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Leonardo de Oliveira Martins1
1. Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, UK

Introduction

Phylogenetic library in python. It will contain python bindings for the low-level biomcmc-lib phylogenetic library in C. Very beta at the moment. Empty, to be precise.

tauari is the name of an endangered Brazilian timber tree. Tree → towa-ree → tauari.

Dependencies

  • python development package (with the API python/C library). Installed with your python conda installation or as python-dev from linux.
  • automake, the check unit test framework, and zlib are required for installing the lowlevel biomcmc-lib.
  • python > 3.6 and a C compiler, e.g. gcc
  • The lowlevel phylogenetic library biomcmc-lib, which should be included here (it will be compiled as well). For a more up-to-date list you may need to check the conda/docker files once they are complete.

Installation

Make sure you clone this repository recursively:

git clone --recursive  https://github.com/leomrtns/tauari.git

tl;dr: You can create a conda environment (or not) and then run pip install .

conda update -n base -c defaults conda # probably not needed, but some machines complained about it
conda env create -f environment.yml
conda activate tauari
pip install .

## since this software is under development, I find these two commands quite useful:

conda env update -f environment.yml # updat conda evironment after changing dependencies
pip install -e . # installs in development mode (modifications to python files are live)
python setup.py develop # same as above, but more verbose and overwriting ./build_setup directory

Details: autotools-based installation

Originally biomcmc-lib is an auxiliary, lowlevel library, and as such should not be directly exposed to the user or shared system-wide (you can do it, btw, but it's intended as a "subdir" for autotools). Therefore tauari compiles biomcmc-lib together with its C components, generating a dynamic library. Just like setuptools.Extension, but using autotools. It still needs setuptools to install the python components and move the library to the correct location.

Calling pip install . (or python setup.py install) will run autotools in the background, but if you want you can run it by hand:

cd build_setup
../configure --prefix="." 
make && make install
ls lib/

The file "tauari_c.so" can be imported in python.

License

SPDX-License-Identifier: GPL-3.0-or-later

Copyright (C) 2020-today Leonardo de Oliveira Martins

Tauari is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version (http://www.gnu.org/copyleft/gpl.html).