feat: one OME-ZARR with image + label pyramids by default (+ hatch-vcs) - #8
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Stop hand-maintaining the version. hatch-vcs reads it from the latest git tag at build time (v0.3.0 -> 0.3.0) and __version__ reads it back through importlib.metadata, so the tag is the single source of truth and releases need no manual version bump. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Refactor the pyramid-writing into shared helpers and expose two new functions: - add_pyramid(group): add downsampled resolution levels to an existing single-resolution zarr in place, lazily (reuses existing multiscales metadata/axes when present) - write_labels(image_store, labels): store a label image inside an OME-ZARR under the NGFF labels/<name>/ group as its own multi-scale pyramid, with image-label metadata and registration in labels/.zattrs so image + segmentation live in one store Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
tile_process now, by default, writes its labels back into the input .zarr store under the NGFF labels/<name>/ group as a multi-scale pyramid (image + segmentation in one file). write_to still overrides to a separate single-resolution store; array inputs use an auto-temp. - labels stream into the store via write_labels/da.to_zarr (OOM-safe) - pyramids downsample X/Y only; Z (and C/T) stay full-resolution, as microscopy stacks are anisotropic - add register_labels helper (pyramid + image-label meta + register) - overlap now defaults to 16 for out-of-the-box boundary context - fix tests for Z-preserving pyramids, overlap default, zarr-v3 API Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Document add_pyramid, write_labels and register_labels on the plugin API page, and rewrite the guide around the new default (tile_process stores image + label pyramids in one OME-ZARR), XY-only downsampling, and plugging in any segmentation function. pdoc picks the functions up automatically. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Builds on the OME-ZARR/napari plugins. Five commits:
hatch-vcs— the tag is now the single source of truth, no manual version bumps.__version__reads it viaimportlib.metadata.add_pyramid(add levels to an existing store) andwrite_labels(store a label image inside an OME-ZARR under NGFFlabels/).tile_processdefault — when input is a.zarrand nowrite_to, labels are written back into the input store underlabels/<name>/as a pyramid, so image + segmentation live in one OME-ZARR. Lazy/streamed (OOM-safe).overlapnow defaults to 16. Pyramids downsample X/Y only — Z kept full-res.Notes
write_to=still overrides to a separate single-resolution store; array inputs use an auto-temp.fn.23 passed), ruff clean,mkdocs build --strictclean. Also fixed two pre-existing zarr-v3 test-API calls (Group.zeros).After merge, tagging
v0.3.0publishes automatically (hatch-vcs → 0.3.0).🤖 Generated with Claude Code