diff --git a/README.md b/README.md index 8fa1107..1f76ada 100644 --- a/README.md +++ b/README.md @@ -5,10 +5,37 @@ Canonically pronouced *nice* -A compositional statistics and visualization toolbox +gneiss is a compositional statistics and visualization toolbox. -You can install Gneiss via pip +Note that gneiss is not compatible with python 2, and is compatible with Python 3.4 or later. +gneiss is currently in alpha. We are actively developing it, and __backward-incompatible interface changes can and will arise__. + +# Installation + +To install this package, it is recommended to setup a conda environment as follows + +``` +conda create -n gneiss_env python=3 pip gneiss +``` + +You can also install Gneiss via pip ``` pip install gneiss ``` + +To run through the tutorials, you'll need a few more packages, namely `seaborn`, `biom-format` and `h5py`. +These packages can be installed with conda as follows +``` +source activate gneiss +conda install seaborn h5py +pip install biom-format +``` + +# Examples + +IPython notebooks demonstrating some of the modules in gneiss can be found as follows + +* [What are balances](https://github.com/biocore/gneiss/blob/master/ipynb/balance_trees.ipynb) +* [Linear regression on balances](https://github.com/biocore/gneiss/blob/master/ipynb/88soils.ipynb) + diff --git a/gneiss/_formula.py b/gneiss/_formula.py index 8136a44..1e8f7d6 100644 --- a/gneiss/_formula.py +++ b/gneiss/_formula.py @@ -1,4 +1,4 @@ -# ---------------------------------------------------------------------------- +`# ---------------------------------------------------------------------------- # Copyright (c) 2016--, gneiss development team. # # Distributed under the terms of the GPLv3 License. diff --git a/gneiss/layouts.py b/gneiss/layouts.py index a831cba..41b0dce 100644 --- a/gneiss/layouts.py +++ b/gneiss/layouts.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------------- # Copyright (c) 2016--, gneiss development team. # -# Distributed under the terms of the Modified BSD License. +# Distributed under the terms of the GPLv3 License. # # The full license is in the file COPYING.txt, distributed with this software. # ---------------------------------------------------------------------------- diff --git a/gneiss/tests/test_balances.py b/gneiss/tests/test_balances.py index 3af8262..7096baf 100644 --- a/gneiss/tests/test_balances.py +++ b/gneiss/tests/test_balances.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------------- # Copyright (c) 2016--, gneiss development team. # -# Distributed under the terms of the Modified BSD License. +# Distributed under the terms of the GPLv3 License. # # The full license is in the file COPYING.txt, distributed with this software. # ---------------------------------------------------------------------------- diff --git a/setup.py b/setup.py index 0d6d7a5..f6480ba 100644 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ # ---------------------------------------------------------------------------- # Copyright (c) 2016--, gneiss development team. # -# Distributed under the terms of the Modified BSD License. +# Distributed under the terms of the GPLv3 License. # # The full license is in the file COPYING.txt, distributed with this software. # ---------------------------------------------------------------------------- @@ -36,7 +36,7 @@ def finalize_options(self): classes = """ Development Status :: 3 - Alpha - License :: OSI Approved :: BSD License + License :: OSI Approved :: GPLv3 License Topic :: Software Development :: Libraries Topic :: Scientific/Engineering Topic :: Scientific/Engineering :: Bio-Informatics