More fixes

bio2zarr/vcf2zarr/vcz.py

@@ -380,13 +380,14 @@ def __init__(self, path):
         if not (path / ".zmetadata").exists():
             raise ValueError("Not in VcfZarr format")  # NEEDS TEST
         self.path = path
-        self.root = zarr.open(path, mode="r")
+        self.root = zarr.open(store=path, mode="r")
 
     def summary_table(self):
         data = []
         arrays = [(core.du(self.path / a.basename), a) for _, a in self.root.arrays()]
         arrays.sort(key=lambda x: x[0])
         for stored, array in reversed(arrays):
+            nbytes = array.size * array.dtype.itemsize
             nchunks = array.metadata.chunk_grid.get_nchunks(array.shape)
             d = {
                 "name": array.name,
@@ -968,7 +969,9 @@ def encode_all_partitions(
         total_bytes = 0
         for array_spec in self.schema.fields:
             # Open the array definition to get the total size
-            total_bytes += zarr.open(self.arrays_path / array_spec.name).nbytes
+            arr = zarr.open(store=self.arrays_path / array_spec.name)
+            nbytes = arr.size * arr.dtype.itemsize
+            total_bytes += nbytes
 
         progress_config = core.ProgressConfig(
             total=total_bytes,

tests/test_vcz.py

@@ -186,7 +186,7 @@ def test_codec(self, tmp_path, icf_path, cname, clevel, shuffle):
         with open(schema_path, "w") as f:
             f.write(schema.asjson())
         vcf2zarr.encode(icf_path, zarr_path, schema_path=schema_path)
-        root = zarr.open(zarr_path)
+        root = zarr.open(store=zarr_path)
         for array_spec in schema.fields:
             a = root[array_spec.name]
             assert a.compressor.cname == cname
@@ -203,7 +203,7 @@ def test_genotype_dtype(self, tmp_path, icf_path, dtype):
         with open(schema_path, "w") as f:
             f.write(schema.asjson())
         vcf2zarr.encode(icf_path, zarr_path, schema_path=schema_path)
-        root = zarr.open(zarr_path)
+        root = zarr.open(store=zarr_path)
         assert root["call_genotype"].dtype == dtype