Carrara group add members - Carrara URI support fixes (#158)

* TileDB Carrara URIs and add memberships

* Cloud URI check

* Pin tifffile version for Zarr 2 support

* Get data protocol from TileDB-Py

* Remove custom DataProtocol type

* Change CI jobs name to reflect python version

* Add weekly nightly CI runs to catch dependency conflicts earlier

* Remove notebooks tests for Windows

* PR fixes

Author: ktsitsi

.github/workflows/ci.yml

@@ -1,10 +1,13 @@
 name: TileDB-BioImaging CI
 
-on: [push]
+on: 
+  push:
+  schedule:
+    - cron: '0 6 * * 1'
 
 jobs:
   build:
-    name: ${{ matrix.sys.os }}
+    name: ${{ matrix.sys.os }} ${{ matrix.python-version }}
     runs-on: ${{ matrix.sys.os }}
     timeout-minutes: 25
     strategy:
@@ -80,8 +83,10 @@ jobs:
 
     - name: Run notebook examples
       run: |
-        micromamba run -n test pip install opencv-python-headless matplotlib nbmake
+        micromamba run -n test pip install opencv-python-headless matplotlib nbmake 
         micromamba run -n test pytest --nbmake examples
+      if: ${{ matrix.sys.os != 'windows-latest' }}
+
 
     - name: Create Test Coverage Badge
       if: ${{ env.run_coverage == 'true' && matrix.sys.os == 'ubuntu-24.04' }}

setup.py

@@ -1,8 +1,8 @@
 import setuptools
 
-zarr = ["ome-zarr>=0.9.0"]
+zarr = ["ome-zarr>=0.9.0,<=0.10.3"]
 openslide = ["openslide-python"]
-tiff = ["tifffile", "imagecodecs"]
+tiff = ["tifffile==v2025.5.10", "imagecodecs"]
 cloud = ["tiledb-cloud"]
 
 full = sorted({*zarr, *openslide, *tiff})

tiledb/bioimg/helpers.py

@@ -71,14 +71,24 @@ def __exit__(self, exc_type: Any, exc_val: Any, exc_tb: Any) -> None:
         self.w_group.close()
         self.m_group.close()
 
+    def _is_tiledbv2_uri(self, uri: str, ctx: tiledb.Ctx) -> bool:
+        """Return True if the URI will use `tiledbv2` semantics."""
+        protocol_name: str = ctx.data_protocol(uri).name
+        return protocol_name == "DATA_PROTOCOL_V2"
+
+    def _is_tiledbv3_uri(self, uri: str, ctx: tiledb.Ctx) -> bool:
+        """Return True if the URI will use `tiledbv3` semantics."""
+        protocol_name: str = ctx.data_protocol(uri).name
+        return protocol_name == "DATA_PROTOCOL_V3"
+
     def get_or_create(self, name: str, schema: tiledb.ArraySchema) -> Tuple[str, bool]:
         create = False
         if name in self.r_group:
             uri = self.r_group[name].uri
         else:
             uri = os.path.join(self._uri, name).replace("\\", "/")
 
-            with tiledb.scope_ctx(self._ctx):
+            with tiledb.scope_ctx(self._ctx) as local_ctx:
                 if not tiledb.array_exists(uri):
                     tiledb.Array.create(uri, schema, ctx=self._ctx)
                     create = True
@@ -100,10 +110,14 @@ def get_or_create(self, name: str, schema: tiledb.ArraySchema) -> Tuple[str, boo
                             # (to allow the add operation)
                             self.w_group.close()
                             self.w_group.open("w")
-            # register the uri with the given name
-            if self._is_cloud:
-                self.w_group.add(uri, name, relative=False)
-            else:
+
+                # In tiledbv3 mode, the array is created with the uri==name and relative=True and registered to the group as a member with the given name from the uri.
+                # so we don't need to add it to the group manually
+
+                if self._is_cloud and self._is_tiledbv2_uri(uri, local_ctx):
+                    # register the uri with the given name
+                    self.w_group.add(uri, name, relative=False)
+            if not self._is_cloud:
                 self.w_group.add(name, name, relative=True)
         return uri, create
 

tiledb/bioimg/wrappers.py

@@ -107,7 +107,6 @@ def from_bioimg(
         else:
             raise _osd_exc
     else:
-
         logger.info("Converting PNG")
         return converters["png_converter"].to_tiledb(
             source=src,