lint

tests/test_annotation.py

@@ -112,9 +112,7 @@ def test_annotation_limit(self, namespace, limit, admin, n_projects):
     @pytest.mark.parametrize("admin", ["private_test"])
     def test_order_by(self, namespace, admin, order_by, first_name):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            result = agent.annotation.get(
-                namespace=namespace, admin=admin, order_by=order_by
-            )
+            result = agent.annotation.get(namespace=namespace, admin=admin, order_by=order_by)
             assert result.results[0].name == first_name
 
     @pytest.mark.parametrize(
@@ -164,9 +162,7 @@ def test_name_search(self, namespace, query, found_number):
     )
     def test_name_search_private(self, namespace, query, found_number):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            result = agent.annotation.get(
-                namespace=namespace, query=query, admin="private_test"
-            )
+            result = agent.annotation.get(namespace=namespace, query=query, admin="private_test")
             assert len(result.results) == found_number
 
     @pytest.mark.parametrize(
@@ -250,9 +246,7 @@ def test_search_filter_zero_prj(self, namespace, query, found_number):
             ["namespace1", "ame", 2],
         ],
     )
-    def test_search_incorrect_filter_by_string(
-        self, namespace, query, found_number
-    ):
+    def test_search_incorrect_filter_by_string(self, namespace, query, found_number):
         with PEPDBAgentContextManager(add_data=True) as agent:
             date_now = datetime.datetime.now() - datetime.timedelta(days=2)
             date_old = date_now - datetime.timedelta(days=2)
@@ -308,9 +302,7 @@ def test_get_annotation_by_rp_enpty_list(self):
             ["namespace1", "ame", 2],
         ],
     )
-    def test_search_incorrect_incorrect_pep_type(
-        self, namespace, query, found_number
-    ):
+    def test_search_incorrect_incorrect_pep_type(self, namespace, query, found_number):
         with PEPDBAgentContextManager(add_data=True) as agent:
 
             with pytest.raises(ValueError):
@@ -322,9 +314,7 @@ def test_search_incorrect_incorrect_pep_type(
             ["namespace1", "ame", 2],
         ],
     )
-    def test_project_list_without_annotation(
-        self, namespace, query, found_number
-    ):
+    def test_project_list_without_annotation(self, namespace, query, found_number):
         with PEPDBAgentContextManager(add_data=True) as agent:
             result = agent.annotation.get_projects_list(
                 namespace=namespace,

tests/test_namespace.py

@@ -94,14 +94,10 @@ def test_count_project_one(self, namespace, name):
     def test_remove_from_favorite(self, namespace, name):
         with PEPDBAgentContextManager(add_data=True) as agent:
             agent.user.add_project_to_favorites("namespace1", namespace, name, "default")
-            agent.user.add_project_to_favorites(
-                "namespace1", namespace, "amendments2", "default"
-            )
+            agent.user.add_project_to_favorites("namespace1", namespace, "amendments2", "default")
             result = agent.user.get_favorites("namespace1")
             assert result.count == len(result.results) == 2
-            agent.user.remove_project_from_favorites(
-                "namespace1", namespace, name, "default"
-            )
+            agent.user.remove_project_from_favorites("namespace1", namespace, name, "default")
             result = agent.user.get_favorites("namespace1")
             assert result.count == len(result.results) == 1
 
@@ -114,9 +110,7 @@ def test_remove_from_favorite(self, namespace, name):
     def test_remove_from_favorite_error(self, namespace, name):
         with PEPDBAgentContextManager(add_data=True) as agent:
             with pytest.raises(ProjectNotInFavorites):
-                agent.user.remove_project_from_favorites(
-                    "namespace1", namespace, name, "default"
-                )
+                agent.user.remove_project_from_favorites("namespace1", namespace, name, "default")
 
     @pytest.mark.parametrize(
         "namespace, name",
@@ -128,9 +122,7 @@ def test_favorites_duplication_error(self, namespace, name):
         with PEPDBAgentContextManager(add_data=True) as agent:
             agent.user.add_project_to_favorites("namespace1", namespace, name, "default")
             with pytest.raises(ProjectAlreadyInFavorites):
-                agent.user.add_project_to_favorites(
-                    "namespace1", namespace, name, "default"
-                )
+                agent.user.add_project_to_favorites("namespace1", namespace, name, "default")
 
     @pytest.mark.parametrize(
         "namespace, name",

tests/test_project.py

@@ -19,9 +19,7 @@ class TestProject:
     def test_create_project(self):
         with PEPDBAgentContextManager(add_data=False) as agent:
             prj = peppy.Project(list_of_available_peps()["namespace3"]["subtables"])
-            agent.project.create(
-                prj, namespace="test", name="imply", overwrite=True
-            )
+            agent.project.create(prj, namespace="test", name="imply", overwrite=True)
             assert True
 
     def test_create_project_from_dict(self):
@@ -49,9 +47,7 @@ def test_create_project_from_dict(self):
     )
     def test_get_project(self, namespace, name):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            kk = agent.project.get(
-                namespace=namespace, name=name, tag="default", raw=False
-            )
+            kk = agent.project.get(namespace=namespace, name=name, tag="default", raw=False)
             ff = peppy.Project(get_path_to_example_file(namespace, name))
             assert kk == ff
 
@@ -108,7 +104,8 @@ def test_get_samples_raw(self, namespace, name):
             orgiginal_prj = peppy.Project(get_path_to_example_file(namespace, name))
 
             assert (
-                prj_samples == orgiginal_prj.to_dict(extended=True, orient="records")["_sample_dict"]
+                prj_samples
+                == orgiginal_prj.to_dict(extended=True, orient="records")["_sample_dict"]
             )
 
     @pytest.mark.parametrize(
@@ -205,9 +202,7 @@ def test_fork_projects(self, namespace, name):
                 fork_tag="new_tag",
             )
 
-            assert agent.project.exists(
-                namespace="new_namespace", name="new_name", tag="new_tag"
-            )
+            assert agent.project.exists(namespace="new_namespace", name="new_name", tag="new_tag")
             result = agent.annotation.get(
                 namespace="new_namespace", name="new_name", tag="new_tag"
             )
@@ -234,13 +229,9 @@ def test_parent_project_delete(self, namespace, name):
                 fork_tag="new_tag",
             )
 
-            assert agent.project.exists(
-                namespace="new_namespace", name="new_name", tag="new_tag"
-            )
+            assert agent.project.exists(namespace="new_namespace", name="new_name", tag="new_tag")
             agent.project.delete(namespace=namespace, name=name, tag="default")
-            assert agent.project.exists(
-                namespace="new_namespace", name="new_name", tag="new_tag"
-            )
+            assert agent.project.exists(namespace="new_namespace", name="new_name", tag="new_tag")
 
     @pytest.mark.parametrize(
         "namespace, name",
@@ -263,13 +254,9 @@ def test_child_project_delete(self, namespace, name):
                 fork_tag="new_tag",
             )
 
-            assert agent.project.exists(
-                namespace="new_namespace", name="new_name", tag="new_tag"
-            )
+            assert agent.project.exists(namespace="new_namespace", name="new_name", tag="new_tag")
             assert agent.project.exists(namespace=namespace, name=name, tag="default")
-            agent.project.delete(
-                namespace="new_namespace", name="new_name", tag="new_tag"
-            )
+            agent.project.delete(namespace="new_namespace", name="new_name", tag="new_tag")
             assert agent.project.exists(namespace=namespace, name=name, tag="default")
 
     @pytest.mark.parametrize(

tests/test_samples.py

@@ -4,6 +4,7 @@
 
 from .utils import PEPDBAgentContextManager
 
+
 @pytest.mark.skipif(
     not PEPDBAgentContextManager().db_setup(),
     reason="DB is not setup",
@@ -39,9 +40,7 @@ def test_retrieve_raw_sample(self, namespace, name, sample_name):
             ["namespace2", "custom_index", "frog_1"],
         ],
     )
-    def test_retrieve_sample_with_modified_sample_id(
-        self, namespace, name, sample_name
-    ):
+    def test_retrieve_sample_with_modified_sample_id(self, namespace, name, sample_name):
         with PEPDBAgentContextManager(add_data=True) as agent:
             one_sample = agent.sample.get(namespace, name, sample_name, raw=False)
             assert isinstance(one_sample, peppy.Sample)
@@ -141,7 +140,9 @@ def test_project_timestamp_was_changed(self, namespace, name, sample_name):
             )
             annotation2 = agent.annotation.get(namespace, name, "default")
 
-            assert annotation1.results[0].last_update_date != annotation2.results[0].last_update_date
+            assert (
+                annotation1.results[0].last_update_date != annotation2.results[0].last_update_date
+            )
 
     @pytest.mark.parametrize(
         "namespace, name, sample_name",
@@ -201,10 +202,7 @@ def test_add_sample(self, namespace, name, tag, sample_dict):
     )
     def test_overwrite_sample(self, namespace, name, tag, sample_dict):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            assert (
-                agent.project.get(namespace, name, raw=False).get_sample("pig_0h").time
-                == "0"
-            )
+            assert agent.project.get(namespace, name, raw=False).get_sample("pig_0h").time == "0"
             agent.sample.add(namespace, name, tag, sample_dict, overwrite=True)
 
             assert (

tests/test_updates.py

@@ -4,6 +4,7 @@
 
 from .utils import PEPDBAgentContextManager
 
+
 @pytest.mark.skipif(
     not PEPDBAgentContextManager().db_setup(),
     reason="DB is not setup",
@@ -35,9 +36,7 @@ def test_update_project_name(self, namespace, name, new_name):
     )
     def test_update_project_name_in_config(self, namespace, name, new_name):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            prj = agent.project.get(
-                namespace=namespace, name=name, raw=False, with_id=True
-            )
+            prj = agent.project.get(namespace=namespace, name=name, raw=False, with_id=True)
             prj.name = new_name
             agent.project.update(
                 namespace=namespace,
@@ -71,9 +70,7 @@ def test_update_project_tag(self, namespace, name, new_tag):
             ["namespace2", "derive", "desc5 f"],
         ],
     )
-    def test_update_project_description(
-        self, namespace, name, new_description
-    ):
+    def test_update_project_description(self, namespace, name, new_description):
         with PEPDBAgentContextManager(add_data=True) as agent:
             prj = agent.project.get(namespace=namespace, name=name, raw=False)
             prj.description = new_description
@@ -95,13 +92,9 @@ def test_update_project_description(
             ["namespace1", "amendments1", "desc1 f"],
         ],
     )
-    def test_update_project_description_in_config(
-        self, namespace, name, new_description
-    ):
+    def test_update_project_description_in_config(self, namespace, name, new_description):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            prj = agent.project.get(
-                namespace=namespace, name=name, raw=False, with_id=True
-            )
+            prj = agent.project.get(namespace=namespace, name=name, raw=False, with_id=True)
             prj.description = new_description
             agent.project.update(
                 namespace=namespace,
@@ -230,13 +223,15 @@ def test_project_can_have_2_sample_names(self, namespace, name):
         ensure that update works correctly
         """
         with PEPDBAgentContextManager(add_data=True) as agent:
-            new_prj = agent.project.get(
-                namespace=namespace, name=name, raw=False, with_id=True
-            )
+            new_prj = agent.project.get(namespace=namespace, name=name, raw=False, with_id=True)
             prj_dict = new_prj.to_dict(extended=True, orient="records")
 
             prj_dict["_sample_dict"].append(
-                {"file": "data/frog23_data.txt", "protocol": "anySample3Type", "sample_name": "frog_2"}
+                {
+                    "file": "data/frog23_data.txt",
+                    "protocol": "anySample3Type",
+                    "sample_name": "frog_2",
+                }
             )
             prj_dict["_sample_dict"].append(
                 {
@@ -282,13 +277,9 @@ def test_update_whole_project_with_id(self, namespace, name):
             ["namespace1", "amendments1"],
         ],
     )
-    def test_update_project_with_duplicated_sample_guids(
-        self, namespace, name
-    ):
+    def test_update_project_with_duplicated_sample_guids(self, namespace, name):
         with PEPDBAgentContextManager(add_data=True) as agent:
-            new_prj = agent.project.get(
-                namespace=namespace, name=name, raw=True, with_id=True
-            )
+            new_prj = agent.project.get(namespace=namespace, name=name, raw=True, with_id=True)
             new_prj["_sample_dict"].append(new_prj["_sample_dict"][0])
 
             with pytest.raises(ProjectDuplicatedSampleGUIDsError):