Update CI workflows, pyproject.toml, and Homebrew docs

[mathomp4]

Summary

This PR brings several improvements to CI configuration, project metadata, and documentation.

CI workflow updates

• All workflows now use actions/checkout@v7 (pinned to SHA)
• All workflows now use astral-sh/setup-uv pinned to SHA (v8.2.0) with uv 0.11.23 and caching disabled (no uv.lock in this repo)
• run-formatter.yaml and run-linter.yaml now use uv run instead of manually activating .venv
• run-tests.yaml: Python version matrix updated — added 3.13, 3.14, pypy@3.11; removed pypy@3.9; added fail-fast: false

pyproject.toml

• Migrated [tool.uv] dev-dependencies to [dependency-groups] dev (modern uv standard)
• Fixed license field to use inline table format ({ file = "LICENSE" })
• Moved repository URL to [project.urls]

Documentation

• Revised Homebrew installation instructions in README.md: clarified recommended install method, added guidance on tap trust, and provided tap management commands

Code formatting

• Reformatted multi-line help strings in src/mepo/cmdline/parser.py and print statements in src/mepo/command/config_get.py for consistency (black)
• Removed an unnecessary blank line in tests/test_mepo_clone.py

[mathomp4]

@pchakraborty I used some ChatGPT suggestions to fix up the CI as it was failing in the black formatter.

Though, I wonder, should we switch to using ruff and ty etc?

[pchakraborty]

Why aren’t the tests running?

[mathomp4]

Why aren’t the tests running?

Looks like one failed and all canceled. Let me fix that so we know which is actually having issues.

[mathomp4]

@pchakraborty Okay. I think things are "better" but only in that things are now failing at pytest time, see: https://github.com/GEOS-ESM/mepo/actions/runs/27146165707/job/80124406229?pr=379

I think there is maybe an update needed in what mepo sees in the tests?