fix(py,ts): gate the RFC-4 orientation checks on 0.9.dev1

[vboussot]

Applies the decision recorded in #667: RFC-4 anatomical orientation is normative from OME-Zarr 0.9.dev1, the version ome/ngff-spec#190 folds RFC-4 into. The released 0.4, 0.5 and 0.6 specs give orientation no normative status, yet the three orientation rules (axis-orientation-anatomical-type, axis-orientation-on-non-space, axis-orientation-unique-axis) and the readers' raw RFC-4 hooks ran at every version. They now gate on the declared version.

Stacked on #611. That PR introduces NgffVersion.V09dev1 and the version parameter on the axis rules; it is not merged yet. The base branch here is an upstream copy of #611's head (fix/rfc3-axes), so the diff shows only this change's two commits. Once #611 lands on main, retarget this PR to main and delete the copy; if #611's branch moves first, refresh the copy. The eventual rebase carries one rename: main's reader hooks call has_any_rfc4_orientation (#661) where this branch still calls has_rfc4_orientation_metadata.

Behavior

• A caller that declares 0.4, 0.5 or 0.6 gets no orientation validation: the rules are a no-op there, not a warning.
• 0.9.dev1 keeps every check.
• No declared version keeps the checks on too, as a strictness choice, exactly like axis-names-unique below 0.9.dev1. Every existing no-version caller and test is unchanged.
• The write path is untouched: orientation is serialized whenever present, for every target version.

Implementation

Mirrors the RFC-3 gate's form with the polarity inverted: RFC-3 lifts the axis restrictions at 0.9.dev1 while RFC-4 adds requirements, so the new helper (is_rfc4_orientation_enforced / isRfc4OrientationEnforced) exits the rules early below 0.9.dev1 rather than at it.

• validate_axis_orientation / validateAxisOrientation take the same optional version parameter as the axis rules, supplied by the orchestrators.
• The Python v0.4 reader now passes the store's declared version to validate_structural, as the TypeScript reader already did.
• The readers' raw RFC-4 hooks (Python v04/v06, TypeScript fromZarrAttrsV04 and the shared v0.6/0.9.dev1 reader) are removed. They ran validate_rfc4_orientation on the raw axis dicts before parsing; the structural pass repeats that on the parsed axes with the same function and the same verdicts (checked for a valid, an out-of-vocabulary, a non-anatomical and a non-object orientation; the RFC-4 JSON Schema's root object declares no properties, so its final pass constrains nothing), and it runs in the canonical evaluation order, which the hooks broke by firing first. The v0.6 Python hook also read a flat axes list the v0.6 layout does not carry. The orientation rule is the single enforcement point per port; a 0.9.dev1 store with a stray orientation is refused on read by that rule, covered by a new reader test.
• No rule is added, renamed or reordered. The parity suites pin the version set as a CANONICAL_RFC4_VERSIONS literal in both ports, and docs/validation/ (rule-reference, overview, parity) says the same.

Updated tests

Two tests pinned the old behavior (a 0.4 store with an out-of-vocabulary orientation was refused on read) and now pin the new acceptance, keeping the module-level validate_rfc4_orientation rejection: test_from_ngff_zarr_invalid_orientation_reads_below_rfc4 and its TypeScript twin in rfc4_validation_test.ts. Their fixtures also declared an (x, y, z) spatial order, a v0.4 violation the early RFC-4 raise had masked from the structural pass; they now use (z, y, x).

Side note

TypeScript's hasRfc4OrientationMetadata only inspects type == "space" axes. With the raw hooks gone its only caller is validateAxisOrientation, which checks the non-space axes itself, so no reader-side blind spot remains.

Verification

Python: 969 passed, 3 skipped (full suite). TypeScript: 577 passed, 0 failed. pixi run --as-is lint clean.

Summary by CodeRabbit

• Bug Fixes

  • Added version-aware RFC 4 orientation validation.
  • Enforced orientation rules for OME-Zarr 0.9.dev1 and when no version is specified.
  • Preserved compatibility with earlier versions, which accept metadata predating RFC 4 requirements.
  • Aligned Python and TypeScript validation behavior across supported versions.

• Documentation

  • Updated validation guidance, rule references, and parity requirements for version-dependent orientation handling.

• Tests

  • Added cross-language coverage for invalid orientations, non-spatial axes, duplicate anatomical axes, and version-specific behavior.

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• py/ngff_zarr/v04/zarr_metadata.py
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📝 Walkthrough

Walkthrough

RFC-4 orientation validation is enforced for OME-Zarr 0.9.dev1 and unspecified versions. Earlier declared versions skip RFC-4 orientation checks. Python and TypeScript readers, validators, tests, and documentation reflect this behavior.

Changes

RFC-4 orientation gating

Layer / File(s)	Summary
Python validation and reader integration py/ngff_zarr/structural_validation.py, py/ngff_zarr/v04/zarr_metadata.py, py/ngff_zarr/v06/zarr_metadata.py, py/test/*orientation*, py/test/*reader*, py/test/test_rfc4_validation.py	Python validators and readers pass the declared version to orientation validation. Earlier versions skip RFC-4 orientation checks.
TypeScript validation and reader integration ts/src/types/supported_versions.ts, ts/src/utils/structural_validation.ts, ts/src/utils/from_zarr_attrs.ts, ts/test/*orientation*, ts/test/*reader*, ts/test/rfc4_validation_test.ts	TypeScript readers resolve the declared version and pass it through structural validation. Earlier versions accept RFC-4-incompatible orientations.
Parity coverage and validation contract py/test/test_structural_validation_parity.py, ts/test/structural_validation_parity_test.ts, docs/validation/*	Parity tests cover the three orientation rules across supported versions. Documentation defines 0.9.dev1 as the canonical enforcing version.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Merge Risk: 🟡 Moderate · up to 03e9c

The change gates RFC-4 orientation validation by declared version, but current reader paths may still read version or axes from incorrect locations and normalize unversioned stores before gating, allowing metadata that should be rejected to pass. Those reader paths need correction or explicit owner acceptance before merge.

Sequence Diagram(s)

sequenceDiagram
  participant Reader as Metadata reader
  participant Orchestrator as Structural orchestrator
  participant Gate as RFC-4 version gate
  participant Validator as Orientation validator
  Reader->>Orchestrator: Pass declared version
  Orchestrator->>Validator: Request orientation validation
  Validator->>Gate: Check version
  Gate-->>Validator: Enforce or skip RFC-4 rules
  Validator-->>Reader: Return validation result

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A rabbit checks the axes in a row,
At nine-dev-one, the rules must show.
Old versions pass with checks asleep,
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Actionable comments posted: 1

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⚠️ Outside diff range comments (1)

py/ngff_zarr/v06/zarr_metadata.py (1)

688-706: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

Read the declared version and intrinsic axes from the v0.6 layout.

Line 688 reads version from the multiscales entry. The v0.6/0.9 layout stores it in ome.version. A valid 0.9.dev1 store therefore defaults to "0.6" here and skips RFC-4 validation.

Lines 695-706 also look for axes on the multiscales entry. v0.6/0.9 axes are in coordinateSystems[0].axes. Even after fixing the version source, the RFC-4 hook remains unreachable for normal v0.9 metadata. Use the group version and intrinsic axes. Add a 0.9.dev1 reader regression with an out-of-vocabulary orientation.

Proposed fix

-            declared_version = root_attrs["ome"]["multiscales"][0].get("version", "0.6")
+            entry = root_attrs["ome"]["multiscales"][0]
+            declared_version = root_attrs["ome"].get("version", "0.6")
             validate_ngff(root_attrs, version=declared_version)
+            intrinsic_axes = entry["coordinateSystems"][0].get("axes")

             if (
                 is_rfc4_orientation_enforced(declared_version)
-                and "axes" in root_attrs["ome"]["multiscales"][0]
-                and isinstance(root_attrs["ome"]["multiscales"][0]["axes"], list)
+                and isinstance(intrinsic_axes, list)
             ):
                 axes_dicts = []
-                for axis in root_attrs["ome"]["multiscales"][0]["axes"]:
+                for axis in intrinsic_axes:
                     if isinstance(axis, dict):
                         axes_dicts.append(axis)

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In `@py/ngff_zarr/v06/zarr_metadata.py` around lines 688 - 706, Update the
metadata reader around validate_ngff to obtain the declared version from
root_attrs["ome"]["version"] and obtain intrinsic axes from
root_attrs["ome"]["coordinateSystems"][0]["axes"]. Feed these values into the
existing RFC-4 enforcement and validation helpers so valid 0.9.dev1 metadata
with an out-of-vocabulary orientation is rejected, and add a reader regression
test covering that case.

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Inline comments:
In `@ts/src/utils/from_zarr_attrs.ts`:
- Around line 175-176: Keep the raw declared version from rootAttrs.version or
multiscalesMetadata.version separate from the normalized metadata.version
fallback in the relevant parsing flows. Pass the raw optional value to
isRfc4OrientationEnforced and validateStructural, while retaining "0.4"/"0.6"
only where the normalized metadata.version requires a fallback.

---

Outside diff comments:
In `@py/ngff_zarr/v06/zarr_metadata.py`:
- Around line 688-706: Update the metadata reader around validate_ngff to obtain
the declared version from root_attrs["ome"]["version"] and obtain intrinsic axes
from root_attrs["ome"]["coordinateSystems"][0]["axes"]. Feed these values into
the existing RFC-4 enforcement and validation helpers so valid 0.9.dev1 metadata
with an out-of-vocabulary orientation is rejected, and add a reader regression
test covering that case.

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• docs/validation/overview.md
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• py/ngff_zarr/structural_validation.py
• py/ngff_zarr/v04/zarr_metadata.py
• py/ngff_zarr/v06/zarr_metadata.py
• py/test/test_rfc4_validation.py
• py/test/test_structural_validation_orientation.py
• py/test/test_structural_validation_parity.py
• py/test/test_structural_validation_reader.py
• ts/src/types/supported_versions.ts
• ts/src/utils/from_zarr_attrs.ts
• ts/src/utils/structural_validation.ts
• ts/test/rfc4_validation_test.ts
• ts/test/structural_validation_orientation_test.ts
• ts/test/structural_validation_parity_test.ts
• ts/test/structural_validation_reader_test.ts

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[vboussot]

@coderabbitai On the outside-diff comment about py/ngff_zarr/v06/zarr_metadata.py lines 688-706: not changed in this PR, for three reasons.

• The gate deliberately reads the same value the adjacent validate_ngff call uses. Sourcing either from ome.version would feed "0.6.dev4" (the on-disk v0.6 string) into validate_ngff, and this branch resolves schema paths literally (spec/0.6.dev4/schemas does not exist). Mapping dev releases to their release tree is fix(py): resolve cross-file JSON Schema references during validation #659, which this stack picks up when it rebases onto main.
• A 0.9.dev1 store cannot reach this hook with validate=True through the public API: from_ngff_zarr routes 0.9.dev1 to the v09 reader, which raises NotImplementedError for validate=True and otherwise delegates with validate=False. Python-side enforcement at 0.9.dev1 is validate_structural's orientation rule, pinned by the parity manifest test. For the same reason a 0.9.dev1 read regression with an out-of-vocabulary orientation cannot be written against the public Python API today; the TypeScript port, whose shared reader does serve 0.9.dev1 under validate, carries exactly that regression test.
• The entry-level flat axes read predates this PR and is inert for conforming v0.6/0.9.dev1 layouts. Restoring real read-path validation for the coordinate-system layout is the from_ome_zarr(validate=True) item tracked in The data model does not follow the schema of its own version #667, out of this PR's scope.

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🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo '== Relevant symbols =='
ast-grep outline py/ngff_zarr/v06/zarr_metadata.py --items all --match '_from_zarr_attrs|validate_ngff|is_rfc4_orientation_enforced'
ast-grep outline py/ngff_zarr --items all --match 'from_ngff_zarr|validate_structural|is_rfc4_orientation_enforced'

echo '== v0.6 reader context =='
nl -ba py/ngff_zarr/v06/zarr_metadata.py | sed -n '670,715p'

echo '== Reader routing and structural gate matches =='
rg -n -A12 -B8 -P '\b(from_ngff_zarr|validate_structural|is_rfc4_orientation_enforced)\b' py/ngff_zarr --glob '*.py'

echo '== Referenced follow-up issues =='
gh issue view 659 --repo fideus-labs/ngff-zarr --json number,title,state,url,body
gh issue view 667 --repo fideus-labs/ngff-zarr --json number,title,state,url,body

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🏁 Script executed:

#!/bin/bash
set -u

echo '== v0.6 reader context =='
sed -n '670,715p' py/ngff_zarr/v06/zarr_metadata.py || true

echo '== Public reader routing =='
rg -n -A18 -B8 -P '\bfrom_ngff_zarr\s*\(' py/ngff_zarr/from_ngff_zarr.py || true

echo '== v0.9 reader validation behavior =='
rg -n -A16 -B8 -P '(NotImplementedError|validate\s*=\s*False|\bvalidate\b)' py/ngff_zarr/v09 --glob '*.py' || true

echo '== Structural version gate =='
rg -n -A20 -B8 -P '\b(is_rfc4_orientation_enforced|validate_axis_orientation|validate_structural)\s*\(' py/ngff_zarr/structural_validation.py || true

echo '== Issue `#659` =='
gh issue view 659 --repo fideus-labs/ngff-zarr --json number,title,state,url,body 2>&1 || true

echo '== Issue `#667` =='
gh issue view 667 --repo fideus-labs/ngff-zarr --json number,title,state,url,body 2>&1 || true

Length of output: 34145

---

@vboussot Thanks for the detailed explanation. I verified the version flow.

declared_version must remain shared with validate_ngff in this v0.6 path. PR #659 resolves the 0.6.dev4 to 0.6 schema-tree mapping.

A 0.9.dev1 store routes to the v0.9 reader. That reader rejects validate=True and delegates with validate=False. validate_structural provides the Python RFC-4 enforcement for 0.9.dev1.

The coordinate-system read-path gap is tracked in #667. It is outside this PR.

I am withdrawing the outside-diff finding.
🐇

---

✏️ Learnings added

Learnt from: vboussot
URL: https://github.com/fideus-labs/ngff-zarr/pull/673

Timestamp: 2026-08-24T12:21:56.081Z
Learning: In the Python `py/ngff_zarr/v06/zarr_metadata.py` reader, `declared_version` must be passed unchanged to both `validate_ngff` and `is_rfc4_orientation_enforced`. The v0.6 on-disk string can be `0.6.dev4`; schema-path resolution for prereleases is handled by the version-to-directory mapping from PR `#659` rather than by this reader.

---

Learnt from: vboussot
URL: https://github.com/fideus-labs/ngff-zarr/pull/673

Timestamp: 2026-08-24T12:21:56.081Z
Learning: For Python OME-Zarr `0.9.dev1` reads, `py/ngff_zarr/from_ngff_zarr.py` routes to `py/ngff_zarr/v09/zarr_metadata.py`. That reader raises `NotImplementedError` when `validate=True` and delegates to the v0.6 reader with `validate=False`; RFC-4 orientation enforcement for `0.9.dev1` is provided by `validate_structural`.

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