lint with black

tests/test_graphkb/test_graphkb.py

@@ -18,6 +18,7 @@ def conn():
     conn.login(os.environ["GRAPHKB_USER"], os.environ["GRAPHKB_PASS"])
     return conn
 
+
 class TestPaginate:
     @mock.patch("pori_python.graphkb.GraphKBConnection.request")
     def test_does_not_paginate_when_false(self, graphkb_request, conn):

tests/test_graphkb/test_match.py

@@ -7,7 +7,10 @@
 
 import pori_python.graphkb
 from pori_python.graphkb import GraphKBConnection, match
-from pori_python.graphkb.constants import DEFAULT_NON_STRUCTURAL_VARIANT_TYPE, STRUCTURAL_VARIANT_SIZE_THRESHOLD
+from pori_python.graphkb.constants import (
+    DEFAULT_NON_STRUCTURAL_VARIANT_TYPE,
+    STRUCTURAL_VARIANT_SIZE_THRESHOLD,
+)
 from pori_python.graphkb.util import FeatureNotFoundError
 
 # Test datasets
@@ -500,6 +503,7 @@ def test_filling_cache(self):
         assert "alice" in match.FEATURES_CACHE
         match.FEATURES_CACHE = None
 
+
 class TestTypeScreening:
     # Types as class variables
     default_type = DEFAULT_NON_STRUCTURAL_VARIANT_TYPE

tests/test_ipr/test_annotate.py

@@ -47,6 +47,7 @@ def graphkb_conn():
     graphkb_conn.login(username, password)
     return graphkb_conn
 
+
 class TestAnnotation:
     def test_annotate_nonsense_vs_missense(self, graphkb_conn):
         """Verify missense (point mutation) is not mistaken for a nonsense (stop codon) mutation."""
@@ -58,7 +59,6 @@ def test_annotate_nonsense_vs_missense(self, graphkb_conn):
             assert not nonsense, f"nonsense matched to {key}: {TP53_MUT_DICT[key]}"
             assert matched, f"should have matched in {key}: {TP53_MUT_DICT[key]}"
 
-
     def test_annotate_nonsense_vs_missense_protein(self, graphkb_conn):
         """Verify missense (point mutation) is not mistaken for a nonsense (stop codon) mutation."""
         disease = 'cancer'
@@ -69,7 +69,6 @@ def test_annotate_nonsense_vs_missense_protein(self, graphkb_conn):
             assert not nonsense, f"nonsense matched to {key}: {TP53_MUT_DICT[key]}"
             assert matched, f"should have matched in {key}: {TP53_MUT_DICT[key]}"
 
-
     def test_annotate_structural_variants_tp53(self, graphkb_conn):
         """Verify alternate TP53 variants match."""
         disease = 'cancer'

tests/test_ipr/test_summary.py

@@ -1,6 +1,10 @@
 from unittest.mock import MagicMock
 
-from pori_python.ipr.summary import GRAPHKB_GUI, get_preferred_drug_representation, substitute_sentence_template
+from pori_python.ipr.summary import (
+    GRAPHKB_GUI,
+    get_preferred_drug_representation,
+    substitute_sentence_template,
+)
 
 
 class TestGetPreferredDrugRepresentation: