUB
------------

Install SNUB using ``pip``::

   pip install systems-neuro-browser

To speed up selections, we recommend installing ``ncls``::

   pip install ncls

To include optional development dependencies, install with the ``[dev]`` option::

   pip install systems-neuro-browser[dev]



Test SNUB
---------

To test the installation, try launching ``snub`` from the command line (make sure the ``snub`` conda environment is activated)::

   snub

A browser window should launch. Download the `example project <https://zenodo.org/records/10578025/files/miniscope_project.zip?download=1>`_, and try opening it by going to ``File > Open Project``, navigating to the project directory, and hitting ``Choose`` with the directory selected. Projects can also be opened by including the path as a command line argument::

   snub /path/to/project/directory


SNUB + Jupyter
--------------

To use SNUB functions in a jupyter notebook, execute the following line with the ``snub`` environment active. The environment should then be listed as an option when creating a new notebook or when switching kernels (``Kernel > Change Kernel > snub``)::

   python -m ipykernel install --user --name=snub