Dependencies

PyNWB has the following minimum requirements, which must be installed before you can get started using PyNWB.

  1. Python 2.7, Python 3.5 or Python 3.6
  2. pip

Installation

Install release from PyPI

The Python Package Index (PyPI) is a repository of software for the Python programming language.

To install or update PyNWB distribution from PyPI simply run:

$ pip install -U pynwb

This will automatically install the following required dependencies:

  1. h5py
  2. numpy
  3. python-dateutil
  4. requests
  5. ruamel.yaml
  6. six

Install release from Conda-forge

Conda-forge is a community led collection of recipes, build infrastructure and distributions for the conda package manager.

To install or update PyNWB distribution from conda-forge using conda simply run:

$ conda install -c conda-forge pynwb

Install latest pre-release

This is useful to tryout the latest features and also setup continuous integration of your own project against the latest version of PyNWB.

$ pip install -U pynwb --find-links https://github.com/NeurodataWithoutBorders/pynwb/releases/tag/latest  --no-index

For developers

Install from Git repository

For development an editable install is recommended.

$ pip install -U virtualenv
$ virtualenv ~/pynwb
$ ~/pynwb/bin/activate
$ git clone git@github.com:NeurodataWithoutBorders/pynwb.git
$ cd pynwb
$ pip install -r requirements.txt -r requirements-dev.txt
$ pip install -e .

Run tests

For running the tests, it is required to install the development requirements.

$ pip install -U virtualenv
$ virtualenv ~/pynwb
$ ~/pynwb/bin/activate
$ git clone git@github.com:NeurodataWithoutBorders/pynwb.git
$ cd pynwb
$ pip install -r requirements.txt -r requirements-dev.txt
$ pip install -e .
$ tox

Following PyNWB Style Guide

Before you create a Pull Request, make sure you are following PyNWB style guide (PEP8). To do that simply run the following command in the project’s root directory.

$ flake8