Merge branch 'dev'

CHANGELOG.txt

@@ -1,3 +1,6 @@
+v0.2.2 (2014-03-31)
+- Fix setup.py
+- Typos fixing
 v0.2.1 (2014-03-31)
 - Improve documentation
 - Add badges and further info to Readme

README.md

@@ -7,7 +7,7 @@ About
 
 READemption is a pipeline for the computational evaluation of RNA-Seq
 data. It was originally developed at the IMIB/ZINF to process dRNA-Seq
-reads (as introduced by Sharma et al., Nature, 2010 originating from
+reads (as introduced by Sharma et al., Nature, 2010) originating from
 bacterial samples. Meanwhile is has been extended to process data
 generated in different experimental setups and originating from all
 domains of life and is under active development. The subcommands which

README.rst

@@ -0,0 +1,66 @@
+About
+-----
+
+READemption is a pipeline for the computational evaluation of RNA-Seq
+data. It was originally developed at the IMIB/ZINF to process dRNA-Seq
+reads (as introduced by Sharma et al., Nature, 2010) originating from
+bacterial samples. Meanwhile is has been extended to process data
+generated in different experimental setups and originating from all
+domains of life and is under active development. The subcommands which
+are accessible viaq command-line interface cover read processing and
+aligning, coverage plot generation, gene expression quantification as
+well as differential gene expression analysis. READemption was applied
+to analyze numerous data sets. In order to set up analyses quickly
+READemption follows the principal of "convention over configuration":
+Once the input files are copied into defined folders no further
+parameters have to be given. Still, READemption's behavior can be
+adapted to specific needs of the user.
+
+Documentation
+-------------
+
+Documentation can be found on
+`here <http://pythonhosted.org/READemption/>`__.
+
+Installation
+------------
+
+Short version (if you have all the requirements installed):
+
+::
+
+    $ pip install READemption
+
+`Long version <http://pythonhosted.org/READemption/installation.html>`__
+(what are the requirements and how do you get them)
+
+License
+-------
+
+`ICSL <https://en.wikipedia.org/wiki/ISC_license>`__ - see LICENSE.txt
+
+Development
+-----------
+
+-  If possible follow the principal of "convention over configuration".
+   This means input file are into a fixed location and the result file
+   are placed in fixed location.
+
+-  The classes should be path agnostic as far a possible. The controller
+   is taking care of that and calls them adequately.
+
+-  The git braching model is very close to the one proposed
+   `here <http://nvie.com/posts/a-successful-git-branching-model/>`__.
+   There two main branches:
+
+   -  master
+   -  dev(elopment)
+
+   And there are further supporting branches:
+
+   -  feature branches - branched off and back to the dev branch
+   -  release branches - branched off from dev and merged back into dev
+      and master
+   -  hotfix branches - branched off from master and merged back into
+      dev and master
+

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2013 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 
 def main():
     parser = argparse.ArgumentParser()

docs/source/conf.py

@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.1'
+release = '0.2.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.2.1',
+    version='0.2.2',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',
@@ -18,8 +18,8 @@
     license='LICENSE.txt',
     long_description=open('README.rst').read(),
     classifiers=[
-        'License :: OSI Approved :: ISC License (ISCL)'
-        'Operating System :: POSIX'
+        'License :: OSI Approved :: ISC License (ISCL)',
+        'Operating System :: POSIX',
         'Programming Language :: Python :: 3',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
     ]