Apply SciPy-like repository suggestions

[Zeitsperre]

Pull Request Checklist:

• This PR addresses an already opened issue (for bug fixes / features)
  • This PR fixes #xyz
• Tests for the changes have been added (for bug fixes / features)
  • (If applicable) Documentation has been added / updated (for bug fixes / features)
• CHANGELOG.rst has been updated (with summary of main changes)
  • Link to issue (:issue:number) and pull request (:pull:number) has been added

What kind of change does this PR introduce?

• Applies several linting suggestions adopted by the scipy community
• Replaces isort with ruff formatting
• Adds Markdown file formatting
• Adds a few strongly encouraged ruff checks (bugbear, pyupgrade)
• Adjust mypy checks

Does this PR introduce a breaking change?

Yes. isort is no longer required. Code checks are marginally stricter.

Other information:

https://github.com/scientific-python/repo-review

If we wanted to replace black as well, this is feasible with ruff, as it nearly replicates its functionality 1-to-1. To be revisited.

I've staged the python-check-blanket-noqa and python-check-blanket-type-ignore hooks since there are several instances where these won't work (numba-based code blocks). These statements should be followed up on at some point, likely when we address more things with mypy.

Repo checks:

(xclim) ~/git/xclim git:[repo-suggestions]
python -m repo_review
General:

 • Detected build backend: flit_core.buildapi                                                                                                                                                                                    
 • Detected license(s): Apache Software 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 ✅
├── PC111 Uses blacken-docs ❌
│   Must have https://github.com/adamchainz/blacken-docs in .pre-commit-config.yaml                                                                                                                                              
├── PC140 Uses a type checker ❌
│   Must have https://github.com/pre-commit/mirrors-mypy in .pre-commit-config.yaml                                                                                                                                              
├── PC160 Uses a spell checker ✅
├── PC170 Uses PyGrep hooks (only needed if rST present) ✅
├── PC180 Uses a markdown formatter ✅
├── PC190 Uses Ruff ✅
├── PC191 Ruff show fixes if fixes enabled ✅
└── PC901 Custom pre-commit CI message ✅

MyPy:
├── MY100 Uses MyPy (pyproject config) ✅
├── MY101 MyPy strict mode ✅
├── MY102 MyPy show_error_codes deprecated ✅
├── MY103 MyPy warn unreachable ✅
├── MY104 MyPy enables ignore-without-code ✅
├── MY105 MyPy enables redundant-expr ✅
└── MY106 MyPy enables truthy-bool ✅

Ruff:
├── RF001 Has Ruff config ✅
├── RF002 Target version must be set ✅
├── RF003 src directory doesn't need to be specified anymore (0.6+) [skipped]
├── RF101 Bugbear must be selected ✅
├── RF102 isort must be selected ✅
├── 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 ✅

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[aulemahal]

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