Tools used for the analysis of neural recording data

Getting started

• Download Miniconda from Continuum Analytics. We recommend the Python 3 version.

• Open a new terminal, create and activate a new conda environment.

  conda create -n yourenv python=3.5
  activate yourenv [Windows] or source activate yourenv [Linux]
  

• Install package dependencies (it's possible to install multiple packages at once or individually). If conda doesn't have a package of interest (eg. shapely), in the terminal try: pip install shapely. In Windows, download the most recent *.whl file here and install using pip install yourshapelyinstall.whl (must be in the directory where this .whl is located).

  conda install numpy scipy shapely pytest matplotlib sphinx numpydoc
  

• Clone the analysis code from Github and developer installation.

  git clone https://github.com/mvdm/vandermeerlab.git
  cd vandermeerlab/code-python
  python setup.py develop
  

• All set!

Documentation

Build documentation (eg. from docstrings) using python setup.py build_sphinx in the vdmlab directory.

Testing

Run tests with pytest.

License

The vdmlab codebase is made available under made available under the MIT license that allows using, copying, and sharing.