Fix failing tests (#1181)

CHANGELOG.md

@@ -24,7 +24,8 @@ dj.FreeTable(dj.conn(), "common_session.session_group").drop()
 - Import `datajoint.dependencies.unite_master_parts` -> `topo_sort` #1116,
     #1137, #1162
 - Fix bool settings imported from dj config file #1117
-- Allow definition of tasks and new probe entries from config #1074, #1120, #1179
+- Allow definition of tasks and new probe entries from config #1074, #1120,
+    #1179
 - Enforce match between ingested nwb probe geometry and existing table entry
     #1074
 - Update DataJoint install and password instructions #1131
@@ -35,9 +36,11 @@ dj.FreeTable(dj.conn(), "common_session.session_group").drop()
     - Remove mambaforge from tests #1153
     - Remove debug statement #1164
     - Add testing for python versions 3.9, 3.10, 3.11, 3.12 #1169
+    - Initialize tables in pytests #1181
 - Allow python \< 3.13 #1169
 - Remove numpy version restriction #1169
 - Merge table delete removes orphaned master entries #1164
+- Edit `merge_fetch` to expect positional before keyword arguments #1181
 
 ### Pipelines
 

src/spyglass/utils/dj_merge_tables.py

@@ -774,7 +774,7 @@ def merge_restrict_class(
         return parent_class & parent_key
 
     def merge_fetch(
-        self, restriction: str = True, log_export=True, *attrs, **kwargs
+        self, *attrs, restriction: str = True, log_export=True, **kwargs
     ) -> list:
         """Perform a fetch across all parts. If >1 result, return as a list.
 

src/spyglass/utils/mixins/export.py

@@ -7,7 +7,7 @@
 from os import environ
 from re import match as re_match
 
-from datajoint.condition import make_condition
+from datajoint.condition import AndList, make_condition
 from datajoint.table import Table
 from packaging.version import parse as version_parse
 
@@ -320,7 +320,7 @@ def restrict(self, restriction):
         log_export = "fetch_nwb" not in self._called_funcs()
         return self._run_with_log(
             super().restrict,
-            restriction=dj.AndList([restriction, self.restriction]),
+            restriction=AndList([restriction, self.restriction]),
             log_export=log_export,
         )
 

tests/common/conftest.py

@@ -56,4 +56,4 @@ def common_ephys(common):
 @pytest.fixture(scope="session")
 def pop_common_electrode_group(common_ephys):
     common_ephys.ElectrodeGroup.populate()
-    yield common_ephys.ElectrodeGroup
+    yield common_ephys.ElectrodeGroup()

tests/common/test_position.py

@@ -97,7 +97,7 @@ def position_video(common_position):
 
 def test_position_video(position_video, upsample_position):
     _ = position_video.populate()
-    assert len(position_video) == 1, "Failed to populate PositionVideo table."
+    assert len(position_video) == 2, "Failed to populate PositionVideo table."
 
 
 def test_convert_to_pixels():

tests/common/test_usage.py

@@ -127,7 +127,7 @@ def test_export_populate(populate_export):
     table, file = populate_export
 
     assert len(file) == 4, "Export tables not captured correctly"
-    assert len(table) == 35, "Export files not captured correctly"
+    assert len(table) == 37, "Export files not captured correctly"
 
 
 def test_invalid_export_id(export_tbls):

tests/utils/conftest.py

@@ -243,14 +243,16 @@ def graph_tables(dj_conn, graph_schema):
     # Merge inserts after declaring tables
     merge_keys = graph_schema["PkNode"].fetch("KEY", offset=1, as_dict=True)
     graph_schema["MergeOutput"].insert(merge_keys, skip_duplicates=True)
-    merge_child_keys = graph_schema["MergeOutput"].merge_fetch(
-        True, "merge_id", offset=1
+    merge_child_keys = graph_schema["MergeOutput"]().merge_fetch(
+        "merge_id", restriction=True, offset=1
     )
     merge_child_inserts = [
         (i, j, k + 10)
         for i, j, k in zip(merge_child_keys, range(4), range(10, 15))
     ]
-    graph_schema["MergeChild"].insert(merge_child_inserts, skip_duplicates=True)
+    graph_schema["MergeChild"]().insert(
+        merge_child_inserts, skip_duplicates=True
+    )
 
     yield graph_schema