Improve position coverage (#1315)

* WIP: improve position coverage

* ✅ : improve position coverage

* Fix import

* Revise skipping dlc tests

* WIP: Add import coverage

* WIP: Fix import tests

* more tests

* Fix tests

* Fix test

* Omit position from cov report in gh-action run

* Update changelog

* Fix alternate gh-action coverage report

* Add alt coverage config

* imported_pose insert transaction

* Incorporate feedback

* Imported pose: no nested transaction

* Abort tests if can't insert session

Author: CBroz1

.github/workflows/test-conda.yml

@@ -76,9 +76,13 @@ jobs:
         curl_opts $RAW_DIR $NWBFILE $NWB_URL
         curl_opts $VID_DIR $VID_ONE $VID1URL
         curl_opts $VID_DIR $VID_TWO $VID2URL
+    - name: Move actions coveragerc
+      run: mv tests/.coveragerc .coveragerc
     - name: Run tests
       run: |
-        pytest --no-docker --no-dlc --cov=spyglass-neuro --cov-report=xml tests/
+        pytest --no-docker --no-dlc \
+          --cov-config=.coveragerc --cov=spyglass-neuro --cov-report=xml \
+          tests/
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v5
       with:

CHANGELOG.md

@@ -86,7 +86,7 @@ ImportedLFP().drop()
 - Track Spyglass version in dedicated table for enforcing updates #1281
 - Pin to `datajoint>=0.14.4` for `dj.Top` and long make call fix #1281
 - Remove outdated code comments #1304
-- Add code coverage badge #1305
+- Add code coverage badge, and increase position coverage #1305, #1315
 
 ### Documentation
 

pyproject.toml

@@ -166,16 +166,18 @@ filterwarnings = [
   "ignore::MissingRequiredBuildWarning:.*",
 ]
 
-[tool.coverage.run]
+[tool.coverage.run] # NOTE: changes need to be mirrored in tests/.coveragerc
 source = ["*/src/spyglass/*"]
 omit = [ # which submodules have no tests
     "*/__init__.py",
     "*/_version.py",
+    # "*/behavior/*",
+    "*/cli/*",
     # "*/common/*",
     "*/data_import/*",
     "*/decoding/v0/*",
-    # "*/decoding/*",
     "*/figurl_views/*",
+    # "*/decoding/*",
     # "*/lfp/*",
     # "*/linearization/*",
     "*/lock/*",

src/spyglass/behavior/v1/moseq.py

@@ -403,7 +403,7 @@ def make(self, key):
         self.insert1(key)
 
     def fetch1_dataframe(self):
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
         dataframe = self.fetch_nwb()[0]["moseq"]
         dataframe.set_index("time", inplace=True)
         return dataframe

src/spyglass/common/common_ephys.py

@@ -575,7 +575,7 @@ def nwb_object(self, key):
 
     def fetch1_dataframe(self, *attrs, **kwargs) -> pd.DataFrame:
         """Fetch the LFP data as a pandas DataFrame."""
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
         nwb_lfp = self.fetch_nwb()[0]
         return pd.DataFrame(
             nwb_lfp["lfp"].data,
@@ -952,7 +952,7 @@ def make(self, key):
 
     def fetch1_dataframe(self, *attrs, **kwargs) -> pd.DataFrame:
         """Fetch the LFP band data as a pandas DataFrame."""
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
         filtered_nwb = self.fetch_nwb()[0]
         return pd.DataFrame(
             filtered_nwb["filtered_data"].data,

src/spyglass/common/common_position.py

@@ -489,7 +489,7 @@ def calculate_position_info(
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Fetches the position data as a pandas dataframe."""
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
         return self._data_to_df(self.fetch_nwb()[0])
 
     @staticmethod

src/spyglass/common/common_sensors.py

@@ -105,7 +105,7 @@ def fetch1_dataframe(
         """
         if len(self) == 0:
             return None
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
 
         nwb = self.fetch_nwb()[0]
         columns = nwb["sensor_data"].description.split()

src/spyglass/common/common_subject.py

@@ -57,7 +57,8 @@ def insert_from_nwbfile(cls, nwbf: NWBFile, config: dict = None):
                 "sex",
             ]
         }
-        if (sex := subject_dict["sex"][0].upper()) in ("M", "F"):
+        sex_field = subject_dict.get("sex") or ["U"]  # If not provided
+        if (sex := sex_field[0].upper()) in ("M", "F", "U"):
             subject_dict["sex"] = sex
         else:
             subject_dict["sex"] = "U"

src/spyglass/decoding/v0/clusterless.py

@@ -451,7 +451,7 @@ def plot_all_marks(
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Convenience function for returning the first dataframe"""
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
         return self.fetch_dataframe()[0]
 
     def fetch_dataframe(self) -> list[pd.DataFrame]:

src/spyglass/decoding/v0/sorted_spikes.py

@@ -164,7 +164,7 @@ def make(self, key):
 
     def fetch1_dataframe(self) -> pd.DataFrame:
         """Return the first spike indicator as a dataframe."""
-        self.ensure_single_entry()
+        _ = self.ensure_single_entry()
         return self.fetch_dataframe()[0]
 
     def fetch_dataframe(self) -> list[pd.DataFrame]: