Migrate from rye to uv for dependency management

[x]

Rye is deprecated in favor of uv. Replace all rye usage with uv equivalents:

• pyproject.toml: [tool.rye] → [tool.uv], merge dev-dependencies into
  [dependency-groups] dev, remove [tool.rye.scripts]
• Shell scripts: rye run → uv run with inlined commands
• CI workflows: rye install → astral-sh/setup-uv@v5 action
• Dev container: install uv instead of rye
• Delete requirements.lock and requirements-dev.lock (replaced by uv.lock)
• Update bootstrap script
• Update all docs, AI assistant configs, and cursor rules

This is definitely a more involved change, no rush on the review.

Greptile Summary

This PR completes a clean migration from the deprecated rye tool to uv for dependency management, environment setup, and script execution across the entire repository. The changes are consistent and well-scoped: pyproject.toml consolidates the two separate dev-dependency lists into a single [dependency-groups] dev block, CI workflows swap the manual curl | bash rye bootstrap for the astral-sh/setup-uv@v5 action, shell scripts inline the old rye run <alias> calls as direct uv run invocations, and all documentation/AI assistant configs are updated to match.

Key changes:

• pyproject.toml: [tool.rye] → [tool.uv], both dev-dependency lists merged into one [dependency-groups] dev, [tool.rye.scripts] removed (scripts now live in shell files directly)
• CI workflows: rye install removed; all three jobs now use astral-sh/setup-uv@v5
• bin/publish-pypi: rye build --clean + rye publish --yes → uv build --clean + uv publish --token; the --yes flag is unnecessary for uv publish which is non-interactive by default
• scripts/bootstrap: simplified to a pre-flight uv availability check + uv sync --all-groups
• .devcontainer/Dockerfile: uses COPY --from=ghcr.io/astral-sh/uv:latest — the only minor concern is the unpinned latest tag (old rye was pinned to 0.44.0)
• All docs (CLAUDE.md, CONTRIBUTING.md, cursor rules, README files) updated consistently

Confidence Score: 5/5

• This PR is safe to merge — it is a mechanical tooling migration with no changes to library code or public API.
• All rye usages have been replaced with correct uv equivalents, dev-dependency lists are fully preserved, CI and publish pipelines are functionally equivalent, and docs/configs are consistent. The only minor concern is the unpinned uv:latest in the devcontainer Dockerfile, which does not affect CI or production.
• .devcontainer/Dockerfile — uses unpinned uv:latest image tag; consider pinning to a specific version for reproducible devcontainer builds.

Important Files Changed

Filename	Overview
pyproject.toml	Moves from [tool.rye] to [tool.uv], merges dev-dependencies from both the old [tool.rye] block and the pre-existing [dependency-groups] dev list into a single [dependency-groups] dev, and removes [tool.rye.scripts] in favour of shell scripts. All dependencies are preserved; [build-system] is simply reordered.
.github/workflows/ci.yml	Replaces `curl
.github/workflows/publish-pypi.yml	Replaces rye bootstrap with astral-sh/setup-uv@v5; publish logic lives in bin/publish-pypi and is unchanged structurally.
bin/publish-pypi	Replaces rye build --clean and rye publish --yes with uv build --clean and uv publish --token $PYPI_TOKEN. Functionally equivalent; uv publish is non-interactive by default so --yes is not needed.
.devcontainer/Dockerfile	Switches from `curl
scripts/bootstrap	Removes optional Homebrew bundle step and rye config call; simply checks that uv is already installed and runs uv sync --all-groups. Cleaner and correct.
scripts/lint	Inlines rye run lint / rye run fix:ruff as direct uv run ruff and uv run pyright calls. Behaviour is equivalent: non-fix path runs ruff + pyright + importability check; fix path only runs ruff check --fix.
scripts/format	Inlines the rye run format chain as explicit uv run ruff format, uv run python ruffen-docs.py, uv run ruff check --fix, uv run ruff format steps. Behaviour is identical to the old rye script chain.
scripts/test	Single-line change replacing rye run pytest with uv run pytest. No functional change.
.claude/settings.json	Updates allowed bash command patterns from rye run * to equivalent uv run * / uv sync / uv build permissions. Also adds a trailing newline.
CLAUDE.md	All command references updated from rye to uv equivalents, trailing whitespace cleaned up, and a trailing newline added. Accurate and complete.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[Developer / CI] --> B{Environment setup}
    B -->|Local| C["scripts/bootstrap\nuv sync --all-groups"]
    B -->|CI| D["astral-sh/setup-uv@v5\nuv sync --all-groups"]
    B -->|Devcontainer| E["Dockerfile\nCOPY uv from ghcr.io/astral-sh/uv:latest\nuv sync --all-groups"]

    C & D & E --> F[.venv ready]

    F --> G[scripts/test\nuv run pytest]
    F --> H[scripts/lint\nuv run ruff check + uv run pyright]
    F --> I[scripts/format\nuv run ruff format/check]
    F --> J[uv build]
    J --> K[bin/publish-pypi\nuv publish --token]

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_{Last reviewed commit: 2ca7af4}