zarr-lint

Inspect, validate, and understand Zarr stores with fast structural, metadata, and compatibility checks. Built for scientific data and reproducible workflows.

What it does

zarr-lint points at a local Zarr store, recognizes Zarr v2 and v3 metadata, and reports structural and metadata problems as diagnostics — in human-readable text or JSON, with stable exit codes suitable for CI.

$ zarr-lint check images.zarr
error[array/rank-mismatch] temperature/.zarray
  Array shape rank (2) does not match chunk shape rank (1).

  Caused by:
    shape [4, 3], chunks [2]

1 finding(s): 1 error(s), 0 warning(s), 0 info.

Install

From PyPI (installs the zarr-lint command and a Python API):

pip install zarr-lint

From source with Cargo (requires Rust 1.82+):

cargo install --path crates/zarr-lint-cli

Or build the binary in-tree:

cargo build --release
# binary at target/release/zarr-lint

Usage

zarr-lint check <PATH>     Check a store (primary form)
zarr-lint <PATH>           Shorthand for `check`
zarr-lint inspect <PATH>   Print a summary of discovered groups and arrays
zarr-lint version          Print version (add --verbose for commit/profile)

Options for check:

--format text|json         Output format (default: text)
--fail-on warning|error|never
                           Severity at/above which findings fail (default: error)
--quiet                    Suppress the summary/success line (text output)

Examples

# Human-readable check
zarr-lint check path/to/store.zarr

# JSON for machines / CI
zarr-lint check --format json path/to/store.zarr

# Report problems but never fail the build
zarr-lint check --fail-on never path/to/store.zarr

# See what the linter discovered
zarr-lint inspect path/to/store.zarr

JSON output:

{
  "version": "0.0.1",
  "store": "images.zarr",
  "diagnostics": [
    {
      "rule": "array/rank-mismatch",
      "severity": "error",
      "path": "temperature/.zarray",
      "message": "Array shape rank (2) does not match chunk shape rank (1).",
      "detail": "shape [4, 3], chunks [2]"
    }
  ]
}

Python API

The PyPI package ships the same zarr-lint command plus a small Python API. The report matches the CLI's JSON schema:

import zarr_lint

zarr_lint.__version__          # "0.0.1"
report = zarr_lint.lint("images.zarr")
report["diagnostics"]          # list of {rule, severity, path, message, ...}
zarr_lint.rules()              # the built-in rule registry

Rules

zarr-lint checks the following rules, each reporting at error severity:

Rule	What it detects
`structure/unrecognized-store`	No recognizable Zarr metadata under the path.
`metadata/invalid-json`	A metadata file is not valid JSON.
`metadata/missing-required-field`	A required field is absent.
`metadata/unsupported-format-version`	`zarr_format` is not `2` or `3`.
`structure/conflicting-node-type`	A path declares both array and group metadata.
`array/rank-mismatch`	Shape rank differs from chunk-shape rank.

Details and per-rule fixtures: docs/rules.md.

Exit codes

Code	Meaning
`0`	No findings reached the failure threshold.
`1`	Findings reached the failure threshold.
`2`	Invalid command usage or configuration.
`3`	Store access or internal execution failure.

Scope

zarr-lint reads store metadata — the .zgroup, .zarray, and zarr.json documents of Zarr v2 and v3 stores — and reports structural and metadata problems. It inspects metadata rather than reading or decoding chunk data, which keeps checks fast and lightweight. Coverage grows with each release; see the rules.

Stores can be local (a filesystem path) or remote over http(s)://, including public object stores reached through their HTTPS endpoints. Because HTTP has no directory listing, remote discovery uses the store's consolidated metadata (.zmetadata) when present, and otherwise reads the root node.

zarr-lint check path/to/store.zarr
zarr-lint check https://example.com/data.zarr
zarr-lint check https://bucket.s3.amazonaws.com/prefix/data.zarr

Native s3:// (and gs://, azure://) access with credentials is not yet supported; use the equivalent https:// URL for public data.

Development

cargo test --workspace          # unit + CLI integration tests
cargo fmt --all --check         # formatting
cargo clippy --all-targets --all-features -- -D warnings
python tools/check_versions.py  # version consistency
prek run --all-files            # all pre-commit hooks (or: pre-commit run)

The test corpus includes small, real stores written by zarr-python, xarray, and tensorstore (under test-data/generated/) to guard against false positives on mainstream tools. Regenerate them with:

uv run --with zarr --with xarray --with tensorstore tools/generate_fixtures.py

Documentation:

docs/architecture.md — pipeline, crates, and model.
docs/rules.md — the rule set and fixtures.
docs/versioning.md — the dynamic versioning model.
docs/test-corpus.md — fixture provenance.

License

BSD 3-Clause. See LICENSE.

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0.0.3

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zarr-lint 0.0.3

zarr-lint

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