Fix test_cli.py test_io.py and test_node.py

ome_zarr/data.py

@@ -129,7 +129,7 @@ def create_zarr(
 
     loc = parse_url(zarr_directory, mode="w")
     assert loc
-    grp = zarr.group(loc.store, zarr_format=2)
+    grp = zarr.group(loc.store, zarr_format=fmt.zarr_format)
     axes = None
     size_c = 1
     if fmt.version not in ("0.1", "0.2"):
@@ -200,7 +200,10 @@ def create_zarr(
 
     if labels:
         labels_grp = grp.create_group("labels")
-        labels_grp.attrs["labels"] = [label_name]
+        if fmt.zarr_format == 2:
+            labels_grp.attrs["labels"] = [label_name]
+        else:
+            labels_grp.attrs["ome"] = {"labels": [label_name]}
 
         label_grp = labels_grp.create_group(label_name)
         if axes is not None:
@@ -214,11 +217,23 @@ def create_zarr(
             rgba = [randrange(0, 256) for i in range(4)]
             colors.append({"label-value": x, "rgba": rgba})
             properties.append({"label-value": x, "class": f"class {x}"})
-        label_grp.attrs["image-label"] = {
-            "version": fmt.version,
-            "colors": colors,
-            "properties": properties,
-            "source": {"image": "../../"},
-        }
+        if fmt.zarr_format == 2:
+            label_grp.attrs["image-label"] = {
+                "version": fmt.version,
+                "colors": colors,
+                "properties": properties,
+                "source": {"image": "../../"},
+            }
+        else:
+            ome_attrs = label_grp.attrs["ome"]
+            label_grp.attrs["ome"] = {
+                "image-label": {
+                    "version": fmt.version,
+                    "colors": colors,
+                    "properties": properties,
+                    "source": {"image": "../../"},
+                },
+                **ome_attrs,
+            }
 
     return grp

ome_zarr/format.py

@@ -55,6 +55,11 @@ class Format(ABC):
     def version(self) -> str:  # pragma: no cover
         raise NotImplementedError()
 
+    @property
+    @abstractmethod
+    def zarr_format(self) -> int:  # pragma: no cover
+        raise NotImplementedError()
+
     @abstractmethod
     def matches(self, metadata: dict) -> bool:  # pragma: no cover
         raise NotImplementedError()
@@ -129,6 +134,10 @@ class FormatV01(Format):
     def version(self) -> str:
         return "0.1"
 
+    @property
+    def zarr_format(self) -> int:
+        return 2
+
     def matches(self, metadata: dict) -> bool:
         version = self._get_metadata_version(metadata)
         LOGGER.debug("%s matches %s?", self.version, version)
@@ -339,5 +348,9 @@ class FormatV05(FormatV04):
     def version(self) -> str:
         return "0.5"
 
+    @property
+    def zarr_format(self) -> int:
+        return 3
+
 
 CurrentFormat = FormatV05

ome_zarr/writer.py

@@ -265,15 +265,15 @@ def write_multiscale(
                 # dimension_separator=group.store.dimension_separator,
                 dimension_separator="/",
                 compute=compute,
-                zarr_format=2,
+                zarr_format=fmt.zarr_format,
             )
 
             if not compute:
                 dask_delayed.append(da_delayed)
 
         else:
             # v2 arguments
-            if fmt.version in ("0.1", "0.2", "0.3", "0.4"):
+            if fmt.zarr_format == 2:
                 options["chunks"] = chunks_opt
                 options["dimension_separator"] = "/"
                 # default to zstd compression
@@ -356,6 +356,8 @@ def write_multiscales_metadata(
             axes = _get_valid_axes(axes=axes, fmt=fmt)
             if axes is not None:
                 ndim = len(axes)
+
+    ome_attrs = {}
     if (
         isinstance(metadata, dict)
         and metadata.get("metadata")
@@ -378,7 +380,7 @@ def write_multiscales_metadata(
                     if not isinstance(c["window"][p], (int, float)):
                         raise TypeError(f"`'{p}'` must be an int or float.")
 
-        group.attrs["omero"] = omero_metadata
+        ome_attrs["omero"] = omero_metadata
 
     # note: we construct the multiscale metadata via dict(), rather than {}
     # to avoid duplication of protected keys like 'version' in **metadata
@@ -393,12 +395,15 @@ def write_multiscales_metadata(
     if axes is not None:
         multiscales[0]["axes"] = axes
 
-    if fmt.version in ("0.1", "0.2", "0.3", "0.4"):
+    ome_attrs["multiscales"] = multiscales
+
+    if fmt.zarr_format == 2:
         multiscales[0]["version"] = fmt.version
-        group.attrs["multiscales"] = multiscales
+        for key, data in ome_attrs.items():
+            group.attrs[key] = data
     else:
         # Zarr v3 metadata under 'ome' with top-level version
-        group.attrs["ome"] = {"version": fmt.version, "multiscales": multiscales}
+        group.attrs["ome"] = {"version": fmt.version, **ome_attrs}
 
 
 def write_plate_metadata(
@@ -446,7 +451,10 @@ def write_plate_metadata(
         plate["field_count"] = field_count
     if acquisitions is not None:
         plate["acquisitions"] = _validate_plate_acquisitions(acquisitions)
-    group.attrs["plate"] = plate
+    if fmt.zarr_format == 2:
+        group.attrs["plate"] = plate
+    else:
+        group.attrs["ome"] = {"plate": plate}
 
 
 def write_well_metadata(
@@ -471,7 +479,10 @@ def write_well_metadata(
         "images": _validate_well_images(images),
         "version": fmt.version,
     }
-    group.attrs["well"] = well
+    if fmt.zarr_format == 2:
+        group.attrs["well"] = well
+    else:
+        group.attrs["ome"] = {"well": well}
 
 
 def write_image(
@@ -730,7 +741,10 @@ def write_label_metadata(
 
     label_list = group.attrs.get("labels", [])
     label_list.append(name)
-    group.attrs["labels"] = label_list
+    if fmt.zarr_format == 2:
+        group.attrs["labels"] = label_list
+    else:
+        group.attrs["ome"] = {"labels": label_list}
 
 
 def write_multiscale_labels(

tests/test_node.py

@@ -3,7 +3,7 @@
 from numpy import zeros
 
 from ome_zarr.data import create_zarr
-from ome_zarr.format import FormatV01, FormatV02, FormatV03
+from ome_zarr.format import FormatV01, FormatV02, FormatV03, FormatV04
 from ome_zarr.io import parse_url
 from ome_zarr.reader import Label, Labels, Multiscales, Node, Plate, Well
 from ome_zarr.writer import write_image, write_plate_metadata, write_well_metadata
@@ -44,7 +44,7 @@ class TestHCSNode:
     @pytest.fixture(autouse=True)
     def initdir(self, tmpdir):
         self.path = tmpdir.mkdir("data")
-        self.store = parse_url(str(self.path), mode="w").store
+        self.store = parse_url(str(self.path), mode="w", fmt=FormatV04()).store
         self.root = zarr.group(store=self.store)
 
     def test_minimal_plate(self):
@@ -53,7 +53,7 @@ def test_minimal_plate(self):
         well = row_group.require_group("1")
         write_well_metadata(well, ["0"])
         image = well.require_group("0")
-        write_image(zeros((1, 1, 1, 256, 256)), image)
+        write_image(zeros((1, 1, 1, 256, 256)), image, fmt=FormatV04())
 
         node = Node(parse_url(str(self.path)), list())
         assert node.data
@@ -85,7 +85,7 @@ def test_multiwells_plate(self, fmt):
             write_well_metadata(well, ["0", "1", "2"], fmt=fmt)
             for field in range(3):
                 image = well.require_group(str(field))
-                write_image(zeros((1, 1, 1, 256, 256)), image)
+                write_image(zeros((1, 1, 1, 256, 256)), image, fmt=fmt)
 
         node = Node(parse_url(str(self.path)), list())
         assert node.data