isort+black

allensdk/brain_observatory/behavior/behavior_session.py

@@ -285,7 +285,7 @@ def from_json(
                     path=session_data["stim_table_file"],
                     behavior_session_id=session_data["behavior_session_id"],
                     exclude_columns=stimulus_presentation_exclude_columns,
-                    trials=trials
+                    trials=trials,
                 ),
                 templates=Templates.from_stimulus_file(
                     stimulus_file=stimulus_file_lookup.behavior_stimulus_file
@@ -358,7 +358,7 @@ def from_lims(
         date_of_acquisition: Optional[DateOfAcquisition] = None,
         eye_tracking_z_threshold: float = 3.0,
         eye_tracking_dilation_frames: int = 2,
-        load_stimulus_movie: bool = True
+        load_stimulus_movie: bool = True,
     ) -> "BehaviorSession":
         """
 
@@ -454,7 +454,7 @@ def from_lims(
             project_code=ProjectCode.from_lims(
                 behavior_session_id=behavior_session_id.value, lims_db=lims_db
             ),
-            load_stimulus_movie=load_stimulus_movie
+            load_stimulus_movie=load_stimulus_movie,
         )
 
         if date_of_acquisition is None:
@@ -1115,8 +1115,10 @@ def stimulus_presentations(self) -> pd.DataFrame:
         table = table.drop(columns=["image_set", "index"], errors="ignore")
         table = table.rename(columns={"stop_time": "end_time"})
 
-        if "trials_id" not in table.columns \
-                and 'stimulus_block' in table.columns:
+        if (
+            "trials_id" not in table.columns
+            and "stimulus_block" in table.columns
+        ):
             table["trials_id"] = compute_trials_id_for_stimulus(
                 table, self.trials
             )
@@ -1173,9 +1175,7 @@ def stimulus_natural_movie_template(self) -> Optional[pd.DataFrame]:
         if self._stimuli.templates.fingerprint_movie_template_key is not None:
             return self._stimuli.templates.value[
                 self._stimuli.templates.fingerprint_movie_template_key
-            ].to_dataframe(
-                index_name='frame_number',
-                index_type='int')
+            ].to_dataframe(index_name="frame_number", index_type="int")
         else:
             return None
 
@@ -1413,7 +1413,7 @@ def _read_stimuli(
         trials: Trials,
         stimulus_presentation_columns: Optional[List[str]] = None,
         project_code: Optional[ProjectCode] = None,
-        load_stimulus_movie: bool = False
+        load_stimulus_movie: bool = False,
     ) -> Stimuli:
         """
         Construct the Stimuli data object for this session
@@ -1432,7 +1432,7 @@ def _read_stimuli(
             presentation_columns=stimulus_presentation_columns,
             project_code=project_code,
             trials=trials,
-            load_stimulus_movie=load_stimulus_movie
+            load_stimulus_movie=load_stimulus_movie,
         )
 
     @classmethod
@@ -1512,7 +1512,7 @@ def _read_data_from_stimulus_file(
         include_stimuli: bool = True,
         stimulus_presentation_columns: Optional[List[str]] = None,
         project_code: Optional[ProjectCode] = None,
-        load_stimulus_movie: bool = False
+        load_stimulus_movie: bool = False,
     ):
         """Helper method to read data from stimulus file"""
 
@@ -1549,7 +1549,7 @@ def _read_data_from_stimulus_file(
                 trials=trials,
                 stimulus_presentation_columns=stimulus_presentation_columns,
                 project_code=project_code,
-                load_stimulus_movie=load_stimulus_movie
+                load_stimulus_movie=load_stimulus_movie,
             )
         else:
             stimuli = None

allensdk/brain_observatory/behavior/data_objects/stimuli/presentations.py

@@ -60,7 +60,7 @@ def __init__(
         columns_to_rename: Optional[Dict[str, str]] = None,
         column_list: Optional[List[str]] = None,
         sort_columns: bool = True,
-        trials: Optional[Trials] = None
+        trials: Optional[Trials] = None,
     ):
         """
 
@@ -102,13 +102,11 @@ def __init__(
             if "active" not in presentations.columns:
                 # Add column marking where the mouse is engaged in active,
                 # trained behavior.
-                presentations = add_active_flag(
-                    presentations, trials.data
-                )
+                presentations = add_active_flag(presentations, trials.data)
             if "trials_id" not in presentations.columns:
                 # Add trials_id to presentations df to allow for joining of the
                 # two tables.
-                presentations['trials_id'] = compute_trials_id_for_stimulus(
+                presentations["trials_id"] = compute_trials_id_for_stimulus(
                     presentations, trials.data
                 )
             if "is_sham_change" not in presentations.columns:
@@ -271,9 +269,9 @@ def from_nwb(
         if add_trials_dependent_values and nwbfile.trials is not None:
             trials = Trials.from_nwb(nwbfile)
 
-        return Presentations(presentations=table,
-                             column_list=column_list,
-                             trials=trials)
+        return Presentations(
+            presentations=table, column_list=column_list, trials=trials
+        )
 
     @classmethod
     def from_stimulus_file(
@@ -324,7 +322,8 @@ def from_stimulus_file(
         )
         raw_stim_pres_df = raw_stim_pres_df.drop(columns=["index"])
         raw_stim_pres_df = cls._check_for_errant_omitted_stimulus(
-            input_df=raw_stim_pres_df)
+            input_df=raw_stim_pres_df
+        )
 
         # Fill in nulls for image_name
         # This makes two assumptions:
@@ -428,9 +427,7 @@ def from_stimulus_file(
             )
 
         return Presentations(
-            presentations=stim_pres_df,
-            column_list=column_list,
-            trials=trials
+            presentations=stim_pres_df, column_list=column_list, trials=trials
         )
 
     @classmethod
@@ -441,7 +438,7 @@ def from_path(
         exclude_columns: Optional[List[str]] = None,
         columns_to_rename: Optional[Dict[str, str]] = None,
         sort_columns: bool = True,
-        trials: Optional[Trials] = None
+        trials: Optional[Trials] = None,
     ) -> "Presentations":
         """
         Reads the table directly from a precomputed csv
@@ -578,7 +575,7 @@ def _postprocess(
 
     @staticmethod
     def _check_for_errant_omitted_stimulus(
-        input_df: pd.DataFrame
+        input_df: pd.DataFrame,
     ) -> pd.DataFrame:
         """Check if the first entry in the DataFrame is an omitted stimulus.