Replace hand-written ty machinery with the official ty-pre-commit hook

[hmgaudecker]

Summary

ty now runs only as pre-commit hooks, under both backends, replacing the dedicated pixi type-checking/type-checking-jax features, environments, and tasks (pixi run ty / pixi run ty-jax no longer exist).

• numpy run: the official astral-sh/ty-pre-commit hook with args: [--no-project]. uv creates no .venv/uv.lock in this pixi-managed repo and resolves no dependencies itself (its default mode fails on the pygraphviz source build anyway); ty resolves third-party imports from the pixi py314 environment via tool.ty.environment.python in pyproject.toml.
• jax run: a minimal local hook running the same pinned ty with --python .pixi/envs/py314-jax. It inherits the entire tool.ty configuration — same rules, only the environment differs. Verified that jax genuinely resolves in this run (passes even with jax dropped from analysis.allowed-unresolved-imports).

The jax variant cannot use the official hook today: uv check forwards nothing to ty (no --python, no -c, no trailing args), and ty rejects conda-style envs handed over via VIRTUAL_ENV (no pyvenv.cfg). The local hook's ty==0.0.48 pin carries a comment to keep it in sync with the hook rev, since prek auto-update bumps only the rev.

Other changes

• The run-ty CI job installs py314/py314-jax and runs the hooks via prek, so the pre-commit config is the single definition of how ty runs everywhere.
• Both ty hooks are skipped on pre-commit.ci (no network at hook runtime, no pixi environments).
• The existing test environments provide everything ty needs (including type stubs), so the dedicated type-checking environments are gone — including their ~1800 lines in pixi.lock. pixi 0.70.2 does not prune removed environments from the lock; the stale blocks and orphaned ty package entries were removed manually and the result validated with pixi lock.
• AGENTS.md: verification is now two steps; prek run --all-files covers type checking under both backends.

Test plan

• pixi run -e py314-jax prek run --all-files — all hooks pass, including both ty variants
• pixi run --locked -e py314 prek run ty --all-files and ... ty-jax --all-files (exact CI commands)
• pixi run --locked -e py314-jax tests -n 7 — 1119 passed, 42 skipped
• pixi lock — lock file validates after pruning

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!