Format with black

Author: kabilar

element_array_ephys/ephys_acute.py

@@ -910,7 +910,7 @@ def make(self, key):
             raise ValueError(f"Unknown task mode: {task_mode}")
 
         creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
-        self.insert1({**key, "clustering_time": creation_time, "package_version":""})
+        self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
 
 
 @schema

element_array_ephys/ephys_chronic.py

@@ -839,7 +839,7 @@ def make(self, key):
             raise ValueError(f"Unknown task mode: {task_mode}")
 
         creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
-        self.insert1({**key, "clustering_time": creation_time, "package_version":""})
+        self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
 
 
 @schema

element_array_ephys/ephys_report.py

@@ -53,7 +53,6 @@ class ProbeLevelReport(dj.Computed):
     """
 
     def make(self, key):
-
         from .plotting.probe_level import plot_driftmap
 
         save_dir = _make_save_dir()
@@ -63,7 +62,6 @@ def make(self, key):
         shanks = set((probe.ProbeType.Electrode & units).fetch("shank"))
 
         for shank_no in shanks:
-
             table = units * ephys.ProbeInsertion * probe.ProbeType.Electrode & {
                 "shank": shank_no
             }
@@ -120,7 +118,6 @@ class UnitLevelReport(dj.Computed):
     """
 
     def make(self, key):
-
         from .plotting.unit_level import (
             plot_auto_correlogram,
             plot_depth_waveforms,
@@ -168,7 +165,7 @@ class QualityMetricCutoffs(dj.Lookup):
         isi_violations_maximum (float): Optional. ISI violation ratio cut-off.
         cutoffs_hash (uuid): uuid for the cut-off values.
     """
-    
+
     definition = """
     cutoffs_id                    : smallint
     ---
@@ -234,7 +231,7 @@ class QualityMetricSet(dj.Manual):
         ephys.QualityMetrics (foreign key): ephys.QualityMetrics primary key.
         QualityMetricCutoffs (foreign key): QualityMetricCutoffs primary key.
     """
-    
+
     definition = """
     -> ephys.QualityMetrics
     -> QualityMetricCutoffs
@@ -249,7 +246,7 @@ class QualityMetricReport(dj.Computed):
         QualityMetricSet (foreign key): QualityMetricSet primary key.
         plot_grid (longblob): Plotly figure object.
     """
-    
+
     definition = """
     -> QualityMetricSet
     ---

element_array_ephys/export/nwb/nwb.py

@@ -219,7 +219,6 @@ def create_units_table(
         (ephys.CuratedClustering.Unit & clustering_query.proj()).fetch(as_dict=True),
         desc=f"creating units table for paramset {paramset_record['paramset_idx']}",
     ):
-
         probe_id, shank_num = (
             ephys.ProbeInsertion
             * ephys.CuratedClustering.Unit

element_array_ephys/plotting/qc.py

@@ -198,7 +198,7 @@ class initialization.
         return fig.add_trace(
             go.Scatter(
                 x=histogram_bins[:-1],
-                y=gaussian_filter1d(histogram, 1),  
+                y=gaussian_filter1d(histogram, 1),
                 mode="lines",
                 line=dict(color="rgb(0, 160, 223)", width=2 * scale),  # DataJoint Blue
                 hovertemplate="%{x:.2f}<br>%{y:.2f}<extra></extra>",

element_array_ephys/plotting/unit_level.py

@@ -183,7 +183,6 @@ def plot_depth_waveforms(
     # Plot figure
     fig = go.Figure()
     for electrode, wf, coord in zip(electrodes_to_plot, waveforms, coords):
-
         wf_scaled = wf * y_scale_factor
         wf_scaled -= wf_scaled.mean()
         color = "red" if electrode == peak_electrode else "rgb(51, 76.5, 204)"

element_array_ephys/plotting/widget.py

@@ -11,7 +11,6 @@
 
 
 def main(ephys: types.ModuleType) -> widgets:
-
     # Build dropdown widgets
     probe_dropdown_wg = widgets.Dropdown(
         options=ephys.CuratedClustering & ephys_report.ProbeLevelReport,
@@ -66,7 +65,6 @@ def probe_dropdown_evt(change):
         )
 
     def plot_probe_widget(probe_key, shank):
-
         fig_name = (
             ephys_report.ProbeLevelReport & probe_key & f"shank={shank}"
         ).fetch1("drift_map_plot")
@@ -92,7 +90,6 @@ def plot_probe_widget(probe_key, shank):
         display(go.FigureWidget(probe_fig))
 
     def plot_unit_widget(unit):
-
         waveform_fig, autocorrelogram_fig, depth_waveform_fig = (
             ephys_report.UnitLevelReport & probe_dropdown_wg.value & f"unit={unit}"
         ).fetch1("waveform_plotly", "autocorrelogram_plotly", "depth_waveform_plotly")

element_array_ephys/probe.py

@@ -218,7 +218,6 @@ def build_electrode_layouts(
     shank_spacing: float = None,
     y_origin="bottom",
 ) -> list[dict]:
-
     """Builds electrode layouts.
 
     Args:

element_array_ephys/readers/kilosort.py

@@ -13,7 +13,6 @@
 
 
 class Kilosort:
-
     _kilosort_core_files = [
         "params.py",
         "amplitudes.npy",

element_array_ephys/readers/openephys.py

@@ -135,7 +135,6 @@ def load_probe_data(self):  # noqa: C901
                     probes[probe.probe_SN] = probe
 
         for probe_index, probe_SN in enumerate(probes):
-
             probe = probes[probe_SN]
 
             for rec in self.experiment.recordings: