Docs now point to GitHub issue tracker.

.gitignore

@@ -34,3 +34,6 @@ tests/draw_results
 .mr.developer.cfg
 .project
 .pydevproject
+
+# vi
+.*.swp

README

@@ -2,7 +2,7 @@ The Readme
 ==========
 
 :Download: `From sourceforge <http://sourceforge.net/projects/pycogent>`_ or follow the :ref:`quick-install` instructions.
-:Registration: To be informed of bugs, new releases please subscribe to the `mailing lists at sourceforge <http://sourceforge.net/projects/pycogent>`_.
+:Registration: To be informed of bugs and new releases, please subscribe to the `News and Announcements Blog <http://pycogent.wordpress.com>`_.
 
 Dependencies
 ------------

doc/cookbook/introduction.rst

@@ -6,7 +6,4 @@ The cookbook remains incomplete with many sections not yet written. Rather than
 
 What we hope is clear from the Cookbook is that PyCogent has extensive capabilities that cover for many areas of genomic biology including, but not limited to: comparative genomics, metagenomics and systems biology.
 
-If you have particular need of an example falling in any of the sections, please post a documentation request on the appropriate projects forums_ page. Better yet, if you write one and attach to such a posting we'll include it!
-
-.. _forums: http://sourceforge.net/projects/pycogent/forums
-
+If you have particular need of an example falling in any of the sections, please create a new issue on our GitHub `issue tracker <https://github.com/pycogent/pycogent/issues>`_. Better yet, if you write one, please consider submitting a `pull request <https://help.github.com/articles/using-pull-requests>`_ to the `PyCogent git repository on GitHub <https://github.com/pycogent/pycogent>`_ and we'll include it in PyCogent!

doc/developer_notes.rst

@@ -1,10 +1,7 @@
 For Developers
 ==============
 
-Anyone can contribute to the development of PyCogent, not just registered developers. If you figure out a solution to something using PyCogent that you'd like to share please post comments on the forums_ page at sourceforge and we'll look at including your tips! If you have ideas for improving the current documentation, then we want to hear from you so please post on the tracker_ page!
-
-.. _forums: http://sourceforge.net/forum/?group_id=186234
-.. _tracker: http://sourceforge.net/tracker2/?group_id=186234
+Anyone can contribute to the development of PyCogent, not just registered developers. If you figure out a solution to something using PyCogent that you'd like to share, or if you have ideas for improving the current documentation, please consider submitting a `pull request <https://help.github.com/articles/using-pull-requests>`_ to the `PyCogent git repository on GitHub <https://github.com/pycogent/pycogent>`_ and we'll look into including it in PyCogent!
 
 Grabbing from GitHub
 --------------------

doc/examples/query_ensembl.rst

@@ -5,7 +5,7 @@ Querying Ensembl
 
 .. sectionauthor:: Gavin Huttley, Hua Ying
 
-We begin this documentation with a note on dependencies, performance and code status. Ensembl_ makes their data available via MySQL servers, so the ``cogent.db.ensembl`` module has additional dependencies of `MySQL-python`_ and SQLAlchemy_. You can use ``easy_install`` to install the latter, but the former is more involved. If you experience trouble, please post to the PyCogent help forums. Regarding performance, significant queries to the UK servers from Australia are very slow. The examples in this documentation, for instance, take ~15 minutes to run when pointed at the UK servers. Running against a local installation, however, is ~50 times faster. On status, the ``cogent.db.ensembl`` module should be considered beta level code. We still strongly advise users to check results for a subset of their analyses against the data from the UK Ensembl web site.
+We begin this documentation with a note on dependencies, performance and code status. Ensembl_ makes their data available via MySQL servers, so the ``cogent.db.ensembl`` module has additional dependencies of `MySQL-python`_ and SQLAlchemy_. You can use ``easy_install`` to install the latter, but the former is more involved. If you experience trouble, please create a new issue on the `issue tracker <https://github.com/pycogent/pycogent/issues>`_ and tag it with the *question* tag. Regarding performance, significant queries to the UK servers from Australia are very slow. The examples in this documentation, for instance, take ~15 minutes to run when pointed at the UK servers. Running against a local installation, however, is ~50 times faster. On status, the ``cogent.db.ensembl`` module should be considered beta level code. We still strongly advise users to check results for a subset of their analyses against the data from the UK Ensembl web site.
 
 .. _`MySQL-python`: http://sourceforge.net/projects/mysql-python
 .. _SQLAlchemy: http://www.sqlalchemy.org/

doc/index.rst

@@ -35,10 +35,7 @@ Our primary goal is to provide a collection of rigourously validated tools for t
 Contacts and contributing
 *************************
 
-If you find a bug, have feature or documentation requests then please post comments on the corresponding tracker_ page at sourceforge. If you have any questions please post on the appropriate projects forums_ page at sourceforge. We appreciate your input!
-
-.. _tracker: http://sourceforge.net/tracker2/?group_id=186234
-.. _forums: http://sourceforge.net/projects/pycogent/forums
+If you find a bug or have feature/documentation requests, please create a new issue on our GitHub `issue tracker <https://github.com/pycogent/pycogent/issues>`_. If you have any questions, please create a new issue on the `issue tracker <https://github.com/pycogent/pycogent/issues>`_ and tag it with the *question* tag. We appreciate your input!
 
 ********
 Citation
@@ -62,6 +59,6 @@ Search
 News and Announcements
 **********************
 
-PyCogent News and Annoucements are available via the News and Announcements Blog at http://pycogent.wordpress.com.
+PyCogent News and Announcements are available via the News and Announcements Blog at http://pycogent.wordpress.com.
 
 `Subscribe to the News and Annoucements RSS Feed <http://pycogent.wordpress.com/feed>`_