Fix transformations

[NicolaCourtier]

Description

Move the cost evaluation error catches to BaseOptimiser, add log_update() and fix inconsistencies in the application of transformations.

Issue reference

Fixes #473

Review

Before you mark your PR as ready for review, please ensure that you've considered the following:

• Updated the CHANGELOG.md in reverse chronological order (newest at the top) with a concise description of the changes, including the PR number.
• Noted any breaking changes, including details on how it might impact existing functionality.

Type of change

• New Feature: A non-breaking change that adds new functionality.
• Optimization: A code change that improves performance.
• Examples: A change to existing or additional examples.
• Bug Fix: A non-breaking change that addresses an issue.
• Documentation: Updates to documentation or new documentation for new features.
• Refactoring: Non-functional changes that improve the codebase.
• Style: Non-functional changes related to code style (formatting, naming, etc).
• Testing: Additional tests to improve coverage or confirm functionality.
• Other: (Insert description of change)

Key checklist:

• No style issues: $ pre-commit run (or $ nox -s pre-commit) (see CONTRIBUTING.md for how to set this up to run automatically when committing locally, in just two lines of code)
• All unit tests pass: $ nox -s tests
• The documentation builds: $ nox -s doctest

You can run integration tests, unit tests, and doctests together at once, using $ nox -s quick.

Further checks:

• Code is well-commented, especially in complex or unclear areas.
• Added tests that prove my fix is effective or that my feature works.
• Checked that coverage remains or improves, and added tests if necessary to maintain or increase coverage.

Thank you for contributing to our project! Your efforts help us to deliver great software.

[codecov]

Codecov Report

Attention: Patch coverage is 98.90110% with 1 line in your changes missing coverage. Please review.

Project coverage is 99.04%. Comparing base (76de36a) to head (a4384e5).
Report is 19 commits behind head on develop.

Files with missing lines	Patch %	Lines
pybop/optimisers/base_pints_optimiser.py	92.85%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #474   +/-   ##
========================================
  Coverage    99.04%   99.04%           
========================================
  Files           52       52           
  Lines         3545     3546    +1     
========================================
+ Hits          3511     3512    +1     
  Misses          34       34           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[BradyPlanden]

Thanks for the updates @NicolaCourtier! The transformation changes look good, I have a few comments on the change from applying transformations within the cost class to optimisation class.

[NicolaCourtier]

I would recommend keeping properties, such as transformations, attached to a single base class for modularity (to reduce the chance of errors and unexpected behaviour). In this case, I think BaseOptimiser is conceptually the correct place for transformations.