AEGeAn Toolkit version 0.16.0

Fixed

• Outer gene in intron gene cases now designated as a ciLocus.
• ciLoci are now exempt from merging into miLoci.
• Fixes to how polycistrons and other edge cases are handled.

AEGeAn Toolkit version 0.15.2

Fixed

• Minor typo in AgnLocus class.
• Correct reporting of iLocus type.

AEGeAn Toolkit version 0.15.1

Fixed

• Updated installation instructions.

AEGeAn Toolkit version 0.15.0

Changed

• Now using a "label" (accession/Name/ID/position) in place of feature IDs in many places.
• iLocus children and grandchildren counts are now prefixed with child_, so as to prevent warning messages for features with an uppercase first letter
  (GFF3 attribute keys starting with an uppercase letter are disallowed except for those declared in the specification).
• Unit tests adjusted to handle GenomeTools 1.5.8's handling of the gff-version pragma (1 space instead of 3).

Fixed

• Bug in miloci.py that prevented the last miLocus from printing.
• Better reporting of issues with gene/mRNA interval containment.
• Make build order deterministic (to facilitate reproducible builds on, i.e., Debian).
• Implemented Python 3 support for all ancillary Python scripts.
• A bug with the locus filtering code that distinguished between reference and prediction loci.
• Improved build and test environment for systems without Cairo installed.