Volume-variable shape support + libvcell bump (and poetry cleanup)

[jcschaff]

Cherry-picked from @LDre398 (Logan Drescher), then verified, lock-fixed, and tidied.

What's in here

Volume-variable shapes (pyvcell/_internal/simdata/zarr_writer.py) — the zarr writer assumed every volume function evaluates to a (z, y, x) array named domain::function. It now handles:

• scalar results (shape == ()) → fill a (z, y, x) array with the value;
• already-sized results → use as-is instead of reshaping;
• function names with 0 or 1 :: separators (domain optional) rather than exactly two — and only applies a domain mask when a domain is present (raises on > 2 parts).

libvcell — bumped to ensure the version that produces the new volume-variable shapes/types:

• the cherry-picked uv.lock had a malformed libvcell entry (a 0.0.15.3 record pointing at a 0.0.15.2 wheel), so it wouldn't even parse — regenerated cleanly, now resolves to libvcell 0.0.15.4;
• bumped the native extra floor to libvcell>=0.0.15.3 so the constraint matches the intent (previously only the lock was touched, so a fresh install could still get an older libvcell).

CI (setup-uv-env action) — the cherry-picked change pins the uv venv to the exact matrix Python. The matrix still listed 3.11 while requires-python = ">=3.12", so that job would now fail uv sync. Aligned the matrix to 3.12–3.14 and retargeted the Codecov upload (3.11 → 3.12).

Poetry cleanup (per request) — the project already moved to uv; removed the leftover poetry.lock and switched the poetry references in CLAUDE.md, CONTRIBUTING.md, and docs/getting-started/installation.md to uv (and documented the new pyvcell[extra] install).

Verification

• make check green — ruff, ruff-format, mypy (310 files), deptry, uv lock --check.
• pytest tests/_internal/simdata tests/vcml tests/sim_results → 60 passed, 5 skipped (includes the zarr_writer tests).

Note

The new scalar / already-sized / no-domain branches in zarr_writer.py aren't covered by a dedicated unit test (they depend on libvcell producing those shapes). The existing zarr_writer suite exercises the normal path; happy to add targeted fixtures for the new branches as a follow-up if wanted.

🤖 Generated with Claude Code