Blackify, edit changelog

CHANGELOG.md

@@ -1,13 +1,18 @@
 # Change Log
 
+## [0.4.4] (Unreleased)
+
+- Additional documentation. #686
+- Refactor input validation in DLC pipeline.
+- Clean up following pre-commit checks.
+
 ## [0.4.3] (November 7, 2023)
 
 - Migrate `config` helper scripts to Spyglass codebase. #662
 - Revise contribution guidelines. #655
 - Minor bug fixes. #656, #657, #659, #651, #671
 - Add setup instruction specificity.
 - Reduce primary key varchar allocation aross may tables. #664
-- Additional documentation. #682, #686
 
 ## [0.4.2] (October 10, 2023)
 
@@ -105,3 +110,4 @@
 [0.4.1]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.1
 [0.4.2]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.2
 [0.4.3]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.3
+[0.4.4]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.4

docs/mkdocs.yml

@@ -112,11 +112,11 @@ plugins:
   - gen-files:
       scripts:
         - ./src/api/make_pages.py
-  # - mkdocs-jupyter: # Comment this block during dev to reduce build time
-  #     execute: False # Very slow, needs gh-action edit to work/link to db
-  #     include_source: False
-  #     ignore_h1_titles: True
-  #     ignore: ["*make_pages.py", "**checkpoints**", "*/py_scripts/*"]
+  - mkdocs-jupyter: # Comment this block during dev to reduce build time
+      execute: False # Very slow, needs gh-action edit to work/link to db
+      include_source: False
+      ignore_h1_titles: True
+      ignore: ["*make_pages.py", "**checkpoints**", "*/py_scripts/*"]
 
 markdown_extensions:
   - attr_list

notebooks/py_scripts/00_Setup.py

@@ -244,7 +244,6 @@
 
 # +
 import os
-
 import datajoint as dj
 
 if os.path.basename(os.getcwd()) == "notebooks":

notebooks/py_scripts/30_Ripple_Detection.py

@@ -38,7 +38,6 @@
 import os
 import datajoint as dj
 import numpy as np
-import pandas as pd
 
 # change to the upper level folder to detect dj_local_conf.json
 if os.path.basename(os.getcwd()) == "notebooks":

src/spyglass/decoding/clusterless.py

@@ -25,8 +25,12 @@
     _DEFAULT_CONTINUOUS_TRANSITIONS,
     _DEFAULT_ENVIRONMENT,
 )
-from replay_trajectory_classification.discrete_state_transitions import DiagonalDiscrete
-from replay_trajectory_classification.initial_conditions import UniformInitialConditions
+from replay_trajectory_classification.discrete_state_transitions import (
+    DiagonalDiscrete,
+)
+from replay_trajectory_classification.initial_conditions import (
+    UniformInitialConditions,
+)
 from ripple_detection import (
     get_multiunit_population_firing_rate,
     multiunit_HSE_detector,

src/spyglass/position/v1/position_dlc_selection.py

@@ -7,14 +7,19 @@
 import pynwb
 from datajoint.utils import to_camel_case
 
-from ...common.common_behav import convert_epoch_interval_name_to_position_interval_name
+from ...common.common_behav import (
+    convert_epoch_interval_name_to_position_interval_name,
+)
 from ...common.common_nwbfile import AnalysisNwbfile
 from ...utils.dj_helper_fn import fetch_nwb
 from .dlc_utils import make_video
 from .position_dlc_centroid import DLCCentroid
 from .position_dlc_cohort import DLCSmoothInterpCohort
 from .position_dlc_orient import DLCOrientation
-from .position_dlc_pose_estimation import DLCPoseEstimation, DLCPoseEstimationSelection
+from .position_dlc_pose_estimation import (
+    DLCPoseEstimation,
+    DLCPoseEstimationSelection,
+)
 from .position_dlc_position import DLCSmoothInterpParams
 
 schema = dj.schema("position_v1_dlc_selection")

tests/conftest.py

@@ -7,7 +7,10 @@
 import datajoint as dj
 
 from .datajoint._config import DATAJOINT_SERVER_PORT
-from .datajoint._datajoint_server import kill_datajoint_server, run_datajoint_server
+from .datajoint._datajoint_server import (
+    kill_datajoint_server,
+    run_datajoint_server,
+)
 
 thisdir = os.path.dirname(os.path.realpath(__file__))
 sys.path.append(thisdir)