[Bug]: pybamm.Simulation.set_parameters and pybamm.Simulation.set_up_and_parameterise_experiment made private in simulation.py

[Akhil-Sharma30]

Description

pybamm.Simulation.set_parameters, pybamm.Simulation.set_up_and_parameterise_experiment and pybamm.Simulation.set_up_and_parameterise_model_for_experiment made private in pybamm/simulation.py
(continuation of #3752 PR)

Fixes #3751

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.

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• 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 run-tests.py --all (or $ nox -s tests)
• The documentation builds: $ python run-tests.py --doctest (or $ nox -s doctests)

You can run integration tests, unit tests, and doctests together at once, using $ python run-tests.py --quick (or $ 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

[kratman]

I think the other question for this is what we do about the function names and tests.

Improvements:

I think that if we intend to deprecate the public functions we should:

1. First rename all the usages to _set_parameters() and _set_up_and_parameterise_experiment()
2. Create new functions called set_parameters() and setup_and_parametrise_experiments()
3. The new functions should be more like this

   def set_parameters(...):
       msg = "pybamm.simulation.set_parameters() is deprecated"
       warnings,warn(msg, DeprecationWarning, stacklevel=2)
       self._set_parameters(...)
   

The renaming is done first so you make sure to catch all usages in the codebase before adding the new one.

Problems:

• The tests use these functions, so this means that we will be accessing private members outside the class.
• In the future I would like to turn on inspections to prevent accessing private methods. This becomes a problem if the tests need to access these methods.
• We should find a solution to having the tests access these members.

[codecov]

Codecov Report

Attention: Patch coverage is 66.66667% with 3 lines in your changes missing coverage. Please review.

Project coverage is 99.25%. Comparing base (bcdd0b5) to head (4051fb6).
Report is 3 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/pybamm/simulation.py	66.66%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4489      +/-   ##
===========================================
- Coverage    99.26%   99.25%   -0.02%     
===========================================
  Files          302      302              
  Lines        22889    22897       +8     
===========================================
+ Hits         22721    22726       +5     
- Misses         168      171       +3     

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[kratman]

@Akhil-Sharma30 I just fixed a couple small things, should be good for now