spiketools
==========
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``spiketools`` is a collection of tools and utilities for analyzing spiking data.
Overview
--------
``spiketools`` is an open-source module for processing and analyzing single-unit activity from neuro-electrophysiological recordings.
Available sub-modules in ``spiketools`` include:
- ``measures`` : measures and conversions that can be applied to spiking data
- ``objects`` : objects that can be used to manage spiking data
- ``spatial`` : space related functionality and measures
- ``stats`` : statistical measures for analyzing spiking data
- ``sim`` : simulations of spiking activity and related functionality
- ``plts`` : plotting functions for visualizing spike data and related measures
- ``utils`` : additional utilities for working with spiking data
Scope
-----
``spiketools`` is currently organized around analyses of single cell activity.
The current scope does not include population measures, though this may be extended in the future.
Note that ``spiketools`` does *not* cover spike sorting.
Check out `spikeinterface <https://github.com/SpikeInterface/>`_ for spike sorting.
Documentation
-------------
Documentation for ``spiketools`` is available
`here <https://spiketools.github.io/>`_.
The documentation includes:
- `Tutorials <https://spiketools.github.io/spiketools/auto_tutorials/index.html>`_: which describe and provide examples for each sub-module
- `API List <https://spiketools.github.io/spiketools/api.html>`_: which lists and describes everything available in the module
- `Glossary <https://spiketools.github.io/spiketools/glossary.html>`_: which defines key terms used in the module
If you have a question about using ``spiketools`` that doesn't seem to be covered by the documentation, feel free to
open an `issue <https://github.com/spiketools/spiketools/issues>`_ and ask!
Dependencies
------------
``spiketools`` is written in Python, and requires Python >= 3.6 to run.
It has the following required dependencies:
- `numpy <https://github.com/numpy/numpy>`_
- `pandas <https://github.com/pandas-dev/pandas>`_
- `scipy <https://github.com/scipy/scipy>`_
- `matplotlib <https://github.com/matplotlib/matplotlib>`_
There are also optional dependencies, that offer extra functionality:
- `statsmodels <https://github.com/statsmodels/statsmodels>`_ is needed for some statistical measures, for example ANOVAs
- `pytest <https://github.com/pytest-dev/pytest>`_ is needed to run the test suite locally
We recommend using the `Anaconda <https://www.anaconda.com/distribution/>`_ distribution to manage these requirements.
Installation
------------
The current release version of `spiketools` is the 0.X.X series.
See the `changelog <https://spiketools.github.io/spiketools/changelog.html>`_ for notes on major version releases.
**Stable Release Version**
To install the latest stable release, you can use pip:
.. code-block:: shell
$ pip install spiketools
Optionally, to include dependencies required for the `stats` module:
.. code-block:: shell
$ pip install spiketools[stats]
**Development Version**
To get the current development version, first clone this repository:
.. code-block:: shell
$ git clone https://github.com/spiketools/spiketools
To install this cloned copy, move into the directory you just cloned, and run:
.. code-block:: shell
$ pip install .
**Editable Version**
To install an editable version, download the development version as above, and run:
.. code-block:: shell
$ pip install -e .
Contribute
----------
This project welcomes and encourages contributions from the community!
To file bug reports and/or ask questions about this project, please use the
`Github issue tracker <https://github.com/spiketools/spiketools/issues>`_.
To see and get involved in discussions about the module, check out:
- the `issues board <https://github.com/spiketools/spiketools/issues>`_ for topics relating to code updates, bugs, and fixes
- the `development page <https://github.com/spiketools/Development>`_ for discussion of potential major updates to the module
When interacting with this project, please use the
`contribution guidelines <https://github.com/spiketools/spiketools/blob/main/CONTRIBUTING.md>`_
and follow the
`code of conduct <https://github.com/spiketools/spiketools/blob/main/CODE_OF_CONDUCT.md>`_.
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not include population measures, though this may be extended in the future.\n\nNote that ``spiketools`` does *not* cover spike sorting.\nCheck out `spikeinterface <https://github.com/SpikeInterface/>`_ for spike sorting.\n\nDocumentation\n-------------\n\nDocumentation for ``spiketools`` is available\n`here <https://spiketools.github.io/>`_.\n\nThe documentation includes:\n\n- `Tutorials <https://spiketools.github.io/spiketools/auto_tutorials/index.html>`_: which describe and provide examples for each sub-module\n- `API List <https://spiketools.github.io/spiketools/api.html>`_: which lists and describes everything available in the module\n- `Glossary <https://spiketools.github.io/spiketools/glossary.html>`_: which defines key terms used in the module\n\nIf you have a question about using ``spiketools`` that doesn't seem to be covered by the documentation, feel free to\nopen an `issue <https://github.com/spiketools/spiketools/issues>`_ and 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