update coverage badge link and links from docs to GitHub

khillion · khillion · commit c44d09c373dd · 2017-01-26T15:04:31.000+01:00
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # python-cwlgen
 
 [![Build Status](https://travis-ci.org/khillion/python-cwlgen.svg?branch=master)](https://travis-ci.org/khillion/python-cwlgen)
-[![codecov](https://codecov.io/gh/khillion/python-cwlgen/branch/master/graph/badge.svg)](https://codecov.io/gh/khillion/python-cwlgen)
+[![codecov](https://codecov.io/gh/common-workflow-language/python-cwlgen/branch/master/graph/badge.svg)](https://codecov.io/gh/common-workflow-language/python-cwlgen)
 [![Documentation Status](https://readthedocs.org/projects/python-cwlgen/badge/?version=latest)](http://python-cwlgen.readthedocs.io/en/latest/?badge=latest)
 
 Python-cwlgen is a python library for the generation of CWL programmatically.
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -11,8 +11,8 @@ Python-cwlgen
 
    introduction
    installation
-   references
    user_guide
+   references
 
 Python-cwlgen API documentation
 ===============================
diff --git a/doc/source/user_guide.rst b/doc/source/user_guide.rst
@@ -10,10 +10,15 @@ This user guide aims to help you through the different steps to build your CWL t
 python-cwlgen.
 
 .. Note::
-    If you find a bug, have any questions or suggestions, please submit an issue on Github.
+    If you find a bug, have any questions or suggestions, please `submit an issue on Github`_.
+
+.. _`submit an issue on Github`: https://github.com/common-workflow-language/python-cwlgen/issues/new
 
 Basic example
 -------------
+Through this little tutorial, we will go step by step through the example you can `find on Github`_.
+
+.. _`find on Github`: https://github.com/common-workflow-language/python-cwlgen/blob/master/examples/example.py
 
 Initialize your tool
 """"""""""""""""""""
