Fix new mypy errors

Author: tomwhite

.pre-commit-config.yaml

@@ -26,4 +26,4 @@ repos:
     hooks:
       - id: mypy
         args: ["--strict", "--show-error-codes"]
-        additional_dependencies: ["numpy>=1.21.2", "xarray>=0.17.0", "dask[array]", "scipy", "typing-extensions", "zarr", "numba", "dask-ml", "networkx"]
+        additional_dependencies: ["numpy>=1.21.2", "xarray", "dask[array]", "scipy", "typing-extensions", "zarr", "numba", "dask-ml", "networkx"]

sgkit/display.py

@@ -108,17 +108,19 @@ def truncate(ds: xr.Dataset, max_sizes: Mapping[Hashable, int]) -> xr.Dataset:
 
     limits = {dims[0]: m_dim[0], dims[1]: m_dim[1]}
     slices = {k: slice(v) for k, v in limits.items()}
-    ds_abbr: xr.Dataset = xr.combine_nested(  # type: ignore[no-untyped-call]
+    ds_abbr: xr.Dataset = xr.combine_nested(
         [
             [
                 # Roll all of these simultaneously along with any indexes/coords
                 # and then clip them using the same slice for each corner
-                ds.roll(dict(zip(limits, roll)), roll_coords=True).isel(**slices)
+                ds.roll(dict(zip(limits, roll)), roll_coords=True).isel(  # type: ignore[misc]
+                    **slices  # type: ignore[arg-type]
+                )
                 for roll in row
             ]
             for row in rows
         ],
-        concat_dim=limits.keys(),
+        concat_dim=limits.keys(),  # type: ignore[arg-type]
     )
 
     assert ds_abbr.sizes[dims[0]] <= max_dim[0] + 2

sgkit/tests/test_association.py

@@ -111,7 +111,7 @@ def _generate_test_dataset(**kwargs: Any) -> Dataset:
         # relationship with trait j where i != j
         data_vars[f"trait_{i}"] = (["samples"], ys[i])
     attrs = dict(beta=bg, n_trait=ys.shape[0], n_covar=x.shape[1])
-    return xr.Dataset(data_vars, attrs=attrs)  # type: ignore[arg-type]
+    return xr.Dataset(data_vars, attrs=attrs)
 
 
 def _generate_regenie_test_dataset(**kwargs: Any) -> Dataset:
@@ -135,7 +135,7 @@ def _generate_regenie_test_dataset(**kwargs: Any) -> Dataset:
     )
 
     attrs = dict(beta=bg, n_trait=ys.shape[0], n_covar=x.shape[1])
-    return xr.Dataset(data_vars, attrs=attrs)  # type: ignore[arg-type]
+    return xr.Dataset(data_vars, attrs=attrs)
 
 
 @pytest.fixture(scope="module")