Installation

ipcoal can be installed using pip or conda, either of which will pull in all required dependencies. We also provide instructions below for installing from source (GitHub).

Conda install (recommended)

$ conda install ipcoal -c conda-forge

Pip install

$ pip install ipcoal

Dependencies

Our goal is to maintain ipcoal as a small library that does not require substantial dependencies outside of the standard Python scientific stack (i.e., numpy, scipy, and pandas).

- python>=3.7
- numpy
- scipy
- pandas
- loguru
- toytree
- msprime

Optional dependencies

ipcoal includes several submodules that provide wrappers around external phylogenetic inference tools, such as raxml-ng, Astral, SNaQ, and others. These tools are optional. When you call the function it will raise an exception if the required binary cannot be found in your path and will provide recommendations for how to install it using conda.

Installing Development Versions

$ conda install ipcoal -c conda-forge --only-deps
$ git clone https://github.com/eaton-lab/ipcoal.git
$ cd ipcoal
$ pip install -e . --no-deps

Building the documentation

$ conda install mkdocs-material mkdocstrings-python mkdocs-jupyter -c conda-forge
$ cd ipcoal/
$ mkdocs serve