zarr-tree v0.3.0
zarr-tree v0.3.0
This release expands zarr-tree from a local Zarr metadata inspector into a
remote and SpatialData-aware inspection tool.
Remote stores
- inspect Zarr stores directly on S3
- inspect HTTP/HTTPS stores using WebDAV-compatible listing
- traverse static HTTP stores using consolidated metadata
- support Zarr V2
.zmetadata - support Zarr V3 inline
consolidated_metadata
SpatialData
- inspect Parquet footer metadata for Points and Shapes
- report rows, columns, file counts and schemas without reading records
- summarize AnnData-backed Tables
- report observations, variables, X representation, obs/var columns and
SpatialData region linkage - distinguish unavailable Points payload metadata with
parquet files: ?
Efficiency
- arrays remain leaves; chunk keys are not enumerated
- remote Parquet metadata uses bounded footer reads
- expression matrices are not read
- consolidated metadata can traverse an entire HTTP hierarchy with a single
metadata document
Validation
Validated against real public data including:
- IDR OME-Zarr 0.3, 0.4 and 0.5
- OME-Zarr HCS
- Janelia COSEM
- Pangeo consolidated Zarr
- SpatialData Xenium
- SpatialData Visium
- SpatialData MERFISH
- SpatialData MIBI-TOF
The final public-data validation found no correctness bugs.
Scope
zarr-tree remains a read-only metadata inspection tool.
No chunk/pixel reads, Parquet row reads or expression-matrix reads are
performed.