Fix up tests

Author: benjeffery

bio2zarr/vcf.py

@@ -281,7 +281,7 @@ def scan_vcfs(paths, show_progress, target_num_partitions, worker_processes=1):
     )
     with core.ParallelWorkManager(worker_processes, progress_config) as pwm:
         for path in paths:
-            pwm.submit(scan_vcf, path, target_num_partitions//len(paths))
+            pwm.submit(scan_vcf, path, max(1, target_num_partitions//len(paths)))
         results = list(pwm.results_as_completed())
 
     # Sort to make the ordering deterministic
@@ -1068,7 +1068,7 @@ def convert_finalise(self):
 
         for field in self.metadata.fields:
             # Clear the summary to avoid problems when running in debug
-            # syncronous mode
+            # synchronous mode
             field.summary = VcfFieldSummary()
             for summary in partition_summaries:
                 field.summary.update(summary["field_summaries"][field.full_name])

tests/test_vcf_examples.py

@@ -791,14 +791,25 @@ def test_split_explode(tmp_path):
         "tests/data/vcf/sample.vcf.gz.3.split/X.vcf.gz",
     ]
     out = tmp_path / "test.explode"
-    pcvcf = vcf.explode_init(paths, out, num_partitions=15)
-    with open(out / "num_partitions.txt", "r") as f:
-        num_partitions = int(f.read())
-    assert pcvcf.num_partitions == num_partitions
-    assert num_partitions == 3
-    vcf.explode_slice(out, 0, num_partitions)
-    vcf.explode_finalise(out)
+    pcvcf = vcf.explode_init(paths, out, target_num_partitions=15)
+    assert pcvcf.num_partitions == 3
+    assert vcf.explode_partition_count(out) == 3
 
-    vcf.encode(out, tmp_path / "test.zarr")
+    with pytest.raises(ValueError):
+        vcf.explode_slice(out, -1, 3)
+    with pytest.raises(ValueError):
+        vcf.explode_slice(out, 0, 42)
 
+    vcf.explode_slice(out, 0, 3)
+    vcf.explode_finalise(out)
+    pcvcf = vcf.PickleChunkedVcf.load(out)
+    assert pcvcf.columns['POS'].vcf_field.summary.asdict() == {
+        'num_chunks': 3,
+        'compressed_size': 587,
+        'uncompressed_size': 1008,
+        'max_number': 1,
+        'max_value': 1235237,
+        'min_value': 10
+    }
+    vcf.encode(out, tmp_path / "test.zarr")
     vcf.validate("tests/data/vcf/sample.vcf.gz", tmp_path / "test.zarr")