fix: remove type ignore comments for improved type checking (#44)

Author: tlambert03

examples/demo_from_uri.py

@@ -15,7 +15,7 @@
 from yaozarrs import validate_ome_uri
 
 try:
-    from rich import print  # ty: ignore
+    from rich import print
 except ImportError:
     print = builtins.print  # type: ignore # noqa
 

scripts/fetch.py

@@ -7,7 +7,7 @@
 from pathlib import Path, PurePosixPath
 from typing import Any
 
-import fsspec  # type: ignore
+import fsspec
 
 META_SUFFIXES = (
     "zarr.json",  # Zarr v3
@@ -115,7 +115,7 @@ def metadata_mirror(remote_url: str, local_parent: str, verbose: bool = True) ->
     str
         Path to the local mirrored store directory.
     """
-    fs, root = fsspec.url_to_fs(remote_url)  # type: ignore
+    fs, root = fsspec.url_to_fs(remote_url)
 
     root_path = PurePosixPath(root.rstrip("/"))
     root_name = root_path.name or root_path.parent.name

src/yaozarrs/_base.py

@@ -22,7 +22,7 @@ class _BaseModel(BaseModel):
         validate_assignment=True,
         validate_default=True,
         serialize_by_alias=True,
-        **_by_name_cfg,  # type: ignore[typeddict-item]
+        **_by_name_cfg,
     )
 
     if not TYPE_CHECKING:

src/yaozarrs/_demo_data.py

@@ -131,11 +131,13 @@ def write_ome_image(
             win_max = 1.0
 
         for i in range(n_channels):
-            channel = {"window": {"start": 0, "min": 0, "end": win_max, "max": win_max}}
+            channel: dict[str, Any] = {
+                "window": {"start": 0, "min": 0, "end": win_max, "max": win_max}
+            }
             if channel_names and i < len(channel_names):
-                channel["label"] = channel_names[i]  # pyright: ignore
+                channel["label"] = channel_names[i]
             if channel_colors and i < len(channel_colors):
-                channel["color"] = f"{channel_colors[i]:06x}"  # pyright: ignore
+                channel["color"] = f"{channel_colors[i]:06x}"
             channels.append(channel)
 
         metadata_kwargs["metadata"] = {"omero": {"channels": channels}}
@@ -377,12 +379,14 @@ def write_ome_plate(
             field_paths: list[str | dict] = [str(i) for i in range(fields_per_well)]
 
             # Write well metadata
-            well_metadata: dict = {"images": [{"path": path} for path in field_paths]}
+            well_metadata: dict[str, Any] = {
+                "images": [{"path": path} for path in field_paths]
+            }
 
             if acquisitions:
                 # Add acquisition references to images
                 for i, img in enumerate(well_metadata["images"]):
-                    img["acquisition"] = i % len(acquisitions)
+                    img["acquisition"] = i % len(acquisitions)  # ty: ignore[invalid-assignment]
 
             writer.write_well_metadata(well_group, field_paths)
 

src/yaozarrs/_storage.py

@@ -94,7 +94,7 @@ def _custom_formatwarning(message, category, *_, **__) -> str:
             # Format like an exception: module.Class: message
             return f"{category.__module__}.{category.__name__}: {message}\n"
 
-        warnings.formatwarning = _custom_formatwarning  # type: ignore
+        warnings.formatwarning = _custom_formatwarning  # ty: ignore[invalid-assignment]
         try:
             warnings.warn(warning_instance, stacklevel=2)
         finally:

src/yaozarrs/_zarr.py

@@ -46,8 +46,8 @@
     from typing import TypeVar
 
     import rich.tree
-    import tensorstore  # type: ignore
-    import zarr  # type: ignore
+    import tensorstore
+    import zarr
     from fsspec import FSMap
     from typing_extensions import Self
 
@@ -509,7 +509,7 @@ def to_zarr_python(self) -> zarr.Array | zarr.Group:
             Requires `zarr-python` to be installed.
         """
         try:
-            import zarr  # type: ignore
+            import zarr
         except ImportError as e:
             raise ImportError("zarr package is required for to_zarr_python()") from e
 
@@ -815,7 +815,7 @@ def _getitem_v2(self, child_path: str, key: str) -> ZarrGroup | ZarrArray:
 
     if TYPE_CHECKING:
 
-        def to_zarr_python(self) -> zarr.Group:  # type: ignore
+        def to_zarr_python(self) -> zarr.Group:
             """Convert to a zarr-python Group object.
 
             !!!important
@@ -856,7 +856,7 @@ def dtype(self) -> str:
 
     if TYPE_CHECKING:
 
-        def to_zarr_python(self) -> zarr.Array:  # type: ignore
+        def to_zarr_python(self) -> zarr.Array:
             """Convert to a zarr-python Array object.
 
             !!!important
@@ -870,7 +870,7 @@ def to_tensorstore(self) -> tensorstore.TensorStore:
             Requires `tensorstore` to be installed.
         """
         try:
-            import tensorstore as ts  # type: ignore
+            import tensorstore as ts
         except ImportError as e:
             raise ImportError(
                 "tensorstore package is required for to_tensorstore()"
@@ -947,7 +947,7 @@ def open_group(
     storage_options = storage_options or {}
     if str(uri).startswith("s3://"):
         storage_options.setdefault("anon", True)
-    mapper = get_mapper(uri, **storage_options)  # type: ignore
+    mapper = get_mapper(uri, **storage_options)
 
     if not isinstance(mapper, FSMap):  # pragma: no cover
         raise TypeError(f"Expected FSMap from get_mapper, got {type(mapper)}")

src/yaozarrs/write/v05/_write.py

@@ -1084,7 +1084,7 @@ def prepare(self) -> tuple[Path, dict[str, Any]]:
             raise ValueError("No series added. Use add_series() before prepare().")
 
         # Create root zarr.json with bioformats2raw.layout
-        bf2raw = Bf2Raw(bioformats2raw_layout=3)  # type: ignore
+        bf2raw = Bf2Raw(bioformats2raw_layout=3)  # ty: ignore[missing-argument,unknown-argument]
         _create_zarr3_group(self._dest, bf2raw, self._overwrite)
 
         # Create OME/zarr.json with series list
@@ -1133,7 +1133,7 @@ def _ensure_initialized(self) -> None:
             return
 
         # Create root zarr.json with bioformats2raw.layout
-        bf2raw = Bf2Raw(bioformats2raw_layout=3)  # type: ignore
+        bf2raw = Bf2Raw(bioformats2raw_layout=3)  # ty: ignore[missing-argument,unknown-argument]
         _create_zarr3_group(self._dest, bf2raw, self._overwrite)
 
         # Create OME directory and write METADATA.ome.xml if provided
@@ -2463,16 +2463,16 @@ def _write_to_array(array: Any, data: ArrayLike, *, progress: bool) -> None:
         with ctx:
             # Handle both zarr and tensorstore
             if hasattr(array, "store"):  # zarr.Array
-                da.store(dask_data, array, lock=False)  # type: ignore
+                da.store(dask_data, array, lock=False)  # ty: ignore[invalid-argument-type]
             else:  # tensorstore
                 computed = dask_data.compute()
                 array[:].write(computed).result()
 
     else:
         if hasattr(array, "store"):  # zarr.Array
-            array[:] = data  # type: ignore
+            array[:] = data
         else:  # tensorstore
-            array[:].write(data).result()  # type: ignore
+            array[:].write(data).result()
 
 
 # ######################## Array Writing Functions #############################

tests/v04/test_bf2raw_v04.py

@@ -1,4 +1,4 @@
 def test_bf2raw_v04():
     from yaozarrs.v04._bf2raw import Bf2Raw
 
-    Bf2Raw(bioformats2raw_layout=3)  # type: ignore
+    Bf2Raw(bioformats2raw_layout=3)  # ty: ignore[missing-argument,unknown-argument]

tests/v04/test_images_v04.py

@@ -714,7 +714,7 @@ def test_v04_axis_name_uniqueness_custom_validation() -> None:
     with pytest.raises(
         ValueError, match=r"Axis names must be unique\. Found duplicates"
     ):
-        _validate_axes_list(axes)
+        _validate_axes_list(axes)  # ty: ignore[invalid-argument-type]
 
 
 def test_multiscale_from_dims() -> None:

tests/v05/test_bf2raw_v05.py

@@ -1,4 +1,4 @@
 def test_bf2raw_v05():
     from yaozarrs.v05._bf2raw import Bf2Raw
 
-    Bf2Raw(bioformats2raw_layout=3)  # type: ignore
+    Bf2Raw(bioformats2raw_layout=3)  # ty: ignore[missing-argument,unknown-argument]