From 1e730fad33de43c1751a946d52da915c119381c0 Mon Sep 17 00:00:00 2001 From: biologyguy Date: Fri, 7 Oct 2016 08:51:14 -0400 Subject: [PATCH] Add README in rst format for PyPi Modify setup files as needed --- README.md | 2 +- README.rst | 89 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ setup.cfg | 2 +- setup.py | 4 +-- 4 files changed, 93 insertions(+), 4 deletions(-) create mode 100644 README.rst diff --git a/README.md b/README.md index b849b8e..434f4ea 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ Each tool in the BuddySuite has been extensively documented in the [wiki](https: * [SeqBuddy](https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy) * [AlignBuddy](https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy) * [PhyloBuddy](https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy) -* [DatabaseBuddy](https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy). +* [DatabaseBuddy](https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy) ## Developers All of the individual Buddy toolkits are located in the 'buddysuite' directory and the diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..5a22f4f --- /dev/null +++ b/README.rst @@ -0,0 +1,89 @@ +|Build Status| |Coverage Status| |PyPi version| + +|BuddySuite| + +-------------- + +Description +----------- + +The BuddySuite modules are 'one-stop-shop' command line tools for common +biological data file manipulations. Formats are detected automatically, +conversions are seamless, and you can pipe into or out of the modules, +allowing you to spend more time analyzing your sequences, alignments, +and phylogenetic trees, instead of wrangling them. + +For example, the following command reads in three sequence files (all in +different formats), pulls out records with RefSeq identifiers, calls +MAFFT to generate an alignment, shifts gaps to force a codon alignment, +calls RAxML to infer a phylogeny, and then roots the tree at its +midpoint. + +``$: seqbuddy seqs1.gb seqs2.embl seqs3.fasta --pull_records "[XN]M" | alignbuddy --generate_alignment mafft | alignbuddy --enforce_triplets | phylobuddy --generate_tree raxmlHPC-SSE3 | phylobuddy --root`` + +BuddySuite is a Python3 project, developed and extensively tested on +Linux and Mac OS X. Full release versions are also tested on Windows +before release, so should work as expected on Vista and above. + +Getting started +--------------- + +The simplest way to get up and running is: + +.. code:: bash + + $: pip install buddysuite + $: buddysuite -setup + +Further instructions are available in the `installation +guide `__. + +There is also a short `Beginners' +Guide `__ +to show you the basics. + +Each tool in the BuddySuite has been extensively documented in the +`wiki `__, complete with +worked examples and explanations for all arguments/options. + +- `SeqBuddy `__ +- `AlignBuddy `__ +- `PhyloBuddy `__ +- `DatabaseBuddy `__ + +Developers +---------- + +All of the individual Buddy toolkits are located in the 'buddysuite' +directory and the `'develop' +branch `__ is +where all new features have been implemented. If you're interested in +contributing, please refer to the `developer +page `__ for +further information on dependencies and instructions. + +Citation +-------- + +We are currently working on a `peer reviewed +manuscript `__, +but until then there is a very short application note on bioRxiv that +can be cited if you use BuddySuite in your work. + +`DOI: 10.1101/040675 `__ + +Contact +------- + +Any comments you have would be really appreciated. Please feel free to +add issues in the GitHub issue tracker or contact Steve Bond (lead +developer) directly at steve.bond@nih.gov. + +.. |Build Status| image:: https://travis-ci.org/biologyguy/BuddySuite.svg?branch=master + :target: https://travis-ci.org/biologyguy/BuddySuite +.. |Coverage Status| image:: https://coveralls.io/repos/github/biologyguy/BuddySuite/badge.svg?branch=master + :target: https://coveralls.io/github/biologyguy/BuddySuite?branch=master +.. |PyPi version| image:: https://img.shields.io/pypi/v/buddysuite.svg + :target: https://pypi.python.org/pypi/buddysuite +.. |BuddySuite| image:: https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/BuddySuite-logo.gif + :target: https://github.com/biologyguy/BuddySuite/wiki \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index b88034e..5aef279 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,2 +1,2 @@ [metadata] -description-file = README.md +description-file = README.rst diff --git a/setup.py b/setup.py index 15175f4..e1c33f4 100755 --- a/setup.py +++ b/setup.py @@ -75,10 +75,10 @@ def run(): } setup(name='buddysuite', - version='1.2b.3', + version='1.2b.6', description='BuddySuite is a collection of command line utilities written in Python for ' 'working with biological data.', - long_description=open(os.path.join(os.path.dirname(__file__), 'README.md'), encoding="utf-8").read(), + long_description=open(os.path.join(os.path.dirname(__file__), 'README.rst'), encoding="utf-8").read(), author='Stephen Bond', author_email='steve.bond@gmail.com', url='https://github.com/biologyguy/BuddySuite',