Transformation fixes

[BradyPlanden]

Description

• Fixes GaussianLogLikelihood's interaction with the transformation class.
• Fixes missing apply_transform arg in cost call for SciPy optimisers. Adds addition costs to transformation integration tests and general refactor.
• Fixes incorrect application of transformed bounds with default or resulting NaN transformation bounds

Issue reference

Fixes #492

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.04%. Comparing base (a3293ed) to head (6569eaa).
Report is 143 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #495   +/-   ##
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  Coverage    99.04%   99.04%           
========================================
  Files           52       52           
  Lines         3556     3559    +3     
========================================
+ Hits          3522     3525    +3     
  Misses          34       34           

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[martinjrobins]

Thanks @BradyPlanden, looks great. I think there is a danger in the lenght of the fail gradient becoming out of sync with the number of parameters in the base cost class, so would suggest a setter on the parameters attribute, what do you think? Can be a separate issue as well if you don't want to deal with it now

[BradyPlanden]

Thanks for the review @martinjrobins, I agree that a setter in the BaseCost would improve stability the fail_gradient() object. It's probably best as a follow on PR though as I think it will require more changes than should be included here. Updated below.

[martinjrobins]

Yea, I think this is better. Should parameters be renamed to `_parameters' to indicate that it shouldn't be set directly?