Fix bio2zarr import

Author: tomwhite

tests/test_stats.py

@@ -3,7 +3,7 @@
 
 import pytest
 import zarr
-from bio2zarr import vcf2zarr
+from bio2zarr import icf
 
 from vcztools.stats import nrecords, stats
 
@@ -39,7 +39,7 @@ def test_stats__no_index(tmp_path):
     original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz"
     # don't use cache here since we want to make sure vcz is not indexed
     vcz = tmp_path.joinpath("intermediate.vcz")
-    vcf2zarr.convert([original], vcz, worker_processes=0, local_alleles=False)
+    icf.convert([original], vcz, worker_processes=0, local_alleles=False)
 
     # delete the index created by vcf2zarr
     root = zarr.open(vcz, mode="a")

tests/test_vcf_writer.py

@@ -6,7 +6,7 @@
 import numpy as np
 import pytest
 import zarr
-from bio2zarr import vcf2zarr
+from bio2zarr import icf
 from cyvcf2 import VCF
 from numpy.testing import assert_array_equal
 
@@ -307,7 +307,7 @@ def test_write_vcf__generate_header(tmp_path):
     original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz"
     # don't use cache here since we mutate the vcz
     vcz = tmp_path.joinpath("intermediate.vcz")
-    vcf2zarr.convert([original], vcz, worker_processes=0, local_alleles=False)
+    icf.convert([original], vcz, worker_processes=0, local_alleles=False)
 
     # remove vcf_header
     root = zarr.open(vcz, mode="r+")

tests/utils.py

@@ -5,7 +5,7 @@
 
 import cyvcf2
 import numpy as np
-from bio2zarr import vcf2zarr
+from bio2zarr import icf
 
 
 @contextmanager
@@ -139,15 +139,15 @@ def vcz_path_cache(vcf_path):
     cached_vcz_path = (cache_path / vcf_path.name).with_suffix(".vcz")
     if not cached_vcz_path.exists():
         if vcf_path.name.startswith("chr22"):
-            vcf2zarr.convert(
+            icf.convert(
                 [vcf_path],
                 cached_vcz_path,
                 worker_processes=0,
                 variants_chunk_size=10,
                 samples_chunk_size=10,
             )
         else:
-            vcf2zarr.convert(
+            icf.convert(
                 [vcf_path], cached_vcz_path, worker_processes=0, local_alleles=False
             )
     return cached_vcz_path