File jquery-3.6.0.js has 6891 lines of code (exceeds 250 allowed). Consider refactoring.

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/*!
 * jQuery JavaScript Library v3.6.0
 * https://jquery.com/
 *
 * Includes Sizzle.js

Function Sizzle has 1510 lines of code (exceeds 25 allowed). Consider refactoring.

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( function( window ) {
var i,
    support,
    Expr,
    getText,

File visuals.py has 2311 lines of code (exceeds 250 allowed). Consider refactoring.

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"""General plotting functions for the deepof package."""
# @author lucasmiranda42
# encoding: utf-8
# module deepof

File data.py has 2050 lines of code (exceeds 250 allowed). Consider refactoring.

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"""Data structures for preprocessing and wrangling of motion tracking output data. This is the main module handled by the user.

There are three main data structures to pay attention to:
- :class:`~deepof.data.Project`, which serves as a configuration hub for the whole pipeline
- :class:`~deepof.data.Coordinates`, which acts as an intermediary between project configuration and data, and contains

File utils.py has 1645 lines of code (exceeds 250 allowed). Consider refactoring.

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# @author lucasmiranda42
# encoding: utf-8
# module deepof

"""Functions and general utilities for the deepof package."""

File models.py has 1637 lines of code (exceeds 250 allowed). Consider refactoring.

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"""deep autoencoder models for unsupervised pose detection.

- VQ-VAE: a variational autoencoder with a vector quantization latent-space (https://arxiv.org/abs/1711.00937).
- VaDE: a variational autoencoder with a Gaussian mixture latent-space.
- Contrastive: an embedding model consisting of a single encoder, trained using a contrastive loss.

File underscore-1.13.1.js has 1445 lines of code (exceeds 250 allowed). Consider refactoring.

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(function (global, factory) {
  typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() :
  typeof define === 'function' && define.amd ? define('underscore', factory) :
  (global = typeof globalThis !== 'undefined' ? globalThis : global || self, (function () {
    var current = global._;

File model_utils.py has 1354 lines of code (exceeds 250 allowed). Consider refactoring.

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# @author lucasmiranda42
# encoding: utf-8
# module deepof

"""Utility functions for both training autoencoder models in deepof.models and tuning hyperparameters with deepof.hypermodels."""

File post_hoc.py has 923 lines of code (exceeds 250 allowed). Consider refactoring.

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# @author lucasmiranda42
# encoding: utf-8
# module deepof

"""Data structures and functions for analyzing supervised and unsupervised model results."""

File annotation_utils.py has 679 lines of code (exceeds 250 allowed). Consider refactoring.

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# @author lucasmiranda42
# encoding: utf-8
# module deepof

"""Functions and general utilities for supervised pose estimation. See documentation for details."""

Function get_coords has a Cognitive Complexity of 67 (exceeds 5 allowed). Consider refactoring.

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    def get_coords(
        self,
        center: str = False,
        polar: bool = False,
        speed: int = 0,

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Function setDocument has 262 lines of code (exceeds 25 allowed). Consider refactoring.

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setDocument = Sizzle.setDocument = function( node ) {
    var hasCompare, subWindow,
        doc = node ? node.ownerDocument || node : preferredDoc;

    // Return early if doc is invalid or already selected

Function ajax has 259 lines of code (exceeds 25 allowed). Consider refactoring.

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    ajax: function( url, options ) {

        // If url is an object, simulate pre-1.5 signature
        if ( typeof url === "object" ) {
            options = url;

Function preprocess has a Cognitive Complexity of 64 (exceeds 5 allowed). Consider refactoring.

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    def preprocess(
        self,
        automatic_changepoints=False,
        handle_ids: str = "concat",
        window_size: int = 25,

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Function tag_annotated_frames has a Cognitive Complexity of 62 (exceeds 5 allowed). Consider refactoring.

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def tag_annotated_frames(
    frame,
    font,
    frame_speeds,
    animal_ids,

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Function Stemmer has a Cognitive Complexity of 58 (exceeds 5 allowed). Consider refactoring.

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var Stemmer = function() {

  var step2list = {
    ational: 'ate',
    tional: 'tion',

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Function plot_gantt has a Cognitive Complexity of 51 (exceeds 5 allowed). Consider refactoring.

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def plot_gantt(
    coordinates: project,
    experiment_id: str,
    soft_counts: table_dict = None,
    supervised_annotations: table_dict = None,

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Function Deferred has 178 lines of code (exceeds 25 allowed). Consider refactoring.

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    Deferred: function( func ) {
        var tuples = [

                // action, add listener, callbacks,
                // ... .then handlers, argument index, [final state]

Function align_deepof_kinematics_with_unsupervised_labels has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.

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def align_deepof_kinematics_with_unsupervised_labels(
    deepof_project: coordinates,
    kin_derivative: int = 1,
    center: str = "Center",
    align: str = "Spine_1",

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Function plot_embeddings has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.

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def plot_embeddings(
    coordinates: coordinates,
    embeddings: table_dict = None,
    soft_counts: table_dict = None,
    breaks: table_dict = None,

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