Installation

Installing pypillometry and its dependencies is automated and can be done by running the following lines (on Mac OS X or Linux).

$ git clone https://github.com/ihrke/pypillometry.git
$ cd pypillometry
$ pip install -r requirements.txt
$ python setup.py install

pypillometry is on PyPI and released versions can be installed with pip (this will also install the dependencies automatically):

$ pip install pypillometry

(link to the PyPI project page).

It is also possible to install the developer’s version directly from github using pip

$ pip install git+https://github.com/ihrke/pypillometry.git

Requirements

pypillometry requires Python3 and a range of standard numerical computing packages (all of which listed in the file requirements.txt)

• numpy, scipy and matplotlib

• cmdstanpy

If you want to ready Eyelink’s .edf files directly, you can install the [eyelinkio](https://github.com/scott-huberty/eyelinkio) package.

It can be useful to access pypillometry through Jupyter or Jupyter Notebook, so installing those packages is also useful but not necessary.

All requirements can be installed by running pip install -r requirements.txt.

Virtual environments

It can sometimes be useful to install a new package in a new virtual environment using either Python’s virtual environments or conda.

$ conda create -n pypil python=3
$ conda activate pypil
$ conda install anaconda
$ pip install -r requirements.txt

The anaconda package contains all the requirements except cmdstanpy which can be installed from conda-forge

$ conda install -c conda-forge cmdstanpy

CmdStanPy

pypillometry uses cmdstanpy to interface with the Stan probabilistic programming language. cmdstanpy is a Python interface to the CmdStan command-line interface to Stan.

Please refer to the CmdStanPy documentation for more information on how to install and use it.