Installation

Ivy is a module for Python 3. You probably want to install it into a virtual environment. A convenient way to do this is using conda, the package/environment manager provided by the Anaconda Python distribution and its minimalist cousin, Miniconda.

Installation using conda

This is the recommended way, unless you prefer another system of managing your environments, in which case adapting the instructions below should be straightforward.

Install Anaconda or Miniconda

Install the Python 3 version of either Anaconda (large, slow to download, includes most dependencies of ivy) or Miniconda (small, fast to download, includes no dependencies).

The following assumes you now have conda in your $PATH and you’re using a Mac or Linux terminal. The same tasks can be done using the Anaconda Navigator’s graphical interface.

Create a new environment for ivy

This is optional, but probably a good idea.

$ conda create -n ivy  # here 'ivy' is just the environment name

Activate the environment. The environment’s name should appear in the shell prompt.

$ source activate ivy
(ivy) $

Install dependencies

Ivy liberally draws from the amazing ecosystem of Python data science libraries, such as scipy, pandas, and especially matplotlib.

The advantage of using conda here is that it pulls in compiled versions of the packages needed by ivy, and all their dependencies; you could use pip instead, but depending on your setup, it may require compiling things that you’re not prepared to compile. (With the exception of biopython, all of ivy’s dependencies are already included in Anaconda.)

(ivy) $ conda install numpy scipy matplotlib pandas biopython pyparsing lxml jupyter

This will pull in many other dependencies, and may take several minutes to complete.

Finally install ivy:

(ivy) $ pip install git+http://github.com/rhr/ivy.git

This pulls the latest source code from the github repository.

Updating ivy

First remove the existing installation:

(ivy) $ pip uninstall ivy-phylo

Then re-install it:

(ivy) $ pip install git+http://github.com/rhr/ivy.git