v0.3.1 Bugfix: ribocount: allow creation of zip files larger than 2GB

ribocount fails to create zip files larger than 2GB due to missing ZIP64 extensions. This is now fixed (zipfile.ZipFile(..., allowZip64=True)).

Thanks @audreymannion for reporting the bug and for the fix.

v0.3 Support for multiple read lengths and offsets

• Support for multiple read lengths and corresponding offsets.
• Optional arguments check is now split into multiple steps.
• Remove the calculation of read lengths present in the BAM alignment.

Bugfix: Use tested versions of libraries as dependencies

• Bugfix: Use tested 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].

Bugfixes for ribocount

• Bugfix: ribocount now returns correct read counts if an offset is provided.
• 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

• Bugfix: Recalculate read frame positions after applying offset.
• Add sequence to CSV output.

Plot style changes, Fix for matplotlib DISPLAY error (Galaxy)

• 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.

Add mock to requirements

Fix: Add mock again to setup requirements. Matplolib install under Galaxy fails otherwise.

v0.2.0 - Color schemes for plots and 5' and 3' read counts

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 -> 600.
• Sample scripts to plot multiple transcripts and multiple color schemes.

ribocount

• Ability to output read counts in 5'(-v) and 3'(-r) regions.

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].

v0.1.1

• Remove invalid Python 3 version (whl).
• Remove unused test data files.
• Remove strict dependence on matplotlib and pysam versions.
• Cleanup MANIFEST.

First release

This is the first release of RiboPlot.