AEGeAn Toolkit Version 0.10
===========================

v0.10.2
-------

The changes associated with this release are mainly corrections and cosmetic
improvements for the documentation.

v0.10.1
-------

Simple usage of the AEGeAn Toolkit and additional functional tests revealed a
couple of issues with the v0.10.0 release.

  - In ParsEval's HTML output mode, the sequence overview pages were only being
    created correctly when there was a single sequence in the input.

  - ParsEval had a memory leak both in text and HTML output mode, stemming from
    AgnTranscriptClique objects that never got freed.

The first issue simply required a bit of refactoring and a different approach to
generating the sequence overview pages. The second issue took some detective
work to find the leak, which was in the core code (AgnLocus class).

Along the way, I extended the functional tests and improved the testing for
memory leaks a bit.

v0.10.0
-------

The core of the AEGeAn Toolkit has been under heavy re-development for several
months. The primary focus of this development has been:

  - implementating analysis components as feature visitors and feature streams
    to facilitate efficient online streaming processing of annotations, as is
    the canonical GenomeTools approach

  - generalizing the comparative analysis code originally implemented in
    ParsEval so that it can be called by other programs via the AEGeAn C API

  - implementation of better software development practices; continuous
    integration and testing (via Travis CI), static code analysis (by Coverity
    Scan), better unit testing, better functional testing, and early correction
    of memory leaks before additional features are implemented

In the refactoring process, several features have been excluded. Most should be
re-introduced when I have time, but some minor features many not make it back in
unless there is a really good motivation to do so.

As a final note, I have only just in the last few months understood how to use
Semantic Versioning and git/Github's tag/release features correctly. AEGeAn is
still pre-1.0, so any changes to the code or API are still on the table, but
moving forward I will be adhering to semantic versioning prescriptions much more
 faithfully.
