Fix GAF lines by adding missing underscore to qualifiers

v3.0.1

fix: restored case sensitive qualifiers

Minor changes following paper reviewers comments

This release introduces minor changes requested by the paper reviewers. These are the highlights:

• removed GO anti-slims from block list to use generic terms as potential common ancestors
• added a function to remapping instead of renaming GO terms
• changes for WB

New trimming classes and improved performance

• Trimming algorithms are now classes
• All algorithms have been improved and are now faster
• Major code refactoring
• Better tests

Expression module and bug fixing

v2.3.3

include terms with no 'type'

Bug fixing

v2.3.2

include terms with no 'type'

Expression module and bug fixing

Added precanned function for expression module + bug fixing

Expression module and bug fixing

Added expression module precanned function + bug fixing

New template options

Description template can be now controlled by defining separator characters for terms and modules

Bug fixing

This release fixes a number of minor bugs found with the help of biological curators at the Alliance and adds unit tests for the same bugs

Simplified interface + new algorithms

This release introduces the following changes:

• New interface with simplified access to core functions. No need to read the configuration file and then pass each option as a separate argument to multiple functions. The new interface is based on a configuration object that can be passed to most high level functions that the latter can use to get global options.
• Major code refactoring
• New core algorithms to trim ontology terms: LCA (pure lowest common ancestor algorithm) and IC (based on information content with boosted values for terms present in a slim)