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

:code:`spikeinterface` is a Python package.

From PyPi
---------

To install the current release version, you can use:

.. code-block:: bash

   pip install spikeinterface[full]

The :code:`[full]` option installs all the extra dependencies for all the different sub-modules.

Note that if using Z shell (:code:`zsh` - the default shell on macOS), you will need to use quotes (:code:`pip install "spikeinterface[full]"`).


To install all interactive widget backends, you can use:

.. code-block:: bash

   pip install spikeinterface[full,widgets]

Note that the :code:`[widgets]` option also installs jupyter (and relative dependencies).


If you wish to only install the :code:`core` module, without optional dependencies, you can use:

.. code-block:: bash

   pip install spikeinterface


From source
-----------

As :code:`spikeinterface` is undergoing a heavy development phase, it is sometimes convenient to install from source
to get the latest bug fixes and improvements. We recommend constructing the package within a
`virtual environment <https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/>`_
to prevent potential conflicts with local dependencies.

.. code-block:: bash


   git clone https://github.com/SpikeInterface/spikeinterface.git
   cd spikeinterface
   pip install -e .
   cd ..

Note that this will install the package in `editable mode <https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs>`_.

It is also recommended in that case to also install :code:`neo` and :code:`probeinterface` from source,
as :code:`spikeinterface` strongly relies on these packages to interface with various formats and handle probes:


.. code-block:: bash


   pip install git+https://github.com/NeuralEnsemble/python-neo.git
   pip install git+https://github.com/SpikeInterface/probeinterface.git


It is also sometimes useful to have local copies of :code:`neo` and :code:`probeinterface` to make changes to the code. To achieve this, repeat the first set of commands,
replacing :code:`https://github.com/SpikeInterface/spikeinterface.git` with the appropriate repository in the first code block of this section.

Testing a PR
------------

If you have submitted an issue and another contributor has attempted to fix your issue by creating a pull request (PR), you
might want to test the PR. To do this, first install spikeinterface "from source" in editable mode by following the
instructions in the above Section.

Now enter the :code:`spikeinterface` folder in your terminal

.. code-block:: bash

   cd path/to/spikeinterface


There are a few ways to checkout a PR. The simplest is to first install the GitHub command line interface (https://cli.github.com/).
After installing this, you can run :code:`gh pr checkout PR_NUMBER`. Every pull request has an ID, which can be found on the
github Pull Request page (https://github.com/SpikeInterface/spikeinterface/pulls). So if you're interested in PR 4200 you should run:

.. code-block:: bash

   gh pr checkout 4200


If successful, the returned message should end "Switched to branch 'blah blah blah'". You're now using :code:`spikeinterface`
including the changes made in PR 4200.

For beginners
-------------

We provide some installation tips for beginners in Python here:

https://github.com/SpikeInterface/spikeinterface/tree/main/installation_tips



Requirements
------------

:code:`spikeinterface.core` itself has only a few dependencies:

  * numpy
  * probeinterface
  * neo
  * threadpoolctl
  * tqdm
  * zarr
  * pydantic
  * numcodecs
  * packaging

Sub-modules have more dependencies, so you should also install:

  * h5py
  * scipy
  * pandas
  * xarray
  * scikit-learn
  * networkx
  * matplotlib
  * numba
  * distinctipy
  * skops
  * huggingface_hub
  * cuda-python (for non-macOS users)


For developers we offer a :code:`[dev]` option which installs testing, documentation, and linting packages necessary
for testing and building the docs.

All external spike sorters can be either run inside containers (Docker or Singularity - see :ref:`containerizedsorters`)
or must be installed independently (see :ref:`get_started/install_sorters:Installing Spike Sorters`).