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 local 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 dependency-free. Coverage grows with each release; see the rules.

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

Aug 10, 2026

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zarr-lint 0.0.1

zarr-lint

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