test_csi passing

Author: tomwhite

bio2zarr/csi.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from sgkit.io.vcf.utils import (
+from bio2zarr.utils import (
     get_file_offset,
     open_gzip,
     read_bytes_as_tuple,

bio2zarr/tbi.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from sgkit.io.vcf.utils import (
+from bio2zarr.utils import (
     get_file_offset,
     open_gzip,
     read_bytes_as_tuple,

bio2zarr/utils.py

@@ -8,7 +8,6 @@
 
 import fsspec
 from numcodecs import Delta, PackBits
-from yarl import URL
 
 from sgkit.typing import PathType
 

bio2zarr/vcf_partition.py

@@ -5,9 +5,9 @@
 import numpy as np
 from cyvcf2 import VCF
 
-from sgkit.io.vcf.csi import CSI_EXTENSION, read_csi
-from sgkit.io.vcf.tbi import TABIX_EXTENSION, read_tabix
-from sgkit.io.vcf.utils import ceildiv, get_file_length
+from bio2zarr.csi import CSI_EXTENSION, read_csi
+from bio2zarr.tbi import TABIX_EXTENSION, read_tabix
+from bio2zarr.utils import ceildiv, get_file_length
 from sgkit.typing import PathType
 
 

tests/__init__.py

@@ -1,11 +1,10 @@
 import pytest
 from cyvcf2 import VCF
 
-from sgkit.io.vcf.csi import read_csi
-from sgkit.io.vcf.vcf_partition import get_csi_path
-from sgkit.io.vcf.vcf_reader import count_variants
+from bio2zarr.csi import read_csi
+from bio2zarr.vcf_partition import get_csi_path
 
-from .utils import path_for_test
+from .utils import count_variants, path_for_test
 
 
 @pytest.mark.parametrize(