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AGENTS.md

zarr-java (dev.zarr:zarr-java) is a Java implementation of the Zarr v2 and v3 array storage specs, plus experimental OME-Zarr support. Public API entry points are dev.zarr.zarrjava.v2.{Array,Group} and dev.zarr.zarrjava.v3.{Array,Group}.

  • Build: Maven, compiled with maven.compiler.release=8 (build with JDK 11).
  • Arrays are backed by ucar.ma2.Array (netCDF-Java).
  • Metadata is (de)serialized with Jackson.

Layout

  • core/ — version-agnostic base types (Array, Group, ArrayMetadata, DataType, Attributes), shared codecs (core/codec) and chunk key encodings.
  • v2/, v3/ — spec-version-specific metadata, codecs and chunk grids.
  • store/ — Store backends: FilesystemStore, HttpStore, S3Store, MemoryStore, ZipStore/ReadOnlyZipStore/BufferedZipStore. Keys are addressed through StoreHandle.
  • experimental/ome/ — OME-Zarr (NGFF) v0.4 / v0.5 / v0.6 metadata models.
  • cli/ — command line wrapper.
  • utils/ — indexing helpers, notably IndexingUtils.

Before implementing a feature

Before implementing a feature, codec, data type, or behaviour change, check whether it already exists or is specified elsewhere, and use that as context. Check in this order:

  1. zarr-specs: the core Zarr v2/v3 specification. Is it specified, and how exactly?
  2. zarr-extensions: codecs, data types, chunk grids etc. that are not part of the core spec.
  3. zarr-python: the reference implementation. Defines the actual behaviour (defaults, edge cases, error handling) that zarr-java must match.
  4. OME-Zarr (NGFF): for anything under experimental/ome/, the current OME-NGFF specification is at https://ngff.openmicroscopy.org/specifications/0.6/index.html.

Prefer the local clones (grep) over fetching the web. If the spec and zarr-python disagree, match zarr-python and mention the discrepancy. If nothing relevant is found, say so before designing the feature from scratch.

Conventions

  • IntelliJ IDEA default Java formatting; run Reformat Code and Optimize Imports before submitting changes.
  • User-facing documentation lives in USERGUIDE.md and USERGUIDE-OME-ZARR.md; update them alongside API changes.
  • When writing code comments, keep them short and concise, do not reference other code or previous behavior.

Pull requests

  • Use the PR template at .github/pull_request_template.md.
  • Keep your summaries short and to the point.
  • When adding comments or replies to PRs, always mention that Claude wrote them.