feat(py,ts): track the OME-Zarr 0.6rc0 schemas and version tag

docs/rfc5.md

@@ -53,7 +53,7 @@ position `i` is the input axis that becomes the `i`-th output axis, and every
 zero-based input axis index appears exactly once.
 
 `ByDimension` builds a high dimensional transform from lower dimensional ones;
-each `ByDimensionItem` wraps a transformation with the `input_axes` and `output_axes`
+each `ByDimensionItem` wraps a transformation with the `inputAxes` and `outputAxes`
 (zero-based indices into the parent's coordinate systems) it applies to, and
 every output axis is produced by exactly one item.
 

py/examples/upgrade_ome_zarr_example.py

@@ -111,7 +111,7 @@ def demo_write_to_new_store(tmp: Path) -> None:
     print(f"  source version (after)  : {src_after!r}  (unchanged)")
     print(f"  new store version       : {dst_after!r}")
     assert src_after == "0.4", src_after
-    assert dst_after == "0.6.dev4", dst_after
+    assert dst_after == "0.6rc0", dst_after
 
     # Confirm the upgraded store reads back with pixel data intact.
     reloaded = from_ome_zarr(dst, version="0.6")
@@ -142,7 +142,7 @@ def demo_in_place(tmp: Path) -> None:
     after_version = read_ome_version(store)
     after_chunks = chunk_digests(store_root)
     print(f"  version (after)         : {after_version!r}")
-    assert after_version == "0.6.dev4", after_version
+    assert after_version == "0.6rc0", after_version
 
     # Prove every array chunk file is byte-for-byte identical.
     assert after_chunks == before_chunks, "array chunk data changed on in-place upgrade"

py/ngff_zarr/__init__.py

@@ -4,7 +4,7 @@
 # SPDX-License-Identifier: MIT
 
 from .__about__ import __version__
-from ._supported_versions import SUPPORTED_VERSIONS
+from ._supported_versions import SUPPORTED_VERSIONS, V06_ONDISK_VERSION
 from .cli_input_to_ngff_image import cli_input_to_ngff_image
 from .codecs import codec_from_name, get_available_codecs
 from .compute_omero import (
@@ -110,6 +110,7 @@
 __all__ = [
     "__version__",
     "SUPPORTED_VERSIONS",
+    "V06_ONDISK_VERSION",
     "config",
     # OMERO computation
     "compute_omero_from_ngff_image",

py/ngff_zarr/_supported_versions.py

@@ -12,8 +12,11 @@ class NgffVersion(StrEnum):
     V04 = "0.4"
     V05 = "0.5"
     V06 = "0.6"
+    #: Pre-release tags of the 0.6 spec. Both remain readable: stores written
+    #: while 0.6 was a draft carry the ``dev4`` tag on disk.
     V06dev4 = "0.6.dev4"
-    LATEST = "0.6.dev4"
+    V06rc0 = "0.6rc0"
+    LATEST = "0.6rc0"
 
 
 # Supported NGFF specification versions
@@ -25,4 +28,19 @@ class NgffVersion(StrEnum):
     NgffVersion.V05,
     NgffVersion.V06,
     NgffVersion.V06dev4,
+    NgffVersion.V06rc0,
 )
+
+#: The ``ome.version`` string written to disk for the API version ``"0.6"``.
+#: The 0.6 spec is a release candidate, so a store is tagged with the
+#: pre-release the bundled ``spec/0.6`` schemas carry rather than with the bare
+#: ``"0.6"`` the public ``version`` option accepts. Mirrors the TypeScript
+#: port's ``V06_ONDISK_VERSION``; this constant is the one place the tag lives.
+V06_ONDISK_VERSION = NgffVersion.V06rc0
+
+#: 0.6 pre-release tags that earlier ngff-zarr releases wrote and that the
+#: bundled schemas no longer accept. A store carrying one differs from a valid
+#: store in that string alone; the validating reader says so and checks the
+#: rest, and ``upgrade_ome_zarr`` rewrites the tag. Any other tag is checked
+#: as given, so a tag from a later spec release is not passed off as this one.
+V06_SUPERSEDED_TAGS = frozenset({NgffVersion.V06dev4.value})

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

@@ -1,10 +1,10 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/_version.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema",
   "title": "OME-Zarr version",
   "description": "OME-Zarr version.",
   "type": "string",
   "enum": [
-    "0.6.dev4"
+    "0.6rc0"
   ]
 }

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

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/axes.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/axes.schema",
   "title": "Axes",
   "description": "OME-Zarr Axes.",
   "type": "array",

py/ngff_zarr/spec/0.6/schemas/bf2raw.schema

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/bf2raw.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/bf2raw.schema",
   "title": "bioformats2raw",
   "description": "OME-Zarr bioformats2raw metadata.",
   "type": "object",
@@ -17,7 +17,7 @@
           ]
         },
         "version": {
-          "$ref": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/_version.schema"
+          "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema"
         }
       },
       "required": [

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

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/coordinate_systems.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_systems.schema",
   "title": "Coordinate systems",
   "description": "OME-Zarr coordinate system.",
   "type": "array",

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

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/coordinate_transformations.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema",
   "title": "Coordinate Transformations",
   "description": "OME-Zarr Coordinate transforms.",
   "type": "array",
@@ -67,6 +67,9 @@
             {
               "$ref": "#/$defs/mapAxis"
             },
+            {
+              "$ref": "#/$defs/projectAxis"
+            },
             {
               "$ref": "#/$defs/scale"
             },
@@ -133,6 +136,51 @@
         "mapAxis"
       ]
     },
+    "projectAxis": {
+      "type": "object",
+      "title": "projectAxis transformation",
+      "description": "Add or drop axes from a coordinate vector.",
+      "allOf": [
+        {
+          "properties": {
+            "type": {
+              "const": "projectAxis"
+            },
+            "droppedInputs": {
+              "type": "array",
+              "minItems": 1,
+              "items": {
+                "type": "integer",
+                "minimum": 0,
+                "maximum": 4
+              },
+              "maxItems": 3,
+              "uniqueItems": true,
+              "description": "An array of integers representing the indices of the input axes to drop."
+            },
+            "createdOutputs": {
+              "type": "array",
+              "minItems": 1,
+              "items": {
+                "type": "integer",
+                "minimum": 0,
+                "maximum": 4
+              },
+              "maxItems": 3,
+              "uniqueItems": true,
+              "description": "An array of integers representing the indices where zeros are inserted in the output coordinate vector."
+            }
+          }
+        },
+        {
+          "anyOf": [
+            {"required": ["droppedInputs"]},
+            {"required": ["createdOutputs"]}
+          ]
+        }
+      ]
+
+    },
     "scale": {
       "type": "object",
       "title": "Scale Transformation",
@@ -319,27 +367,25 @@
               "transformation": {
                 "$ref": "#/$defs/coordinateTransformation"
               },
-              "input_axes": {
+              "inputAxes": {
                 "type": "array",
                 "items": {
-                  "type": "integer",
-                  "minimum": 0
+                  "type": "number"
                 },
-                "description": "Zero-based axis indices into the parent byDimension transformation's input coordinate system."
+                "description": "Names of the input axes for this transformation."
               },
-              "output_axes": {
+              "outputAxes": {
                 "type": "array",
                 "items": {
-                  "type": "integer",
-                  "minimum": 0
+                  "type": "number"
                 },
-                "description": "Zero-based axis indices into the parent byDimension transformation's output coordinate system."
+                "description": "Names of the output axes for this transformation."
               }
             },
             "required": [
               "transformation",
-              "input_axes",
-              "output_axes"
+              "inputAxes",
+              "outputAxes"
             ]
           }
         }