Mypy type checking

tiled/_tests/adapters/test_sql.py

@@ -205,11 +205,11 @@ def test_psql(adapter_psql_one_partition: SQLAdapter) -> None:
     ],
 )
 def test_write_read_one_batch_one_part(
-    adapter: SQLAdapter, request: pytest.FixtureRequest
+    adapter: str, request: pytest.FixtureRequest
 ) -> None:
     # get adapter from fixture
     adapter = request.getfixturevalue(adapter)
-
+    assert isinstance(adapter, SQLAdapter)
     # test appending and reading a table as a whole
     test_table = pa.Table.from_arrays(data0, names)
 
@@ -237,11 +237,11 @@ def test_write_read_one_batch_one_part(
     ],
 )
 def test_write_read_list_batch_one_part(
-    adapter: SQLAdapter, request: pytest.FixtureRequest
+    adapter: str, request: pytest.FixtureRequest
 ) -> None:
     # get adapter from fixture
     adapter = request.getfixturevalue(adapter)
-
+    assert isinstance(adapter, SQLAdapter)
     test_table = pa.Table.from_batches([batch0, batch1, batch2])
     # test appending a list of batches to a table and read as a whole
     adapter.append_partition([batch0, batch1, batch2], 0)
@@ -293,12 +293,10 @@ def assert_same_rows(table1: pa.Table, table2: pa.Table) -> None:
         ("adapter_psql_many_partitions"),
     ],
 )
-def test_append_single_partition(
-    adapter: SQLAdapter, request: pytest.FixtureRequest
-) -> None:
+def test_append_single_partition(adapter: str, request: pytest.FixtureRequest) -> None:
     # get adapter from fixture
     adapter = request.getfixturevalue(adapter)
-
+    assert isinstance(adapter, SQLAdapter)
     # test writing an entire pyarrow table to a single partition
     table = pa.Table.from_batches([batch0, batch1, batch2])
     adapter.append_partition(table, 0)
@@ -321,11 +319,11 @@ def test_append_single_partition(
     ],
 )
 def test_write_read_one_batch_many_part(
-    adapter: SQLAdapter, request: pytest.FixtureRequest
+    adapter: str, request: pytest.FixtureRequest
 ) -> None:
     # get adapter from fixture
     adapter = request.getfixturevalue(adapter)
-
+    assert isinstance(adapter, SQLAdapter)
     # test writing to many partitions and reading it whole
     adapter.append_partition(batch0, 0)
     adapter.append_partition(batch1, 1)

tiled/_tests/adapters/test_sql_types.py

@@ -27,12 +27,12 @@ async def postgresql_uri() -> AsyncGenerator[str, None]:
         # yield uri_with_database_name.rsplit("/", 1)[0]
 
 
-@pytest_asyncio.fixture
+@pytest.fixture
 def sqlite_uri(tmp_path: Path) -> Generator[str, None, None]:
     yield f"sqlite:///{tmp_path}/test.db"
 
 
-@pytest_asyncio.fixture
+@pytest.fixture
 def duckdb_uri(tmp_path: Path) -> Generator[str, None, None]:
     yield f"duckdb:///{tmp_path}/test.db"
 

tiled/_tests/test_protocols.py

@@ -1,3 +1,4 @@
+import uuid
 from pathlib import Path
 from typing import Any, Dict, List, Literal, Optional, Set, Tuple, Union
 
@@ -420,7 +421,7 @@ async def test_accesspolicy_protocol(mocker: MockFixture) -> None:
     metadata: JSON = {"foo": "bar"}
     container = DirectoryContainer(directory=Path("somedirectory"), form={})
     principal = Principal(
-        uuid="12345678124123412345678123456781", type=PrincipalType.user
+        uuid=uuid.UUID(int=0x12345678124123412345678123456781), type=PrincipalType.user
     )
     authn_scopes = {"abc", "baz"}
     scopes = {"abc"}

tiled/adapters/hdf5.py

@@ -232,12 +232,12 @@ def from_catalog(
         array = cls.lazy_load_hdf5_array(
             *file_paths, dataset=dataset, swmr=swmr, libver=libver
         )
-
         if slice:
             if isinstance(slice, str):
                 slice = NDSlice.from_numpy_str(slice)
             array = array[slice]
         if squeeze:
+            assert isinstance(array, dask.array.Array)
             array = array.squeeze()
 
         if array.shape != tuple(structure.shape):

tiled/adapters/mapping.py

@@ -36,7 +36,7 @@
     StructureFamilyQuery,
 )
 from ..query_registration import QueryTranslationRegistry
-from ..server.schemas import SortingItem
+from ..server.schemas import SortingDirection, SortingItem
 from ..storage import Storage
 from ..structures.core import Spec, StructureFamily
 from ..structures.table import TableStructure
@@ -111,7 +111,7 @@ def __init__(
             # This is a special case that means, "the given ordering".
             # By giving that a name ("_") we enable requests to asking for the
             # last N by requesting the sorting ("_", -1).
-            sorting = [SortingItem(key="_", direction=1)]
+            sorting = [SortingItem(key="_", direction=SortingDirection.ASCENDING)]
         self._sorting = sorting
         self._metadata = metadata or {}
         self.specs = specs or []

tiled/adapters/netcdf.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Any, List, Optional, Set, Union
+from typing import Any, Optional, Set
 
 import xarray
 
@@ -10,7 +10,7 @@
 from .xarray import DatasetAdapter
 
 
-def read_netcdf(filepath: Union[str, List[str], Path]) -> DatasetAdapter:
+def read_netcdf(filepath: str | Path) -> DatasetAdapter:
     """
 
     Parameters

tiled/adapters/sequence.py

@@ -18,7 +18,7 @@
 from .utils import init_adapter_from_catalog
 
 
-def force_reshape(arr: np.array, desired_shape: Tuple[int, ...]) -> np.array:
+def force_reshape(arr: np.ndarray, desired_shape: Tuple[int, ...]) -> np.ndarray:
     """Reshape a numpy array to match the desired shape, if possible.
 
     Parameters