Remove internal use of deprecated set_parameters method

[MarcBerliner]

Description

The set_parameters method in Simulation was deprecated, but it was still used internally, which caused warnings.

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

• Bug fix (non-breaking change which fixes an issue)

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 tests pass: $ python -m pytest (or $ nox -s tests)
• The documentation builds: $ python -m pytest --doctest-plus src (or $ nox -s doctests)

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

Further checks:

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[agriyakhetarpal]

Thanks, @MarcBerliner!

[kratman]

This is one of the tricky parts of the change that did the deprecation. The private method should not really be used here since it is outside of the class

[kratman]

We do not have the SLF inspection turned on in PyBaMM, but it probably should be enabled

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.20%. Comparing base (72c23ea) to head (d45d388).
Report is 6 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4638      +/-   ##
===========================================
- Coverage    99.21%   99.20%   -0.02%     
===========================================
  Files          302      302              
  Lines        22858    22863       +5     
===========================================
+ Hits         22679    22681       +2     
- Misses         179      182       +3     

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