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Curate, visualize, and annotate your behavioral ephys data using Python

Project description

Curate, visualize, and annotate your behavioral ephys data using Python

PyPI project GitHub source code Build status Coverage status

Installing dependencies

Because neurotic depends on some pre-release changes in a couple libraries, pip cannot automatically fetch all dependencies during normal installation. Therefore, dependencies must be installed manually.

With conda

A recipe for installing neurotic via conda directly is not yet available. However, the file environment.yml is provided for installing its dependencies into a conda environment. To install into a new conda environment named neurotic, use these commands:

git clone https://github.com/jpgill86/neurotic.git
conda env create -f neurotic/environment.yml -n neurotic

To update an existing environment, replace conda env create with conda env update.

Remember to switch environments if necessary before proceeding with installation (conda activate neurotic or source activate neurotic).

Without conda

The file requirements.txt is provided for installing dependencies with pip. Dependencies can be installed using these commands:

git clone https://github.com/jpgill86/neurotic.git
pip install -U -r neurotic/requirements.txt

If you get an error while installing PyAV, especially on Windows, you may need to build it from scratch or get it from another source, such as conda-forge:

conda install -c conda-forge av

Installing neurotic

To reiterate, you must install dependencies manually. They will not be installed with neurotic.

To install the latest release version from PyPI, use

pip install neurotic

To install the latest development version from GitHub, use

pip install git+https://github.com/jpgill86/neurotic.git

To install from a local copy of the source code, use

python setup.py install

Getting started

Launch the standalone app from the command line:

neurotic

A simple example is provided. Select the “example dataset”, download the associated data, and then click launch.

Command line arguments can be listed using

neurotic --help

Questions and support

Please post any questions, problems, comments, or suggestions in the GitHub issue tracker.

Changes

0.2.0 (2019-06-28)

Improvements

  • Add basic command line arguments (#14)

  • Add continuous integration with Travis CI for automated testing (#13)

  • Add some tests (#15, #16)

  • Migrate example data to GIN (#18)

Bug fixes

  • Fix crash when downloading from a server that does not report file size (#17)

  • Raise an exception if a Neo RawIO cannot be found for the data file (#12)

0.1.1 (2019-06-22)

Bug fixes

  • Fix various downloader errors (#7)

0.1.0 (2019-06-22)

  • First release

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