Bugfix: ribocount: allow creation of zip files larger than 2GB

Fix version number (0.3 -> 0.3.0)

Release 0.3

* Bugfix: Use known versions of libraries as dependencies in setup.py.

  Otherwise, pip installs latest versions which haven't been tested.
* Remove Codons label, change START to AUG [riboplot].

* Bugfix: ribocount now returns correct read counts if an offset is p…

…rovided.

* Bugfix: Don't include read counts in the longest ORF start or stop positions
  i.e., only include reads upstream or downstream of the start or stop positions.

* Bugfix: Recalculate read frame positions after applying offset.

* Add sequence to CSV output.

* Use default linewidth (riboplot), Minor changes to default plot style.

* Use 'Agg' as the default matplotlib backend (prevent $DISPLAY errors).
* Use smaller images for the help section.
* Fix typo in HISTORY.rst.
* Update Github repository URL.

Fix: Add mock again to setup requirements. Matplolib install under Ga…

…laxy fails otherwise.

**riboplot**

* Support for color schemes - options: default, colorbrewer, rgb, greyorfs.
* Plot changes - colored, light background for ORF architecture, legend moved down.
* Image DPI change 300 |srarr| 600.
* Sample scripts to plot multiple transcripts and multiple color schemes.

**ribocount**

* Ability to output read counts in 5'(``-v``) and 3'(``-r``) leader region.

Bugfixes

1. Report error if a bam index could not be generated (ex. bam sorted using
   reference names instead of chromosome coordinates).
2. No start/stop values when transcript sequences are in lower case.

Tests

* Split into three different files.
* Updated test configuration.

Minor

* XML wrapper changes - remove 'leader', add help text and output label change [ribocount].
* Remove unused pysam import [riboplot].
* Replace doc includes with sym links (breaks Galaxy toolshed otherwise).
* Updated CSS/Table styles (removed number column from table).
* y limit is now 1.25x [riboplot].
* Removed line width on bars [riboplot].

* Remove invalid Python 3 version (whl).

* Remove unused test data files.
* Remove strict dependence on matplotlib and pysam versions.
* Cleanup MANIFEST.