pre-commit passing

Author: ACEnglish

bio2zarr/vcf2zarr/icf.py

@@ -196,11 +196,11 @@ def __eq__(self, other):
         if not isinstance(other, IcfMetadata):
             return NotImplemented
         return (
-                self.samples == other.samples and 
-                self.contigs == other.contigs and
-                self.filters == other.filters and
-                sorted(self.fields) == sorted(other.fields)
-               )
+            self.samples == other.samples
+            and self.contigs == other.contigs
+            and self.filters == other.filters
+            and sorted(self.fields) == sorted(other.fields)
+        )
 
 
 def fixed_vcf_field_definitions():

tests/test_vcf_examples.py

@@ -1101,14 +1101,16 @@ def test_missing_filter(tmp_path):
     with pytest.raises(ValueError, match="Filter 'q10' was not defined in the header"):
         vcf2zarr.convert([path], zarr_path)
 
+
 class TestOutOfOrderFields:
-    data_paths = ["tests/data/vcf/out_of_order_fields/input1.bcf",
-                  "tests/data/vcf/out_of_order_fields/input2.bcf"]
+    # Mixing on purpose
+    data_path1 = "tests/data/vcf/out_of_order_fields/input2.bcf"
+    data_path2 = "tests/data/vcf/out_of_order_fields/input1.bcf"
 
     @pytest.fixture(scope="class")
     def ds(self, tmp_path_factory):
         out = tmp_path_factory.mktemp("data") / "ooo_example.vcf.zarr"
-        vcf2zarr.convert(self.data_paths, out)
+        vcf2zarr.convert([self.data_path1, self.data_path2], out)
         return sg.load_dataset(out)
 
     def test_filters(self, ds):
@@ -1127,7 +1129,7 @@ def test_source(self, ds):
 
     def test_contigs(self, ds):
         nt.assert_array_equal(ds["contig_id"], ["chr20", "chr21"])
-        nt.assert_array_equal(ds['contig_length'], [64444167., 46709983.])
+        nt.assert_array_equal(ds["contig_length"], [64444167.0, 46709983.0])
         nt.assert_array_equal(ds["variant_contig"], [0, 1, 1])
 
     def test_position(self, ds):
@@ -1139,19 +1141,14 @@ def test_length(self, ds):
     def test_info_fields(self, ds):
         nt.assert_array_equal(
             ds["variant_QNAME"],
-            ['cluster19_000000F', '.', 'cluster19_000000F'],
+            ["cluster19_000000F", ".", "cluster19_000000F"],
         )
         nt.assert_array_equal(ds["variant_QSTART"], [25698928, 25698928, -1])
 
     def test_allele(self, ds):
-        fill = constants.STR_FILL
         nt.assert_array_equal(
             ds["variant_allele"].values.tolist(),
-            [
-                ['TTCCATTCCAC', 'T'],
-                ['C', 'CTCCAT'],
-                ['G', 'A']
-            ]
+            [["TTCCATTCCAC", "T"], ["C", "CTCCAT"], ["G", "A"]],
         )
         assert ds["variant_allele"].dtype == "O"