Carry fix/rfc3-axes into main: the RFC-4 version gate and the bundled 0.9.dev1 schemas

docs/cli.md

@@ -197,9 +197,8 @@ ngff-zarr upgrade src.zarr -o dst.zarr --to 0.5
 
 The target version is selected with `--to` (alias `--version`), one of `0.4`,
 `0.5`, `0.6`, or `0.9.dev1` (default `0.6`). `0.9.dev1` is the development
-version that adopts RFC-3; OME publishes no JSON Schema for it yet, so
-`--validate` cannot check a store at that version. Add `--validate` to validate
-the source metadata against the NGFF schema while reading. For the write-to-new-store mode,
+version that adopts RFC-3. Add `--validate` to validate the source metadata
+against the NGFF schema while reading. For the write-to-new-store mode,
 `--overwrite` (the default) replaces any pre-existing data at the output store,
 while `--no-overwrite` refuses to; both flags are ignored for an in-place
 upgrade, which never overwrites array data.

docs/spec_features.md

@@ -40,9 +40,9 @@ supported by `ngff-zarr`.
   and transformations.
 - **OME-Zarr 0.9.dev1**: Reads and writes the development version that adopts
   RFC-3, which extends support for the number, names, types and order
-  of axes. It is opt-in: pass `version="0.9.dev1"` explicitly. The default
-  target is unchanged, and OME publishes no JSON Schema for it yet, so schema
-  validation is unavailable at that version.
+  of axes. It is opt-in: pass `version="0.9.dev1"` explicitly, the default
+  target is unchanged. The schemas of the `0.9.dev1` release are bundled, so
+  `validate=True` checks a store at that version as it does at any other.
 
 ## High Content Screening (HCS)
 

docs/validation/overview.md

@@ -26,6 +26,9 @@ finest-to-coarsest dataset ordering, OMERO channel color format, RFC 4
 anatomical orientation, and HCS plate/well consistency. Most rules enforce v0.4
 MUSTs; two additional rules (`zarr-format`, `ome-namespace`) enforce the v0.5
 `ome`-namespace and Zarr v3 store conventions and fire only for v0.5 metadata.
+The three RFC 4 orientation rules are normative from OME-Zarr 0.9.dev1: they
+are inert when the caller declares an earlier version and stay on, as a
+strictness choice, when no version is declared (see [[rule-reference]]).
 
 The rules operate on the already-parsed metadata object (the `Metadata`,
 `Plate`, and `Well` dataclasses in Python; their equivalents in TypeScript), so

docs/validation/parity.md

@@ -26,7 +26,7 @@ for usage, see [[api]].
 
 ## The contract
 
-Both ports must agree on five observable dimensions:
+Both ports must agree on six observable dimensions:
 
 1. **Rule identifiers** — the same `SpecRule` string values, in the same
    canonical declaration/iteration order.
@@ -42,6 +42,10 @@ Both ports must agree on five observable dimensions:
    inert for the versions that adopt the RFC-3 free-form axis model. Both ports
    must treat exactly the same version strings as RFC-3, or the same metadata
    validates in one language and not the other.
+6. **The RFC-4 orientation version set** — the three orientation rules gate the
+   opposite way: they are normative at exactly the versions that adopt RFC-4
+   (and when no version is given), and inert below. Both ports must treat the
+   same version strings as RFC-4 for the same reason.
 
 Because both test suites assert these facts against the **same literal
 identifier list**, adding, removing, renaming, or reordering a rule — or
@@ -85,6 +89,15 @@ at every other. Rule 4, `axis-names-unique`, is never inert: RFC-3 *adds* it,
 and ngff-zarr applies it at all versions as a strictness choice (see
 [[rule-reference]]).
 
+The versions at which the RFC-4 orientation rules are normative are pinned the
+same way, as a `CANONICAL_RFC4_VERSIONS` literal:
+
+1. `0.9.dev1`
+
+Rules 9–11 gate the opposite way from the RFC-3 set: they are enforced at
+those versions and when no version is given, and inert at every earlier
+version, where RFC-4 has no normative status (see [[rule-reference]]).
+
 ## The parity tests
 
 | Language   | Test file |
@@ -116,6 +129,10 @@ Each suite independently locks:
   `CANONICAL_RFC3_VERSIONS` and enforced at every other supported version and
   when no version is given, asserted through the public orchestrator rather
   than through the internal predicate.
+- **RFC-4 orientation version set** — the orientation rules are enforced at
+  exactly the versions in `CANONICAL_RFC4_VERSIONS` (and when no version is
+  given) and inert at every other supported version, asserted the same way,
+  once per orientation rule.
 
 Four of the fifteen rules never appear in `EXPECTED_EVALUATION_ORDER`, each for
 its own reason. The two v0.5 namespacing rules (`zarr-format`, `ome-namespace`)

docs/validation/rule-reference.md

@@ -23,8 +23,12 @@ stable, lower-kebab-case identifier (the `SpecRule` value) that is identical
 across the Python and TypeScript ports — see [[parity]] for the guarantee. Most
 rules enforce OME-Zarr v0.4 MUSTs; the two v0.5 namespacing rules
 (`zarr-format`, `ome-namespace`) fire only for v0.5 metadata and are inert (a
-no-op) for v0.4. For the conceptual background and the two validation levels,
-see [[overview]]; for invocation, see [[api]].
+no-op) for v0.4. The three RFC 4 orientation rules (9–11) are normative from
+OME-Zarr 0.9.dev1, which incorporates RFC-4 through `ome/ngff-spec#190`: they are
+inert when the caller declares 0.4, 0.5 or 0.6, where RFC 4 has no normative
+status, and stay on when no version is declared — a strictness choice, like
+`axis-names-unique` below 0.9.dev1. For the conceptual background and the two
+validation levels, see [[overview]]; for invocation, see [[api]].
 
 Location strings are dotted-segment, JSON-Pointer-style identifiers of the
 offending metadata node, emitted byte-for-byte identically in both languages.
@@ -44,9 +48,9 @@ the `SpecRule` enum declares them and the orchestrators evaluate them.
 | 6 | `global-coord-transform-after-per-level` | images/multiscales | Exactly one `scale` per dataset, and a `translation` must follow — not precede — its `scale`. | v0.4: each dataset defines exactly one scale; a translation follows its scale. | `multiscales[0].datasets[1].coordinateTransformations` |
 | 7 | `dataset-order-highest-to-lowest` | images/multiscales | Datasets ordered finest → coarsest; the spatial scale must not decrease as the level index rises. | v0.4: multiscale datasets ordered from highest to lowest resolution. | `multiscales[0].datasets[2]` |
 | 8 | `omero-channel-color-format` | OMERO | Each OMERO channel `color` is exactly six hexadecimal digits (RGB). | v0.4: OMERO channel color is 6 hex digits. | `multiscales[0].omero.channels[0].color` |
-| 9 | `axis-orientation-anatomical-type` | RFC 4 orientation | Every declared spatial-axis `orientation` has `type` `anatomical`. | RFC 4: an orientation's `type` is `anatomical`. | `multiscales[0].axes` |
-| 10| `axis-orientation-on-non-space` | RFC 4 orientation | An `orientation` is declared only on `space` axes, never on a non-spatial axis. | RFC 4: orientation applies to spatial axes only. | `multiscales[0].axes[0]` |
-| 11| `axis-orientation-unique-axis` | RFC 4 orientation | No two spatial axes declare orientations describing the same anatomical axis. | RFC 4: each spatial axis describes a distinct anatomical axis. | `multiscales[0].axes` |
+| 9 | `axis-orientation-anatomical-type` | RFC 4 orientation | Every declared spatial-axis `orientation` has `type` `anatomical`. Inert below 0.9.dev1 when the caller declares a version; kept on when none is given. | RFC 4 (normative from 0.9.dev1): an orientation's `type` is `anatomical`. No released spec below 0.9.dev1 adopts RFC 4, so enforcement without a declared version is a strictness choice, not a spec MUST of those versions. | `multiscales[0].axes` |
+| 10| `axis-orientation-on-non-space` | RFC 4 orientation | An `orientation` is declared only on `space` axes, never on a non-spatial axis. Inert below 0.9.dev1 when the caller declares a version; kept on when none is given. | RFC 4 (normative from 0.9.dev1): orientation applies to spatial axes only. Same below-0.9.dev1 status as rule 9. | `multiscales[0].axes[0]` |
+| 11| `axis-orientation-unique-axis` | RFC 4 orientation | No two spatial axes declare orientations describing the same anatomical axis. Inert below 0.9.dev1 when the caller declares a version; kept on when none is given. | RFC 4 (normative from 0.9.dev1): each spatial axis describes a distinct anatomical axis. Same below-0.9.dev1 status as rule 9. | `multiscales[0].axes` |
 | 12| `zarr-format` | images/multiscales (v0.5) | A v0.5 entry implies a Zarr v3 store; a `zarr_format` value that leaked into the entry must be exactly `3`. Inert for v0.4. | v0.5: metadata is backed by a Zarr v3 store (`zarr_format == 3`). | `multiscales[0]` |
 | 13| `ome-namespace` | images/multiscales (v0.5) | A v0.5 entry must not retain a group-level `ome` or `multiscales` wrapper key — the `ome` namespace wraps the group attributes, not each entry. Inert for v0.4. | v0.5: multiscales live under the top-level `ome` namespace, with `version` hoisted to `ome.version`. | `multiscales[0]` |
 | 14| `plate-row-index-consistency` | HCS plate | Each well's `path` is `<row>/<column>`, naming declared row/column entries, with `rowIndex`/`columnIndex` equal to those entries' positions. | v0.4: well `rowIndex`/`columnIndex` match the named row/column positions in `plate.rows`/`plate.columns`. | `plate.wells[3]` |
@@ -65,11 +69,12 @@ rules:
   class-ordering then spatial-name ordering for `axis-order`; per-dataset
   scale-count then transform-ordering for
   `global-coord-transform-after-per-level`. The v0.5 namespacing rules (12 and
-  13) run last and are inert for v0.4 input. The orientation rules
-  `axis-orientation-on-non-space` (10) and `axis-orientation-unique-axis` (11)
-  fire only for specific axis shapes, so the linear fail-fast cascade for a v0.4
-  metadata is an 11-step sequence ending at
-  `axis-orientation-anatomical-type`.
+  13) run last and are inert for v0.4 input, and the orientation rules (9–11)
+  are inert when the caller declares a version below 0.9.dev1. The orientation
+  rules `axis-orientation-on-non-space` (10) and `axis-orientation-unique-axis`
+  (11) fire only for specific axis shapes, so the linear fail-fast cascade for
+  a v0.4-shaped metadata validated with no declared version is an 11-step
+  sequence ending at `axis-orientation-anatomical-type`.
 - **`validate_plate` / `validatePlate`** evaluates rule **14**
   (`plate-row-index-consistency`).
 - **`validate_well` / `validateWell`** evaluates rule **15**
@@ -96,8 +101,9 @@ TypeScript by checking the target version in `axisViews`.
   `global-coord-transform-after-per-level`,
   `dataset-order-highest-to-lowest`.
 - **OMERO** — `omero-channel-color-format`.
-- **RFC 4 orientation** — `axis-orientation-anatomical-type`,
-  `axis-orientation-on-non-space`, `axis-orientation-unique-axis`.
+- **RFC 4 orientation** (normative from 0.9.dev1) —
+  `axis-orientation-anatomical-type`, `axis-orientation-on-non-space`,
+  `axis-orientation-unique-axis`.
 - **v0.5 namespacing** — `zarr-format`, `ome-namespace` (inert for v0.4).
 - **HCS plate / well** — `plate-row-index-consistency`,
   `well-acquisition-missing`.

py/ngff_zarr/spec/0.6/schemas/coordinate_transformations.schema

@@ -372,14 +372,14 @@
                 "items": {
                   "type": "number"
                 },
-                "description": "Names of the input axes for this transformation."
+                "description": "Indices of the input axes for this transformation."
               },
               "outputAxes": {
                 "type": "array",
                 "items": {
                   "type": "number"
                 },
-                "description": "Names of the output axes for this transformation."
+                "description": "Indices of the output axes for this transformation."
               }
             },
             "required": [

py/ngff_zarr/spec/0.6/schemas/image.schema

@@ -113,7 +113,7 @@
                         ]
                       },
                       {
-                        "description": "A sequence of a ingle scale followed by a single translation",
+                        "description": "A sequence of a single scale followed by a single translation",
                         "type": "object",
                         "properties": {
                           "type": {"const": "sequence"},

py/ngff_zarr/spec/0.9/schemas/_version.schema

@@ -0,0 +1,10 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema",
+  "title": "OME-Zarr version",
+  "description": "OME-Zarr version.",
+  "type": "string",
+  "enum": [
+    "0.9.dev1"
+  ]
+}

py/ngff_zarr/spec/0.9/schemas/axes.schema

@@ -0,0 +1,46 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/axes.schema",
+  "title": "Axes",
+  "description": "OME-Zarr Axes.",
+  "type": "array",
+  "uniqueItems": true,
+  "minItems": 1,
+  "items": {
+    "$ref": "#/$defs/axis"
+  },
+  "$defs": {
+    "axis": {
+      "type": "object",
+      "properties": {
+        "name": {
+          "type": "string",
+          "minLength": 1,
+          "description": "Name of the axis. Must be unique within the coordinate system."
+        },
+        "longName": {
+          "type": "string",
+          "description": "Longer name or description of the axis."
+        },
+        "type": {
+          "type": "string",
+          "description": "Type of the axis. Can be a predefined type or custom type."
+        },
+        "discrete": {
+          "type": "boolean",
+          "description": "Whether the dimension is discrete"
+        },
+        "unit": {
+          "type": "string",
+          "description": "Unit for the axis"
+        },
+        "orientation": {
+          "$ref": "axis_orientation.schema"
+        }
+      },
+      "required": [
+        "name"
+      ]
+    }
+  }
+}

py/ngff_zarr/spec/0.9/schemas/axis_orientation.schema

@@ -0,0 +1,41 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/axis_orientation.schema",
+  "title": "Axis Orientation",
+  "description": "Controlled vocabulary for orientation of each spatial axis according to subject or subject-global reference.",
+  "type": "object",
+      "properties": {
+        "type": {
+          "enum": ["anatomical"]
+        },
+        "value": {
+          "enum": [
+            "left-to-right",
+            "right-to-left",
+            "anterior-to-posterior",
+            "posterior-to-anterior",
+            "inferior-to-superior",
+            "superior-to-inferior",
+            "dorsal-to-ventral",
+            "ventral-to-dorsal",
+            "dorsal-to-palmar",
+            "palmar-to-dorsal",
+            "dorsal-to-plantar",
+            "plantar-to-dorsal",
+            "rostral-to-caudal",
+            "caudal-to-rostral",
+            "cranial-to-caudal",
+            "caudal-to-cranial",
+            "proximal-to-distal",
+            "distal-to-proximal",
+            "superficial-to-deep",
+            "deep-to-superficial",
+            "apical-to-basal",
+            "basal-to-apical",
+            "apex-to-base",
+            "base-to-apex"
+          ]
+        }
+      },
+      "required": ["type", "value"]
+}

py/ngff_zarr/spec/0.9/schemas/bf2raw.schema

@@ -0,0 +1,32 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/bf2raw.schema",
+  "title": "bioformats2raw",
+  "description": "OME-Zarr bioformats2raw metadata.",
+  "type": "object",
+  "properties": {
+    "ome": {
+      "description": "The versioned OME-Zarr Metadata namespace",
+      "type": "object",
+      "properties": {
+        "bioformats2raw.layout": {
+          "description": "The top-level identifier metadata added by bioformats2raw",
+          "type": "number",
+          "enum": [
+            3
+          ]
+        },
+        "version": {
+          "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema"
+        }
+      },
+      "required": [
+        "bioformats2raw.layout",
+        "version"
+      ]
+    }
+  },
+  "required": [
+    "ome"
+  ]
+}

py/ngff_zarr/spec/0.9/schemas/coordinate_systems.schema

@@ -0,0 +1,31 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_systems.schema",
+  "title": "Coordinate systems",
+  "description": "OME-Zarr coordinate system.",
+  "type": "array",
+  "uniqueItems": true,
+  "items": {
+    "$ref": "#/$defs/coordinateSystem"
+  },
+  "$defs": {
+    "coordinateSystem": {
+      "description": "Coordinate Systems for OME-NGFF",
+      "type": "object",
+      "properties": {
+        "name": {
+          "type": "string",
+          "minLength": 1,
+          "description": "Name of coordinate system. Must be unique among all coordinate systems."
+        },
+        "axes": {
+          "$ref": "axes.schema"
+        }
+      },
+      "required": [
+        "name",
+        "axes"
+      ]
+    }
+  }
+}