STYLE: Format with black (#237)

aehrc · Sep 19, 2024 · d671f35 · d671f35
1 parent 8f11e62
commit d671f35
Showing 1 changed file with 30 additions and 16 deletions.
diff --git a/python/varspark/test/test_core.py b/python/varspark/test/test_core.py
@@ -16,10 +16,15 @@ class VariantSparkPySparkTestCase(unittest.TestCase):
 
     @classmethod
     def setUpClass(self):
-        sconf = SparkConf(loadDefaults=False) \
-            .set("spark.driver.extraClassPath", find_variants_jar())
-        spark = SparkSession.builder.config(conf=sconf) \
-            .appName("test").master("local").getOrCreate()
+        sconf = SparkConf(loadDefaults=False).set(
+            "spark.driver.extraClassPath", find_variants_jar()
+        )
+        spark = (
+            SparkSession.builder.config(conf=sconf)
+            .appName("test")
+            .master("local")
+            .getOrCreate()
+        )
         self.sc = spark.sparkContext
 
     @classmethod
@@ -37,28 +42,37 @@ def setUp(self):
     def test_variants_context_parameter_type(self):
         with self.assertRaises(TypeError) as cm:
             self.vc.load_label(label_file_path=123, col_name=456)
-        self.assertEqual('keyword argument label_file_path = 123 doesn\'t match signature str',
-                         str(cm.exception))
+        self.assertEqual(
+            "keyword argument label_file_path = 123 doesn't match signature str",
+            str(cm.exception),
+        )
 
     def test_rfmodel(self):
-        label_data_path = os.path.join(PROJECT_DIR, 'data/chr22-labels.csv')
-        label = self.vc.load_label(label_file_path=label_data_path, col_name='22_16050678')
-        feature_data_path = os.path.join(PROJECT_DIR, 'data/chr22_1000.vcf')
+        label_data_path = os.path.join(PROJECT_DIR, "data/chr22-labels.csv")
+        label = self.vc.load_label(
+            label_file_path=label_data_path, col_name="22_16050678"
+        )
+        feature_data_path = os.path.join(PROJECT_DIR, "data/chr22_1000.vcf")
         features = self.vc.import_vcf(vcf_file_path=feature_data_path)
-        rf = RFModelContext(self.spark, mtry_fraction=None, oob=True, seed=17, var_ordinal_levels=3)
+        rf = RFModelContext(
+            self.spark, mtry_fraction=None, oob=True, seed=17, var_ordinal_levels=3
+        )
         rf.fit_trees(features, label, n_trees=200, batch_size=50)
         imp_analysis = rf.importance_analysis()
         imp_vars = imp_analysis.important_variables(20)
-        most_imp_var = imp_vars['variable'][0]
-        self.assertEqual('22_16050678_C_T', most_imp_var)
+        most_imp_var = imp_vars["variable"][0]
+        self.assertEqual("22_16050678_C_T", most_imp_var)
         df = imp_analysis.variable_importance(normalized=True)
-        self.assertEqual('22_16050678_C_T',
-                         str(df.sort_values(by='importance', ascending=False)['variant_id'].iloc[0]))
+        self.assertEqual(
+            "22_16050678_C_T",
+            str(df.sort_values(by="importance", ascending=False)["variant_id"].iloc[0]),
+        )
         oob_error = rf.oob_error()
         self.assertEqual(0.004578754578754579, oob_error)
         fdrCalc = rf.get_lfdr()
-        _, fdr = fdrCalc.compute_fdr(countThreshold = 2, local_fdr_cutoff = 0.05)
+        _, fdr = fdrCalc.compute_fdr(countThreshold=2, local_fdr_cutoff=0.05)
         self.assertEqual(0.0002976892628282768, fdr)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     unittest.main(verbosity=2)