fix more ty errors

Author: pattonw

tests/process_block/argmax.py

@@ -36,7 +36,7 @@ def test_argmax(tmpdir):
     # create labels array
     prepare_ds(
         tmpdir / "test_data.zarr" / "labels",
-        shape=probs_data[1:],
+        shape=probs_data.shape[1:],
         voxel_size=Coordinate(1, 1),
         dtype=np.uint32,
         mode="w",

tests/process_block/graph_mws.py

@@ -56,6 +56,8 @@ def test_graph_mws(tmpdir, y_bias: float):
     with config.process_block_func() as process_block:
         process_block(block)
 
-    fragments, segments = config.lut.load()
+    lut = config.lut.load()
+    assert lut is not None
+    fragments, segments = lut
     assert len(np.unique(fragments)) == 2, fragments
     assert len(np.unique(segments)) == 1 + (y_bias < 0), segments

tests/test_dataset.py

@@ -217,7 +217,7 @@ def test_attrs_affs_validation(tmp_path):
     # Case 3: Mismatch -> Error
     with pytest.raises(ValidationError):
         # Disk has [[0,1], [1,0]], we provide [[5,5]]
-        Affs(store=path, neighborhood=[[5, 5]])
+        Affs(store=path, neighborhood=[Coordinate(5, 5)])
 
 
 def test_attrs_labels_lsd():

volara/blockwise/__init__.py

@@ -18,7 +18,7 @@
 from .seeded_extract_frags import SeededExtractFrags as SeededExtractFrags
 from .threshold import Threshold as Threshold
 
-BLOCKWISE_TASKS = []
+BLOCKWISE_TASKS: list[BlockwiseTask] = []
 
 
 def register_task(task: BlockwiseTask):
@@ -57,7 +57,7 @@ def get_blockwise_tasks_type():
         TASKS_DISCOVERED = True
     return TypeAdapter(
         Annotated[
-            Union[tuple(BLOCKWISE_TASKS)],
+            Union[tuple[BLOCKWISE_TASKS]],
             Field(discriminator="task_type"),
         ]
     )

volara/blockwise/graph_mws.py

@@ -117,7 +117,9 @@ def process_block_func(self):
             out_rag_provider = self.out_db.open("w")
 
         if self.starting_lut is not None:
-            starting_frags, starting_segs = self.starting_lut.load()
+            starting_lut = self.starting_lut.load()
+            assert starting_lut is not None, "Unable to load starting LUT"
+            starting_frags, starting_segs = starting_lut
             starting_map = {
                 in_frag: out_frag
                 for in_frag, out_frag in zip(starting_frags, starting_segs)

volara/datasets.py

@@ -196,7 +196,7 @@ class Raw(Dataset):
     def bounds(self) -> list[tuple[float, float]] | None:
         if self.ome_norm is not None:
             array = open_ds(self.store, mode="r", **self.zarr_kwargs)
-            metadata_group = zarr.open(self.ome_norm)
+            metadata_group = zarr.open(str(self.ome_norm))
             channels_meta = metadata_group.attrs["omero"]["channels"]
             bounds = [
                 (channels_meta[c]["window"]["min"], channels_meta[c]["window"]["max"])
@@ -339,8 +339,8 @@ def array(self, mode: str = "r") -> Array:
 
         if hasattr(vol, "to_dask") and callable(vol.to_dask):
             return Array(
-                vol.to_dask(),
-                **{k: v for k, v in metadata.items() if v is not None},  # type: ignore[invalid-argument]
+                vol.to_dask(),  # type: ignore
+                **{k: v for k, v in metadata.items() if v is not None},  # type: ignore
             )
         else:
             raise Exception(

volara/dbs.py

@@ -247,7 +247,7 @@ def open(self, mode="r") -> PgSQLGraphDatabase:
             mode=mode,
         )
 
-    def spoof(self):
+    def spoof(self, nodes: bool = True):
         raise NotImplementedError(
             "Spoofing PostgreSQL databases is not implemented yet."
         )

volara/logging.py

@@ -4,7 +4,7 @@
 
 # default log dir
 LOG_BASEDIR = Path("./volara_logs")
-daisy.logging.set_log_basedir(LOG_BASEDIR)  # type: ignore[unresolved-attribute]
+daisy.logging.set_log_basedir(LOG_BASEDIR)
 
 
 def set_log_basedir(path: Path | str):
@@ -24,7 +24,7 @@ def set_log_basedir(path: Path | str):
         raise NotImplementedError("None is not a valid log directory")
         LOG_BASEDIR = None
 
-    daisy.logging.set_log_basedir(LOG_BASEDIR)  # type: ignore[unresolved-attribute]
+    daisy.logging.set_log_basedir(LOG_BASEDIR)
 
 
 def get_log_basedir():

volara/lut.py

@@ -40,9 +40,12 @@ def drop(self):
             self.file.unlink()
 
     def save(self, lut: np.ndarray, edges=None):
-        np.savez_compressed(
-            self.file, fragment_segment_lut=lut.astype(int), edges=edges
-        )
+        if edges is not None:
+            np.savez_compressed(
+                self.file, fragment_segment_lut=lut.astype(int), edges=edges
+            )
+        else:
+            np.savez_compressed(self.file, fragment_segment_lut=lut.astype(int))
 
     def load(self) -> np.ndarray | None:
         if not self.file.exists():
@@ -73,7 +76,7 @@ def __add__(self, other):
     def load(self):
         return np.concatenate(
             [lut.load() for lut in self.luts if lut.load() is not None], axis=1
-        )
+        )  # type: ignore
 
     def load_iterated(self):
         starting_map = self.luts[0].load()