diff --git a/README.md b/README.md index 6cf8798..a247ad8 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,11 @@ # BIRDMAn [![GitHub Actions CI](https://github.com/gibsramen/birdman/workflows/BIRDMAn%20CI/badge.svg)](https://github.com/gibsramen/BIRDMAn/actions) -[![Documentation Status](https://readthedocs.org/projects/birdman/badge/?version=latest)](https://birdman.readthedocs.io/en/latest/?badge=latest) +[![Documentation Status](https://readthedocs.org/projects/birdman/badge/?version=stable)](https://birdman.readthedocs.io/en/stable/?badge=stable) [![PyPI](https://img.shields.io/pypi/v/birdman.svg)](https://pypi.org/project/birdman) **B**ayesian **I**nferential **R**egression for **D**ifferential **M**icrobiome **An**alysis (**BIRDMAn**) is a framework for performing differential abundance analysis through Bayesian inference. -Much of the code in this repository has been adapted from and inspired by [Jamie Morton](https://mortonjt.github.io/probable-bug-bytes/probable-bug-bytes/differential-abundance/). - ## Installation Currently BIRDMAn requires Python 3.7 or higher. @@ -21,4 +19,4 @@ pip install birdman You have to install `cmdstan` through the `cmdstanpy.install_cmdstan` function first. See the [CmdStanPy documentation](https://mc-stan.org/cmdstanpy/installation.html#install-cmdstan) for details. -See the [documentation](https://birdman.readthedocs.io/en/latest/?badge=latest) for details on usage. +See the [documentation](https://birdman.readthedocs.io/en/stable/?badge=stable) for details on usage. diff --git a/setup.py b/setup.py index 73113c1..2120f5d 100644 --- a/setup.py +++ b/setup.py @@ -1,10 +1,10 @@ +# Inspired by the EMPress setup.py file from setuptools import find_packages, setup -__version__ = "0.0.1" +__version__ = "0.0.2" -# Inspired by the EMPress classifiers classifiers = """ - Development Status :: 2 - Pre-Alpha + Development Status :: 3 - Alpha License :: OSI Approved :: BSD License Programming Language :: Python :: 3.7 Programming Language :: Python :: 3.8 @@ -14,13 +14,21 @@ Operating System :: MacOS :: MacOS X Topic :: Scientific/Engineering :: Bio-Informatics """ -short_desc = "Framework for differential abundance using Bayesian inference" +short_desc = ( + "Framework for differential microbiome abundance using Bayesian " + "inference" +) + +with open('README.md') as f: + long_description = f.read() setup( name="birdman", author="Gibraan Rahman", author_email="grahman@eng.ucsd.edu", description=short_desc, + long_description=long_description, + long_description_content_type="text/markdown", url="https://github.com/gibsramen/BIRDMAn", version=__version__, license='BSD-3-Clause', @@ -38,5 +46,5 @@ "arviz" ], extras_require={"dev": ["pytest", "scikit-bio", "sphinx"]}, - classifiers=classifiers + classifiers=[s.strip() for s in classifiers.split('\n') if s] )