Remove typing-extensions dependency and just use standard library

Author: tomwhite

pyproject.toml

@@ -28,7 +28,6 @@ dependencies = [
   "scipy < 1.16",
   "zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3",
   "numba",
-  "typing-extensions",
   "fsspec != 2021.6.*",
   "scikit-learn",
   "pandas",
@@ -97,7 +96,6 @@ known_third_party = [
   "sgkit_plink",
   "sklearn",
   "sphinx",
-  "typing_extensions",
   "xarray",
   "yaml",
   "zarr",

requirements-numpy1.txt

@@ -2,7 +2,6 @@ numpy < 2
 xarray < 2025.03.1
 dask[array,dataframe] >= 2023.01.0, <= 2024.8.0
 scipy < 1.16
-typing-extensions
 numba
 zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3
 fsspec != 2021.6.*

requirements.txt

@@ -2,7 +2,6 @@ numpy < 2.2
 xarray < 2025.03.1
 dask[array,dataframe] >= 2023.01.0, <= 2024.8.0
 scipy < 1.16
-typing-extensions
 numba
 zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3
 fsspec != 2021.6.*

sgkit/distance/api.py

@@ -1,8 +1,8 @@
 import typing
+from typing import Literal
 
 import dask.array as da
 import numpy as np
-from typing_extensions import Literal
 
 from sgkit.typing import ArrayLike
 

sgkit/stats/aggregation.py

@@ -1,8 +1,7 @@
-from typing import Hashable
+from typing import Hashable, Literal
 
 import numpy as np
 import xarray as xr
-from typing_extensions import Literal
 from xarray import Dataset
 
 import sgkit.distarray as da

sgkit/stats/genedrop.py

@@ -1,9 +1,8 @@
-from typing import Hashable, Optional
+from typing import Hashable, Literal, Optional
 
 import dask.array as da
 import numpy as np
 import xarray as xr
-from typing_extensions import Literal
 from xarray import Dataset
 
 from sgkit import variables

sgkit/stats/grm.py

@@ -1,8 +1,7 @@
-from typing import Hashable, Optional, Tuple
+from typing import Hashable, Literal, Optional, Tuple
 
 import dask.array as da
 import numpy as np
-from typing_extensions import Literal
 from xarray import Dataset
 
 from sgkit import variables

sgkit/stats/ibs.py

@@ -1,7 +1,6 @@
-from typing import Hashable
+from typing import Hashable, Literal
 
 import dask.array as da
-from typing_extensions import Literal
 from xarray import Dataset
 
 from sgkit import variables

sgkit/stats/pca.py

@@ -1,10 +1,9 @@
-from typing import Any, Optional, Union
+from typing import Any, Literal, Optional, Union
 
 import numpy as np
 import xarray as xr
 from sklearn.base import BaseEstimator
 from sklearn.pipeline import Pipeline
-from typing_extensions import Literal
 from xarray import DataArray, Dataset
 
 import sgkit.distarray as da

sgkit/stats/pedigree.py

@@ -1,10 +1,9 @@
 import warnings
-from typing import Hashable, Tuple
+from typing import Hashable, Literal, Optional, Tuple
 
 import dask.array as da
 import numpy as np
 import xarray as xr
-from typing_extensions import Literal, Optional
 from xarray import Dataset
 
 from sgkit import variables