Getting Started with PARROT

Installation

PARROT is available through GitHub or the Python Package Index (PyPI). To install through PyPI, run

$ pip install idptools-parrot

To clone the GitHub repository and gain the ability to modify a local copy of the code, run

$ git clone https://github.com/idptools/parrot.git
$ cd parrot
$ pip install .

This will install PARROT locally. If you modify the source code in the local repository, be sure to reinstall with pip.

JULY 2022 UPDATE

To mitigate package version dependency issues involving Python, GPy, and PyTorch, new releases of PARROT have separated parrot-optimize as an optional add-on installation. All of the documentation for using parrot-optimize is unchanged. However, if you wish to use the hyperparameter optimization, there are now slight differences in how you install PARROT.

To install the PARROT that is compatible with parrot-optimize install via pip using:

$ pip install idptools-parrot[optimize]

or

$ pip install "idptools-parrot[optimize]"

Alternatively if you have the PARROT repository cloned locally you can install using

$ pip install ".[optimize]"

Testing

To see if your local installation of PARROT is working properly, first install the “pytest” package:

$ pip install pytest

Then, you can run the unit test included in the package by navigating to the /tests folder within the installation directory and running:

$ pytest -v

Note that this only works if the package is installed as a repository via GitHub. Installation through PyPI does not include the necessary datafiles to run the tests.

Example datasets

Example data that can be used with PARROT can be found in the /data folder on GitHub. Examples of usage with these datasets can be found in the documentation.