There are a lot of changes here. A brief summary of the key ones are given below:
Lots of refactoring, both in optimisers and problems.
Added utils module for common functions.
Bug fixes in some optimisers.
Changes to rate bounds.
Sped up the moreno problem so that it can now be used.
Staircase protocol now uses myokit.Protocol.
Added cost thresholds.
Added penalty function for out of bounds.
More information now tracked with the Tracker.
Updated modifications, removing some unnecessary options.
Staircase problem now has rate bounds built in fully.
Increased frequency of simulated data.
Fixed bugs in Loewe IKr and IKur.
Improvements to profile likelihood calculations and plots.
Standardised assumptions in optimisers.
Introduced standard termination criteria across all optimisers.