Blackify 24.1.1

.pre-commit-config.yaml

@@ -77,7 +77,7 @@ repos:
           - tomli
 
   - repo: https://github.com/ambv/black
-    rev: 23.11.0
+    rev: 24.1.1
     hooks:
       - id: black
         language_version: python3.9

config/dj_config.py

@@ -15,9 +15,7 @@ def main(*args):
     save_method = (
         "local"
         if filename == "dj_local_conf.json"
-        else "global"
-        if filename is None
-        else "custom"
+        else "global" if filename is None else "custom"
     )
 
     config.save_dj_config(

src/spyglass/common/common_behav.py

@@ -191,10 +191,12 @@ def _get_column_names(rp, pos_id):
             INDEX_ADJUST = 1  # adjust 0-index to 1-index (e.g., xloc0 -> xloc1)
             n_pos_dims = rp.data.shape[1]
             column_names = [
-                col  # use existing columns if already numbered
-                if "1" in rp.description or "2" in rp.description
-                # else number them by id
-                else col + str(pos_id + INDEX_ADJUST)
+                (
+                    col  # use existing columns if already numbered
+                    if "1" in rp.description or "2" in rp.description
+                    # else number them by id
+                    else col + str(pos_id + INDEX_ADJUST)
+                )
                 for col in rp.description.split(", ")
             ]
             if len(column_names) != n_pos_dims:

src/spyglass/common/common_device.py

@@ -476,9 +476,9 @@ def __read_ndx_probe_data(
             {
                 "probe_id": nwb_probe_obj.probe_type,
                 "probe_type": nwb_probe_obj.probe_type,
-                "contact_side_numbering": "True"
-                if nwb_probe_obj.contact_side_numbering
-                else "False",
+                "contact_side_numbering": (
+                    "True" if nwb_probe_obj.contact_side_numbering else "False"
+                ),
             }
         )
         # go through the shanks and add each one to the Shank table

src/spyglass/common/common_filter.py

@@ -500,9 +500,9 @@ def filter_data(
         for ii, (start, stop) in enumerate(indices):
             extracted_ts = timestamps[start:stop:decimation]
 
-            new_timestamps[
-                ts_offset : ts_offset + len(extracted_ts)
-            ] = extracted_ts
+            new_timestamps[ts_offset : ts_offset + len(extracted_ts)] = (
+                extracted_ts
+            )
             ts_offset += len(extracted_ts)
 
             # finally ready to filter data!

src/spyglass/common/common_interval.py

@@ -56,9 +56,11 @@ def insert_from_nwbfile(cls, nwbf, *, nwb_file_name):
         for _, epoch_data in epochs.iterrows():
             epoch_dict = {
                 "nwb_file_name": nwb_file_name,
-                "interval_list_name": epoch_data.tags[0]
-                if epoch_data.tags
-                else f"interval_{epoch_data[0]}",
+                "interval_list_name": (
+                    epoch_data.tags[0]
+                    if epoch_data.tags
+                    else f"interval_{epoch_data[0]}"
+                ),
                 "valid_times": np.asarray(
                     [[epoch_data.start_time, epoch_data.stop_time]]
                 ),

src/spyglass/common/common_lab.py

@@ -1,4 +1,5 @@
 """Schema for institution, lab team/name/members. Session-independent."""
+
 import datajoint as dj
 
 from spyglass.utils import SpyglassMixin, logger

src/spyglass/decoding/v0/clusterless.py

@@ -6,6 +6,7 @@
 [1] Denovellis, E. L. et al. Hippocampal replay of experience at real-world
 speeds. eLife 10, e64505 (2021).
 """
+
 import os
 import shutil
 import uuid
@@ -654,11 +655,11 @@ def make(self, key):
             key["nwb_file_name"]
         )
 
-        key[
-            "multiunit_firing_rate_object_id"
-        ] = nwb_analysis_file.add_nwb_object(
-            analysis_file_name=key["analysis_file_name"],
-            nwb_object=multiunit_firing_rate.reset_index(),
+        key["multiunit_firing_rate_object_id"] = (
+            nwb_analysis_file.add_nwb_object(
+                analysis_file_name=key["analysis_file_name"],
+                nwb_object=multiunit_firing_rate.reset_index(),
+            )
         )
 
         nwb_analysis_file.add(

src/spyglass/decoding/v0/dj_decoder_conversion.py

@@ -1,5 +1,6 @@
 """Converts decoder classes into dictionaries and dictionaries into classes
 so that datajoint can store them in tables."""
+
 from spyglass.utils import logger
 
 try:
@@ -116,17 +117,17 @@ def restore_classes(params: dict) -> dict:
         _convert_env_dict(env_params)
         for env_params in params["classifier_params"]["environments"]
     ]
-    params["classifier_params"][
-        "discrete_transition_type"
-    ] = _convert_dict_to_class(
-        params["classifier_params"]["discrete_transition_type"],
-        discrete_state_transition_types,
+    params["classifier_params"]["discrete_transition_type"] = (
+        _convert_dict_to_class(
+            params["classifier_params"]["discrete_transition_type"],
+            discrete_state_transition_types,
+        )
     )
-    params["classifier_params"][
-        "initial_conditions_type"
-    ] = _convert_dict_to_class(
-        params["classifier_params"]["initial_conditions_type"],
-        initial_conditions_types,
+    params["classifier_params"]["initial_conditions_type"] = (
+        _convert_dict_to_class(
+            params["classifier_params"]["initial_conditions_type"],
+            initial_conditions_types,
+        )
     )
 
     if params["classifier_params"].get("observation_models"):
@@ -176,10 +177,10 @@ def convert_classes_to_dict(key: dict) -> dict:
                 key["classifier_params"]["environments"]
             )
         ]
-    key["classifier_params"][
-        "continuous_transition_types"
-    ] = _convert_transitions_to_dict(
-        key["classifier_params"]["continuous_transition_types"]
+    key["classifier_params"]["continuous_transition_types"] = (
+        _convert_transitions_to_dict(
+            key["classifier_params"]["continuous_transition_types"]
+        )
     )
     key["classifier_params"]["discrete_transition_type"] = _to_dict(
         key["classifier_params"]["discrete_transition_type"]
@@ -194,10 +195,10 @@ def convert_classes_to_dict(key: dict) -> dict:
         ]
 
     try:
-        key["classifier_params"][
-            "clusterless_algorithm_params"
-        ] = _convert_algorithm_params(
-            key["classifier_params"]["clusterless_algorithm_params"]
+        key["classifier_params"]["clusterless_algorithm_params"] = (
+            _convert_algorithm_params(
+                key["classifier_params"]["clusterless_algorithm_params"]
+            )
         )
     except KeyError:
         pass

src/spyglass/decoding/v0/sorted_spikes.py

@@ -7,6 +7,7 @@
 speeds. eLife 10, e64505 (2021).
 
 """
+
 import pprint
 
 import datajoint as dj

src/spyglass/decoding/v0/visualization_2D_view.py

@@ -38,7 +38,7 @@ def create_static_track_animation(
         "xmin": np.min(ul_corners[0]),
         "xmax": np.max(ul_corners[0]) + track_rect_width,
         "ymin": np.min(ul_corners[1]),
-        "ymax": np.max(ul_corners[1]) + track_rect_height
+        "ymax": np.max(ul_corners[1]) + track_rect_height,
         # Speed: should this be displayed?
         # TODO: Better approach for accommodating further data streams
     }

src/spyglass/decoding/v1/clusterless.py

@@ -240,9 +240,9 @@ def make(self, key):
             vars(classifier).get("discrete_transition_coefficients_")
             is not None
         ):
-            results[
-                "discrete_transition_coefficients"
-            ] = classifier.discrete_transition_coefficients_
+            results["discrete_transition_coefficients"] = (
+                classifier.discrete_transition_coefficients_
+            )
 
         # Insert results
         # in future use https://github.com/rly/ndx-xarray and analysis nwb file?

src/spyglass/decoding/v1/dj_decoder_conversion.py

@@ -1,7 +1,6 @@
 """Converts decoder classes into dictionaries and dictionaries into classes
 so that datajoint can store them in tables."""
 
-
 import copy
 
 import datajoint as dj

src/spyglass/decoding/v1/sorted_spikes.py

@@ -232,9 +232,9 @@ def make(self, key):
             vars(classifier).get("discrete_transition_coefficients_")
             is not None
         ):
-            results[
-                "discrete_transition_coefficients"
-            ] = classifier.discrete_transition_coefficients_
+            results["discrete_transition_coefficients"] = (
+                classifier.discrete_transition_coefficients_
+            )
 
         # Insert results
         # in future use https://github.com/rly/ndx-xarray and analysis nwb file?

src/spyglass/position/v1/position_dlc_orient.py

@@ -241,15 +241,15 @@ def interp_orientation(orientation, spans_to_interp, **kwargs):
     # TODO: add parameters to refine interpolation
     for ind, (span_start, span_stop) in enumerate(spans_to_interp):
         if (span_stop + 1) >= len(orientation):
-            orientation.loc[
-                idx[span_start:span_stop], idx["orientation"]
-            ] = np.nan
+            orientation.loc[idx[span_start:span_stop], idx["orientation"]] = (
+                np.nan
+            )
             print(f"ind: {ind} has no endpoint with which to interpolate")
             continue
         if span_start < 1:
-            orientation.loc[
-                idx[span_start:span_stop], idx["orientation"]
-            ] = np.nan
+            orientation.loc[idx[span_start:span_stop], idx["orientation"]] = (
+                np.nan
+            )
             print(f"ind: {ind} has no startpoint with which to interpolate")
             continue
         orient = [
@@ -263,7 +263,7 @@ def interp_orientation(orientation, spans_to_interp, **kwargs):
             xp=[start_time, stop_time],
             fp=[orient[0], orient[-1]],
         )
-        orientation.loc[
-            idx[start_time:stop_time], idx["orientation"]
-        ] = orientnew
+        orientation.loc[idx[start_time:stop_time], idx["orientation"]] = (
+            orientnew
+        )
     return orientation

src/spyglass/position/v1/position_dlc_pose_estimation.py

@@ -309,17 +309,17 @@ def make(self, key):
                     description="video_frame_ind",
                 )
                 nwb_analysis_file = AnalysisNwbfile()
-                key[
-                    "dlc_pose_estimation_position_object_id"
-                ] = nwb_analysis_file.add_nwb_object(
-                    analysis_file_name=key["analysis_file_name"],
-                    nwb_object=position,
+                key["dlc_pose_estimation_position_object_id"] = (
+                    nwb_analysis_file.add_nwb_object(
+                        analysis_file_name=key["analysis_file_name"],
+                        nwb_object=position,
+                    )
                 )
-                key[
-                    "dlc_pose_estimation_likelihood_object_id"
-                ] = nwb_analysis_file.add_nwb_object(
-                    analysis_file_name=key["analysis_file_name"],
-                    nwb_object=likelihood,
+                key["dlc_pose_estimation_likelihood_object_id"] = (
+                    nwb_analysis_file.add_nwb_object(
+                        analysis_file_name=key["analysis_file_name"],
+                        nwb_object=likelihood,
+                    )
                 )
                 nwb_analysis_file.add(
                     nwb_file_name=key["nwb_file_name"],

src/spyglass/position/v1/position_dlc_position.py

@@ -248,17 +248,17 @@ def make(self, key):
                 comments="no comments",
                 description="video_frame_ind",
             )
-            key[
-                "dlc_smooth_interp_position_object_id"
-            ] = nwb_analysis_file.add_nwb_object(
-                analysis_file_name=key["analysis_file_name"],
-                nwb_object=position,
+            key["dlc_smooth_interp_position_object_id"] = (
+                nwb_analysis_file.add_nwb_object(
+                    analysis_file_name=key["analysis_file_name"],
+                    nwb_object=position,
+                )
             )
-            key[
-                "dlc_smooth_interp_info_object_id"
-            ] = nwb_analysis_file.add_nwb_object(
-                analysis_file_name=key["analysis_file_name"],
-                nwb_object=video_frame_ind,
+            key["dlc_smooth_interp_info_object_id"] = (
+                nwb_analysis_file.add_nwb_object(
+                    analysis_file_name=key["analysis_file_name"],
+                    nwb_object=video_frame_ind,
+                )
             )
             nwb_analysis_file.add(
                 nwb_file_name=key["nwb_file_name"],

src/spyglass/sharing/sharing_kachery.py

@@ -105,9 +105,9 @@ def set_resource_url(key: dict):
     def reset_resource_url():
         KacheryZone.reset_zone()
         if default_kachery_resource_url is not None:
-            os.environ[
-                kachery_resource_url_envar
-            ] = default_kachery_resource_url
+            os.environ[kachery_resource_url_envar] = (
+                default_kachery_resource_url
+            )
 
 
 @schema

src/spyglass/spikesorting/figurl_views/prepare_spikesortingview_data.py

@@ -102,16 +102,16 @@ def prepare_spikesortingview_data(
                             channel_neighborhood_size=channel_neighborhood_size,
                         )
                         if len(spike_train) >= 10:
-                            unit_peak_channel_ids[
-                                str(unit_id)
-                            ] = peak_channel_id
+                            unit_peak_channel_ids[str(unit_id)] = (
+                                peak_channel_id
+                            )
                         else:
-                            fallback_unit_peak_channel_ids[
-                                str(unit_id)
-                            ] = peak_channel_id
-                        unit_channel_neighborhoods[
-                            str(unit_id)
-                        ] = channel_neighborhood
+                            fallback_unit_peak_channel_ids[str(unit_id)] = (
+                                peak_channel_id
+                            )
+                        unit_channel_neighborhoods[str(unit_id)] = (
+                            channel_neighborhood
+                        )
         for unit_id in unit_ids:
             peak_channel_id = unit_peak_channel_ids.get(str(unit_id), None)
             if peak_channel_id is None:

src/spyglass/spikesorting/v1/recording.py

@@ -318,9 +318,9 @@ def _get_recording_timestamps(recording):
 
             timestamps = np.zeros((total_frames,))
             for i in range(recording.get_num_segments()):
-                timestamps[
-                    cumsum_frames[i] : cumsum_frames[i + 1]
-                ] = recording.get_times(segment_index=i)
+                timestamps[cumsum_frames[i] : cumsum_frames[i + 1]] = (
+                    recording.get_times(segment_index=i)
+                )
         else:
             timestamps = recording.get_times()
         return timestamps

src/spyglass/utils/dj_helper_fn.py

@@ -1,4 +1,5 @@
 """Helper functions for manipulating information from DataJoint fetch calls."""
+
 import inspect
 import os
 from typing import Type
@@ -193,9 +194,11 @@ def get_child_tables(table):
     return [
         dj.FreeTable(
             table.connection,
-            s
-            if not s.isdigit()
-            else next(iter(table.connection.dependencies.children(s))),
+            (
+                s
+                if not s.isdigit()
+                else next(iter(table.connection.dependencies.children(s)))
+            ),
         )
         for s in table.children()
     ]