Finish Release-2.11

Updated documentation

Removed dependency on sphinx extensions in order to keep both readthedocs and homebrew happy.

Fixed representation of labels and plotting coordinates based on whether the matrix should be interpretted transposed or not.

Added shebang to python library files, in order for homebrew to be happy including them in the bin directory.

Author: maplesond

README.md

@@ -104,6 +104,13 @@ Both commands do the same thing.
 
 GNU GPL V3.  See COPYING file for more details.
 
+##Cite:
+
+The KAT paper is currently in submission.  In the meantime, if you use our software
+and wish to cite us please use our bioRxiv preprint:
+
+Daniel Mapleson et al. 2016. KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. bioRxiv doi: 10.1101/064733
+
 
 ##Authors:
 
@@ -118,7 +125,7 @@ See AUTHORS file for more details.
 
 ##Acknowledgements:
 
- * Affiliation: The Genome Analysis Centre (TGAC)
+ * Affiliation: Earlham Institute (EI)
  * Funding: The Biotechnology and Biological Sciences Research Council (BBSRC)
 
 We would also like to thank the authors of Jellyfish: https://github.com/gmarcais/Jellyfish; 

configure.ac

@@ -4,7 +4,7 @@
 
 # Autoconf initialistion.  Sets package name version and contact details
 AC_PREREQ([2.68])
-AC_INIT([kat],[2.1.0],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
+AC_INIT([kat],[2.1.1],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
 AC_CONFIG_SRCDIR([src/kat.cc])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])

doc/source/conf.py

@@ -28,9 +28,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.pngmath',
-    'sphinx.ext.mathjax',
+extensions = [    
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -54,9 +52,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.1.0'
+version = '2.1.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.1.0'
+release = '2.1.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/conf.py.in

@@ -28,9 +28,7 @@ needs_sphinx = '1.3'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.pngmath',
-    'sphinx.ext.mathjax',
+extensions = [    
 ]
 
 # Add any paths that contain templates here, relative to this directory.