Fix multiple configurations and adhere to scientific python guidelines

[Saransh-cpp]

Description

Looks much better now:

saransh@saranshs-air PyBaMM % python3 -m pipx run "sp-repo-review[cli]" .
General:

 • Detected build backend: setuptools.build_meta                                                                                                    
 • Detected license(s): BSD License                                                                                                                 

├── PY001 Has a pyproject.toml ✅
├── PY002 Has a README.(md|rst) file ✅
├── PY003 Has a LICENSE* file ✅
├── PY004 Has docs folder ✅
├── PY005 Has tests folder ✅
├── PY006 Has pre-commit config ✅
└── PY007 Supports an easy task runner (nox or tox) ✅

PyProject:
├── PP002 Has a proper build-system table ✅
├── PP003 Does not list wheel as a build-dep ✅
├── PP301 Has pytest in pyproject ✅
├── PP302 Sets a minimum pytest to at least 6 ✅
├── PP303 Sets the test paths ✅
├── PP304 Sets the log level in pytest ✅
├── PP305 Specifies xfail_strict ✅
├── PP306 Specifies strict config ✅
├── PP307 Specifies strict markers ✅
├── PP308 Specifies useful pytest summary ✅
└── PP309 Filter warnings specified ✅

GitHub Actions:
├── GH100 Has GitHub Actions config ✅
├── GH101 Has nice names ✅
├── GH102 Auto-cancel on repeated PRs ✅
├── GH103 At least one workflow with manual dispatch trigger ✅
├── GH104 Use unique names for upload-artifact ✅
├── GH200 Maintained by Dependabot ✅
├── GH210 Maintains the GitHub action versions with Dependabot ✅
├── GH211 Do not pin core actions as major versions ✅
└── GH212 Require GHA update grouping ✅

Pre-commit:
├── PC100 Has pre-commit-hooks ✅
├── PC110 Uses black or ruff-format ❌
│   Must have https://github.com/psf/black-pre-commit-mirror or https://github.com/astral-sh/ruff-pre-commit + id: ruff-format in                   
│   .pre-commit-config.yaml                                                                                                                         
├── PC111 Uses blacken-docs [skipped]
├── PC140 Uses mypy ❌
│   Must have https://github.com/pre-commit/mirrors-mypy repo in .pre-commit-config.yaml                                                            
├── PC160 Uses codespell ❌
│   Must have https://github.com/codespell-project/codespell repo in .pre-commit-config.yaml                                                        
├── PC170 Uses PyGrep hooks (only needed if RST present) ✅
├── PC180 Uses prettier ❌
│   Must have https://github.com/pre-commit/mirrors-prettier repo in .pre-commit-config.yaml                                                        
├── PC190 Uses Ruff ✅
├── PC191 Ruff show fixes if fixes enabled ✅
└── PC901 Custom pre-commit CI message ✅

MyPy:
├── MY100 Uses MyPy (pyproject config) ❌
│   Must have tool.mypy section in pyproject.toml. Other forms of configuration are not supported by this check.                                    
├── MY101 MyPy strict mode [skipped]
├── MY102 MyPy show_error_codes deprecated [skipped]
├── MY103 MyPy warn unreachable [skipped]
├── MY104 MyPy enables ignore-without-code [skipped]
├── MY105 MyPy enables redundant-expr [skipped]
└── MY106 MyPy enables truthy-bool [skipped]

Ruff:
├── RF001 Has Ruff config ✅
├── RF002 Target version must be set ✅
├── RF003 src directory specified if used [skipped]
├── RF101 Bugbear must be selected ❌
│   Must select the flake8-bugbear B checks. Recommended:                                                                                           
│   
│                                                                                                                                                   
│    [tool.ruff.lint]                                                                                                                               
│    extend-select = [                                                                                                                              
│      "B",  # flake8-bugbear                                                                                                                       
│    ]                                                                                                                                              
│                                                                                                                                                   
├── RF102 isort must be selected ❌
│   Must select the isort I checks. Recommended:                                                                                                    
│   
│                                                                                                                                                   
│    [tool.ruff.lint]                                                                                                                               
│    extend-select = [                                                                                                                              
│      "I",  # isort                                                                                                                                
│    ]                                                                                                                                              
│                                                                                                                                                   
├── RF103 pyupgrade must be selected ✅
├── RF201 Avoid using deprecated config settings ✅
└── RF202 Use (new) lint config section ✅

Documentation:
├── RTD100 Uses ReadTheDocs (pyproject config) ✅
├── RTD101 You have to set the RTD version number to 2 ✅
├── RTD102 You have to set the RTD build image ✅
└── RTD103 You have to set the RTD python version ✅

XRef #3489

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 (7e72c38) 99.59% compared to head (a704571) 99.59%.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #3654   +/-   ##
========================================
  Coverage    99.59%   99.59%           
========================================
  Files          258      258           
  Lines        20797    20797           
========================================
  Hits         20712    20712           
  Misses          85       85           

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[agriyakhetarpal]

Thanks, @Saransh-cpp!

[agriyakhetarpal]

Some of the notebooks are failing due to an internal nbmake error even on a re-run I triggered, I don't think that's related to any of the changes here though