[Jan-Williams]

Adopt uv for environment/dependency management and clean up packaging cruft that had accumulated in pyproject.toml.

Packaging:

• Switch build backend from setuptools+setuptools_scm to hatchling+hatch-vcs. hatch-vcs wraps setuptools_scm, so git-tag-derived version strings are unchanged (verified: 0.3.4.dev2+gc0e77dd2b before and after).
• Drop dead build requirements (wheel, numpy, cython) -- there are no C or Cython sources in the tree.
• Remove setuptools_scm from runtime dependencies; it is a build-time tool and nothing imports it, but every installed user was pulling it in.
• Pin the sdist contents with only-include. docs/examples is a symlink to ../examples, and hatchling's tree walk follows symlinks while de-duplicating on (st_dev, st_ino), so whichever directory was visited first won and the other was silently dropped -- a non-deterministic sdist. only-include bypasses the walk entirely. Sdist also shrinks 2.8M -> 140K.

Dependencies:

• Move dev/docs dependencies to PEP 735 [dependency-groups]; keep gpu and notebooks as extras. Note this breaks pip install -e ".[dev]" in favour of uv sync (or pip install --group dev on pip >= 25.1).
• Add notebook/ipykernel to the docs group: mkdocs-jupyter runs with execute: true, so the docs build executes every example notebook and needs a kernel. It previously worked only by transitive luck.
• Mark the gpu extra sys_platform == "linux". JAX publishes CUDA wheels for Linux only, so uv sync --all-extras failed outright on macOS. No capability is lost: Windows GPU users go through WSL2, which reports as Linux.
• Commit uv.lock for reproducible environments.

CI:

• Replace pip with astral-sh/setup-uv (cached) across tests/docs/publish.
• Split lint into its own job that runs once with uv sync --locked, so a lockfile out of sync with pyproject.toml fails loudly. The test matrix deliberately resolves fresh (--upgrade) so upstream jax/equinox/diffrax breakage still surfaces.
• Add fetch-depth: 0 to tests.yml. It was checking out shallow, so the version derived during install was wrong (0.1.dev1+... rather than the real version).
• Assert in publish.yml that the built artifact version matches the release tag, since hatch-vcs derives it from git rather than from the tag itself.
• Narrow publish.yml's top-level permissions to {}; only the publish job needs id-token: write.
• Add a concurrency group to docs.yml -- gh-deploy force-pushes gh-pages, so overlapping runs raced.

Also adds a coverage config canonicalizing editable vs non-editable paths, and drops a per-file-ignores entry for a setup.py that does not exist.

Co-authored by Claude Opus 5