Add PathType

Author: tomwhite

bio2zarr/csi.py

@@ -8,13 +8,13 @@
 
 import numpy as np
 
+from bio2zarr.typing import PathType
 from bio2zarr.utils import (
     get_file_offset,
     open_gzip,
     read_bytes_as_tuple,
     read_bytes_as_value,
 )
-from sgkit.typing import PathType
 
 CSI_EXTENSION = ".csi"
 

bio2zarr/tbi.py

@@ -8,13 +8,13 @@
 
 import numpy as np
 
+from bio2zarr.typing import PathType
 from bio2zarr.utils import (
     get_file_offset,
     open_gzip,
     read_bytes_as_tuple,
     read_bytes_as_value,
 )
-from sgkit.typing import PathType
 
 TABIX_EXTENSION = ".tbi"
 TABIX_LINEAR_INDEX_INTERVAL_SIZE = 1 << 14  # 16kb interval size

bio2zarr/typing.py

@@ -0,0 +1,4 @@
+from pathlib import Path
+from typing import Union
+
+PathType = Union[str, Path]

bio2zarr/vcf_partition.py

@@ -7,8 +7,8 @@
 
 from bio2zarr.csi import CSI_EXTENSION, read_csi
 from bio2zarr.tbi import TABIX_EXTENSION, read_tabix
+from bio2zarr.typing import PathType
 from bio2zarr.utils import ceildiv, get_file_length
-from sgkit.typing import PathType
 
 
 def region_string(contig: str, start: int, end: Optional[int] = None) -> str:

tests/utils.py

@@ -6,7 +6,7 @@
 
 from cyvcf2 import VCF, Variant
 
-from sgkit.typing import PathType
+from bio2zarr.typing import PathType
 
 
 def path_for_test(shared_datadir: Path, file: str, is_path: bool = True) -> PathType: