deps: Upgrade Python (3.12.4 -> 3.12.6) and common dependencies

[achimnol]

• Upgrade Python (3.12.4 → 3.12.6)
  • https://docs.python.org/3/whatsnew/changelog.html#python-3-12-6-final
  • https://docs.python.org/3/whatsnew/changelog.html#python-3-12-5-final
  • Update pants.toml and pyproject.toml (the interpreter versions for pants and ruff)
  • Update tools/pants-plugins/scie/config.py (the date version for the indygreg distro)
    20240713 → 20240909
  • Update the bootstrapping Python version in scripts (used by git pre-commit/pre-push hooks, etc.)
• Upgrade common dependencies (root requirements.txt)
  • Now many wheels are being updated to support Python 3.13 and nogil (free-threaded) builds. This is a preparation for Python 3.13 migration after releasing 24.09.
  • Notable locked version changes: (bold for typing/code changes required)
    • aiohttp (3.9.5 → 3.10.5)
    • attrs (23.2 → 24.2)
    • typeguard (2.10 → 4.3.0)
    • pyzmq (25.1.2 → 26.2.0)
    • asyncpg (0.27.0 → 0.29.0)
    • textual (0.59.4 → 0.79.1) – fix: Installer regression after upgrading Textual #2867
    • pydantic (2.6.4 → 2.9.2)
    • hiredis (2.2.3 → 3.0.0)
    • msgpack (1.0.5rc1 → 1.1.0)
    • yarl (1.9.x → 1.11.1)
    • uvloop (0.19.0 → 0.20.0)
  • Regenerate lockfiles
• Upgrade tool dependencies (tools/*-requirements.txt)
  • Regenerate lockfiles
• Fix up newly found type check errors
  • Update type annotations and defaults for the ssl parameter passed to aiohttp client APIs: use False instead of None.
  • Use the officially provided aiohttp.typedefs.Middleware instead of custom-defined one.
• Fix up newly occurring test failures
  • Replace common.types.check_typed_dict() with typeguard.check_type() as typeguard has the intrinsic support for typed dicts.
• Upgrade krunner packages (static-gnu, alpine)
  • chore: Update Python version and krunner dependencies backend.ai-krunner-static-gnu#7
  • chore: Update Python version and krunner dependencies backend.ai-krunner-alpine#5
• doc: Update mentions on Python versions and indygreg builds in docs and READMEs.
• Let pants test :: skip the tests marked as "integration" (@pytest.mark.integration) by default, unless the user gives an explicit --integration custom CLI option when executing the pytest.
  • This will lower the bar for new contributors without making them embarrassed.
  • To enable it, pass it as pytest arguments like pants test :: -- --integration.

Reference: #2449

Checklist: (if applicable)

• Milestone metadata specifying the target backport version
• Mention to the original issue
• Documentation

[achimnol]

Confirmed working of manager-agent with a simple session creation and ssh connection into it.

[github-actions]

Backport to 24.03 is failed. Please backport manually.