package dependency update + enabling worktrees - #21
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #21 +/- ##
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+ Coverage 41.28% 42.46% +1.18%
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Files 10 10
Lines 1015 1015
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+ Hits 419 431 +12
+ Misses 596 584 -12 🚀 New features to boost your workflow:
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…full `uv sync` failed to resolve because the `segmentation` extra listed `instanseg`, and the PyPI project of that name is a dead 0.0.2 release pinned to numpy<2, which conflicts with our numpy>=2 floor. uv resolves every extra together even when it is not selected, so the stale pin broke the base install too. The maintained InstanSeg ships as `instanseg-torch`. The sibling repo peng-lab/spatialrefinery already carries the numpy-2-compatible segmentation stack (instanseg-torch, scikit-image, openslide-python + openslide-bin, verified against zarr 3 / spatialdata 0.8 in its lockfile), so the `full` extra now depends on `spatialrefinery[segmentation]` from its git main and the `segmentation` extra is removed. spatialrefinery is not on PyPI, hence the direct reference, which also needs `tool.hatch.metadata.allow-direct-references`; the wheel is therefore not PyPI-uploadable, which is fine as phoenix installs from git. Consequences: `full` gains spatialrefinery's base dependencies (dask, geopandas, opencv-python-headless, spatialdata-io/-plot, ...) and an anndata>=0.13 floor; helpers/segmentor.py is now importable in CI and the docs env, so its import test moved to the `full` case and NucleiPatchExtractor joins the API reference. `.vscode/settings.json` and `.worktreeinclude` only carry prek formatter fixes. Verified on CPU against spatialrefinery 799472d: `uv lock`, `uv sync`, `uv sync --all-extras`, importing spatialrefinery/instanseg/openslide/skimage and phoenix.helpers.segmentor, `pytest tests` (28 passed, 4 apex skips), `uv build` + `twine check --strict`, a dry-run `phoenix[full]` install into an empty venv resolving spatialrefinery from GitHub, `prek run -a`, and `hatch check types`. The `-W` docs build fails before and after with the same 381 torch/lightning cross-reference warnings; no new warnings, tracked separately. Claude-Session: https://claude.ai/code/session_01GG873AhByfhuLZcPrMabwL
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Updating package dependency to python 3.12 with newer zarr > 3 and numpy > 2 support. This is important to maintain the python stack.