ci: 💚 refactor ci/cd

[amd989]

Summary

• Upgrade Python version matrix from 3.8–3.10 to 3.11–3.13 and bump all backend dependencies to compatible versions
• Fix all static analysis issues: 0 flake8 errors, 0 black reformats, 0 pyre type errors, 69/69 tests passing
• Add pyre type stubs for typedstruct, png, toml, and rewrite serial stubs for self-contained resolution

Details

Python version & dependency upgrades

All pinned dependencies have been bumped to current releases with flexible version ranges:

Package	Before	After
python	^3.11 (CI: 3.8/3.9/3.10)	^3.11 (CI: 3.11/3.12/3.13)
flask	^2.3.0	^3.0
flask-caching	1.10.1	^2.1
Flask-WTF	^1.1.0	^1.2
waitress	2.1.1	^3.0
whitenoise	6.0.0	^6.5
pyre-extensions	0.0.27	^0.0.29
black	22.3.0	^24.0
flake8	4.0.1	^7.0
freezegun	1.2.1	^1.4
green	3.4.1	^4.0
pyfakefs	4.5.6	^5.3
pyre-check	0.9.10	0.9.25

Removed python-language-server (unmaintained, not needed).

pyre type checking (159 → 0 errors)

• Rewrote .pyre_configuration to use site-package search paths for all third-party deps and exclude frontend/
• Created type stubs: stubs/typedstruct/__init__.pyi, stubs/png/__init__.pyi, stubs/toml/__init__.pyi
• Rewrote stubs/serial/__init__.pyi to be fully self-contained (no broken submodule imports)
• Fixed mariner/server/api.py return types to Union[str, Response] for Flask 3.x compatibility
• Used none_throws() for proper type narrowing on nullable file uploads
• Added type annotations to test classes for pyre strict mode
• Removed stale # pyre-fixme comments from printer.py and test_mars.py

Test fixes

• assertEquals → assertEqual (removed in Python 3.12)
• setUpPyfakefs(additional_skip_names=["importlib.metadata"]) to prevent pyfakefs from breaking Flask's werkzeug version lookup
• _get_config.cache_clear() before fake filesystem setup to avoid stale LRU-cached config
• Updated test expectations to match corrected layer calculation from prior commit
• freezegun bumped to ^1.4 for Python 3.13 support (uuid._uuid_generate_time was removed)

Lint fixes

• Added node_modules to .flake8 exclude list (new flake8 was picking up vendored Python in node_modules)
• Added # noqa: E701 for inline exception class definitions (black/flake8 disagreement)
• black 24.x auto-reformatted minor whitespace changes

CI workflow

• Python matrix: ["3.8", "3.9", "3.10"] → ["3.11", "3.12", "3.13"]
• Coverage artifact upload pinned to matrix.python-version == '3.11'

Test plan

• poetry run flake8 — 0 errors
• poetry run black --check . — 0 reformats needed
• poetry run pyre check — 0 type errors
• poetry run green — 69/69 tests pass
• CI green on Python 3.11, 3.12, 3.13