Add zarr v2 endpoints to Tiled

.gitignore

@@ -58,6 +58,7 @@ config.yml
 prometheus_data
 grafana_data
 data
+alembic.ini
 
 tiled/_version.py
 

CHANGELOG.md

@@ -3,6 +3,12 @@ Write the date in place of the "Unreleased" in the case a new version is release
 
 # Changelog
 
+## Unreleased
+
+### Added
+
+- zarr v2 endpoints for read access
+
 ## v0.1.0b10 (2024-10-11)
 
 - Add kwarg to client logout to auto-clear default identity.

pyproject.toml

@@ -145,6 +145,7 @@ dataframe = [
 # These are required for developing the package (running the tests, building
 # the documentation) but not necessarily required for _using_ it.
 dev = [
+    "aiohttp",
     "coverage",
     "flake8",
     "importlib_resources;python_version < \"3.9\"",

tiled/_tests/test_protocols.py

@@ -247,9 +247,13 @@ def test_sparseadapter_protocol(mocker: MockFixture) -> None:
     mock_call4 = mocker.patch.object(CustomSparseAdapter, "specs")
     mock_call5 = mocker.patch.object(CustomSparseAdapter, "metadata")
 
-    structure = COOStructure(shape=(2 * 5,), chunks=((5, 5),))
-
     array = numpy.random.rand(2, 512, 512)
+
+    structure = COOStructure(
+        shape=(2 * 5,),
+        chunks=((5, 5),),
+        data_type=BuiltinDtype.from_numpy_dtype(array.dtype),
+    )
     blocks: Dict[Tuple[int, ...], Tuple[NDArray[Any], Any]] = {(1,): (array, (1,))}
     metadata: JSON = {"foo": "bar"}
     anyslice = (1, 1, 1)

tiled/_tests/test_server.py

@@ -1,7 +1,3 @@
-import contextlib
-import threading
-import time
-
 import pytest
 import uvicorn
 from fastapi import APIRouter
@@ -11,35 +7,10 @@
 from ..client import from_uri
 from ..server.app import build_app
 from ..server.logging_config import LOGGING_CONFIG
+from .utils import ThreadedServer
 
 router = APIRouter()
 
-
-class Server(uvicorn.Server):
-    # https://github.com/encode/uvicorn/discussions/1103#discussioncomment-941726
-
-    def install_signal_handlers(self):
-        pass
-
-    @contextlib.contextmanager
-    def run_in_thread(self):
-        thread = threading.Thread(target=self.run)
-        thread.start()
-        try:
-            # Wait for server to start up, or raise TimeoutError.
-            for _ in range(100):
-                time.sleep(0.1)
-                if self.started:
-                    break
-            else:
-                raise TimeoutError("Server did not start in 10 seconds.")
-            host, port = self.servers[0].sockets[0].getsockname()
-            yield f"http://{host}:{port}"
-        finally:
-            self.should_exit = True
-            thread.join()
-
-
 API_KEY = "secret"
 
 
@@ -49,7 +20,7 @@ def server(tmpdir):
     app = build_app(catalog, {"single_user_api_key": API_KEY})
     app.include_router(router)
     config = uvicorn.Config(app, port=0, loop="asyncio", log_config=LOGGING_CONFIG)
-    server = Server(config)
+    server = ThreadedServer(config)
     with server.run_in_thread() as url:
         yield url
 

tiled/_tests/test_writing.py

@@ -26,6 +26,7 @@
 from ..mimetypes import PARQUET_MIMETYPE
 from ..queries import Key
 from ..server.app import build_app
+from ..structures.array import BuiltinDtype
 from ..structures.core import Spec, StructureFamily
 from ..structures.data_source import DataSource
 from ..structures.sparse import COOStructure
@@ -245,7 +246,13 @@ def test_write_sparse_chunked(tree):
                 "sparse",
                 [
                     DataSource(
-                        structure=COOStructure(shape=(2 * N,), chunks=((N, N),)),
+                        structure=COOStructure(
+                            shape=(2 * N,),
+                            chunks=((N, N),),
+                            data_type=BuiltinDtype.from_numpy_dtype(
+                                numpy.dtype("float64")
+                            ),
+                        ),
                         structure_family="sparse",
                     )
                 ],