Installation

species is compatible with Python 3.6/3.7/3.8 and is available in the PyPI repository and on Github.

Installation from PyPI

The Python package can be installed with the pip package manager:

$ pip install species

Or, to update to the most recent version:

$ pip install --upgrade species

Important

Currently it is recommended to install species from Github (see below) in order to benefit from the most recent implementations. The available package on PyPI is also stable but it usually trails behind the version on Github.

Installation from Github

Installation from Github is done by cloning the repository:

$ git clone git@github.com:tomasstolker/species.git

And running the setup script to install the package and its dependencies:

$ python setup.py install

Important

If an error occurs when running setup.py then possibly pip needs to be updated to the latest version:

$ pip install --upgrade pip

Alternatively to running the setup.py file, the folder where species is located can also be added to the PYTHONPATH environment variable such that the package is found by Python. The command may depend on the OS that is used, but is often something like:

$ export PYTHONPATH=$PYTHONPATH:/path/to/species

New commits can be pulled from Github once a local copy of the repository exists:

$ git pull origin master

Do you want to make changes to the code? Please fork the species repository on the Github page and clone your own fork instead of the main repository. Contributions and pull requests are very welcome (see Contributing section).

Testing species

The installation can now be tested, for example by starting Python in interactive mode and printing the version number of the installed package:

>>> import species
>>> species.__version__