From ff63090159995bf4edb2c10f9c650dab1dc64251 Mon Sep 17 00:00:00 2001 From: CBroz1 Date: Fri, 17 Nov 2023 16:45:41 -0600 Subject: [PATCH] Blackify, edit changelog --- CHANGELOG.md | 8 +++++++- docs/mkdocs.yml | 10 +++++----- notebooks/py_scripts/00_Setup.py | 1 - notebooks/py_scripts/30_Ripple_Detection.py | 1 - src/spyglass/decoding/clusterless.py | 8 ++++++-- src/spyglass/position/v1/position_dlc_selection.py | 9 +++++++-- tests/conftest.py | 5 ++++- 7 files changed, 29 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4169af2a2..dba384f10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # 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 @@ -7,7 +13,6 @@ - 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 diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 2bbed90ea..32f789bb9 100644 --- a/docs/mkdocs.yml +++ b/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 diff --git a/notebooks/py_scripts/00_Setup.py b/notebooks/py_scripts/00_Setup.py index 21bb57083..4bb37987c 100644 --- a/notebooks/py_scripts/00_Setup.py +++ b/notebooks/py_scripts/00_Setup.py @@ -244,7 +244,6 @@ # + import os - import datajoint as dj if os.path.basename(os.getcwd()) == "notebooks": diff --git a/notebooks/py_scripts/30_Ripple_Detection.py b/notebooks/py_scripts/30_Ripple_Detection.py index ed61ed523..dd1b14fc1 100644 --- a/notebooks/py_scripts/30_Ripple_Detection.py +++ b/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": diff --git a/src/spyglass/decoding/clusterless.py b/src/spyglass/decoding/clusterless.py index 66d79fda4..281a66762 100644 --- a/src/spyglass/decoding/clusterless.py +++ b/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, diff --git a/src/spyglass/position/v1/position_dlc_selection.py b/src/spyglass/position/v1/position_dlc_selection.py index 5b9caab13..5d23d575b 100644 --- a/src/spyglass/position/v1/position_dlc_selection.py +++ b/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") diff --git a/tests/conftest.py b/tests/conftest.py index 5f41c7bf4..ac1539abf 100644 --- a/tests/conftest.py +++ b/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)