Refactor get_initial_stoichiometries with custom and default tolerance

[AlessioBugetti]

Description

This commit enhances the get_initial_stoichiometries method by introducing a new parameter, solver_tolerance. The primary change allows users to specify a custom tolerance level for the solver.

The method now includes a default solver tolerance set at 1e-6, maintaining a balance between precision and computational efficiency for general use cases. Additionally, users can adjust this tolerance level as needed, catering to specific requirements of different battery modeling scenarios.

Fixes #3688

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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (2f4a928) 99.59% compared to head (96dbb38) 99.59%.
Report is 2 commits behind head on develop.

Additional details and impacted files

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  Coverage    99.59%   99.59%           
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  Files          258      258           
  Lines        20823    20825    +2     
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+ Hits         20738    20740    +2     
  Misses          85       85           

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[agriyakhetarpal]

Question: should we set the function argument to be just tol, instead of solver_tolerance – to be in line with that for the AlgebraicSolver class?

[AlessioBugetti]

I've updated the function argument name from solver_tolerance to tol in the latest commit. This change brings consistency with the naming convention used in the AlgebraicSolver class.

[kratman]

This seems fine to me as long as the tests pass

[AlessioBugetti]

I see that the Run benchmarks on push / benchmarks fail, let me know if any changes are required or if the PR can be merged

[agriyakhetarpal]

I see that the Run benchmarks on push / benchmarks fail, let me know if any changes are required or if the PR can be merged

Not to worry, the benchmarks on PRs have always been flaky, and I don't think the changes here can influence them in any way. Let's wait till @rtimms's review as the author of the linked issue, and it should be good to merge after that

[kratman]

@AlessioBugetti Can you just add a small summary to the change log?

[AlessioBugetti]

@AlessioBugetti Can you just add a small summary to the change log?

Yes, of course. I have updated the change log as requested.

[kratman]

@AlessioBugetti Sorry to do this, but I think it should be in the unreleased section not the RC section for the change log

[AlessioBugetti]

@AlessioBugetti Sorry to do this, but I think it should be in the unreleased section not the RC section for the change log

Yes, I have made the corrections as requested

[kratman]

Thanks, just waiting for the tests to pass now