Align develop and main

[roomrys]

• Remove no-op code from Do not try to remove item if already deleted #1498

• Add options to set background color when exporting video (Add options to set background color when exporting video #1328)

• implement Skeleton without video #921

• simplified form / refractor

• Add test function and update cli docs

• Improve test function to check background color

• Improve comments

• Change background options to lowercase

• Use coderabbitai suggested fill

---

• Increase range on batch size (Increase range on batch size #1513)

• Increase range on batch size

• Set maximum to a factor of 2

• Set default callable for match_lists_function (Set default callable for match_lists_function #1520)

• Set default for match_lists_function

• Move test code to official tests

• Check using expected values

• Allow passing in Labels to app.main (Allow passing in Labels to app.main #1524)

• Allow passing in Labels to app.main

• Load the labels object through command

• Add warning when unable to switch back to CPU mode

• Replace (broken) --unrag with --ragged (Replace (broken) --unrag with --ragged #1539)

• Fix unrag always set to true in sleap-export

• Replace unrag with ragged

• Fix typos

• Add function to create app (Add function to create app #1546)

• Refactor AddInstance command (Refactor AddInstance command #1561)

• Refactor AddInstance command

• Add staticmethod wrappers

• Return early from set_visible_nodes

• Import DLC with uniquebodyparts, add Tracks (Import DLC with uniquebodyparts, add Tracks #1562)

• Import DLC with uniquebodyparts, add Tracks

• add tests

• correct tests

• Make the hdf5 videos store as int8 format (Make the hdf5 videos store as int8 format #1559)

• make the hdf5 video dataset type as proper int8 by padding with zeros

• add gzip compression

• Scale new instances to new frame size (Scale new instances to new frame size #1568)

• Fix typehinting in AddInstance

• brought over changes from my own branch

• added suggestions

• Ensured google style comments

---

• Fix package export (Fix package export #1619)

Add check for empty videos

• Add resize/scroll to training GUI (Add resize/scroll to training GUI #1565)

• Make resizable training GUI and add adaptive scroll bar

• Set a maximum window size

---

• support loading slp files with non-compound types and str in metadata (support loading slp files with non-compound types and str in metadata #1566)

• change inference pipeline option to tracking-only (change inference pipeline option to tracking-only #1666)

change inference pipeline none option to tracking-only

• Add ABL:AOC 2023 Workshop link (Add ABL:AOC 2023 Workshop link #1673)

• Add ABL:AOC 2023 Workshop link

• Trigger website build

• Graceful failing with seeking errors (Graceful failing with seeking errors #1712)

• Don't try to seek to faulty last frame on provider initialization

• Catch seeking errors and pass

• Lint

• Fix IndexError for hdf5 file import for single instance analysis files (Fix IndexError for hdf5 file import for single instance analysis files #1695)

• Fix hdf5 read for single instance analysis files

• Add test

• Small test files

• removing unneccessary fixtures

• Replace imgaug with albumentations (Replace imgaug with albumentations #1623)

What's the worst that could happen?

• Initial commit

• Fix augmentation

• Update more deps requirements

• Use pip for installing albumentations and avoid reinstalling OpenCV

• Update other conda envs

• Fix out of bounds albumentations issues and update dependencies (Fix out of bounds albumentations issues and update dependencies #1724)

• Install albumentations using conda-forge in environment file

• Conda install albumentations

• Add ndx-pose to pypi requirements

• Keep out of bounds points

• Black

• Add ndx-pose to conda install in environment file

• Match environment file without cuda

• Ordered dependencies

• Add test

• Delete comments

• Add conda packages to mac environment file

• Order dependencies in pypi requirements

• Add tests with zeroes and NaNs for augmentation

• Back

• Black

• Make comment one line

• Add todo for later

• Black

• Update to new TensorFlow conda package (Update to new TensorFlow conda package #1726)

• Build conda package locally

• Try 2.8.4

• Merge develop into branch to fix dependencies

• Change tensorflow version to 2.7.4 in where conda packages are used

• Make tensorflow requirements in pypi looser

• Conda package has TensorFlow 2.7.0 and h5py and numpy installed via conda

• Change tensorflow version in environment_no_cuda.yml to test using CI

• Test new sleap/tensorflow package

• Reset build number

• Bump version

• Update mac deps

• Update to Arm64 Mac runners

• pin importlib-metadata

• Pin more stuff on mac

• constrain opencv version due to new qt dependencies

• Update more mac stuff

• Patches to get to green

• More mac skipping

---

• Fix CI on macosx-arm64 (Fix CI on macosx-arm64 #1734)

• Build conda package locally

• Try 2.8.4

• Merge develop into branch to fix dependencies

• Change tensorflow version to 2.7.4 in where conda packages are used

• Make tensorflow requirements in pypi looser

• Conda package has TensorFlow 2.7.0 and h5py and numpy installed via conda

• Change tensorflow version in environment_no_cuda.yml to test using CI

• Test new sleap/tensorflow package

• Reset build number

• Bump version

• Update mac deps

• Update to Arm64 Mac runners

• pin importlib-metadata

• Pin more stuff on mac

• constrain opencv version due to new qt dependencies

• Update more mac stuff

• Patches to get to green

• More mac skipping

• Re-enable mac tests

• Handle GPU re-init

• Fix mac build CI

• Widen tolerance for movenet correctness test

• Fix build ci

• Try for manual build without upload

• Try to reduce training CI time

• Rework actions

• Fix miniforge usage

• Tweaks

• Fix build ci

• Disable manual build

• Try merging CI coverage

• GPU/CPU usage in tests

• Lint

• Clean up

• Fix test skip condition

• Remove scratch test

---

• Add option to export to CSV via sleap-convert and API (Add option to export to CSV via sleap-convert and API #1730)

• Add csv as a format option

• Add analysis to format

• Add csv suffix to output path

• Add condition for csv analysis file

• Add export function to Labels class

• delete print statement

• lint

• Add analysis.csv as parametrize input for sleap-convert tests

• test export_csv method added to Labels class

• black formatting

• use Path to construct filename

• add analysis.csv to cli guide for sleap-convert

---

• Only propagate Transpose Tracks when propagate is checked (Only propagate Transpose Tracks when propagate is checked #1748)

Fix always-propagate transpose tracks issue

• View Hyperparameter nonetype fix (View Hyperparameter nonetype fix #1766)

Pass config getter argument to fetch hyperparameters

• Adding ragged metadata to info.json (Adding ragged metadata to info.json #1765)

Add ragged metadata to info.json file

• Add batch size to GUI for inference (Add batch size to GUI for inference #1771)

• Fix conda builds (Fix conda builds #1776)

• test conda packages in a test environment as part of CI

• do not test sleap import using conda build

• use github environment variables to define build path for each OS in the matrix and add print statements for testing

• figure out paths one OS at a time

• github environment variables work in subsequent steps not current step

• use local builds first

• print env info

• try simple environment creation

• try conda instead of mamba

• fix windows build path

• fix windows build path

• add comment to reference pull request

• remove test stage from conda build for macs and test instead by creating the environment in a workflow

• test workflow by pushing to current branch

• test conda package on macos runner

• Mac build does not need nvidia channel

• qudida and albumentations are conda installed now

• add comment with original issue

• use python 3.9

• use conda match specifications syntax

• make print statements more readable for troubleshooting python versioning

• clean up build file

• update version for pre-release

• add TODO

• add tests for conda packages before uploading

• update ci comments and branches

• remove macos test of pip wheel since python 3.9 is not supported by setup-python action

• Upgrade build actions for release (Upgrade build actions for release #1779)

• update build.yml so it matches updates from build_manual.yml

• test build.yml without uploading

• test again using build_manual.yml

• build pip wheel with Ubuntu and turn off caching so build.yml exactly matches build_manual.yml

• build.yml on release only and upload

• testing caching

• use-only-tar-bz2: true makes environment unsolvable, change it back

• Update .github/workflows/build_manual.yml

• Update .github/workflows/build.yml

• bump pre-release version

• fix version for pre-release

• run build and upload on release!

• try setting CACHE_NUMBER to 1 with use-only-tar-bz2 set to true

• increasing the cache number to reset the cache does work when use-only-tar-bz2 is set to true

• publish and upload on release only

---

• Add ZMQ support via GUI and CLI (Add ZMQ support via GUI and CLI #1780)

• Add ZMQ support via GUI and CLI, automatic port handler, separate utils module for the functions

• Change menu name to match deleting predictions beyond max instance (Change menu name to match deleting predictions beyond max instance #1790)

Change menu and function names

• Fix website build and remove build cache across workflows (Fix website build and remove build cache across workflows #1786)

• test with build_manual on push

• comment out caching in build manual

• remove cache step from builad manual since environment resolves when this is commented out

• comment out cache in build ci

• remove cache from build on release

• remove cache from website build

• test website build on push

• add name to checkout step

• update checkout to v4

• update checkout to v4 in build ci

• remove cache since build ci works without it

• update upload-artifact to v4 in build ci

• update second chechout to v4 in build ci

• update setup-python to v5 in build ci

• update download-artifact to v4 in build ci

• update checkout to v4 in build ci

• update checkout to v4 in website build

• update setup-miniconda to v3.0.3 in website build

• update actions-gh-pages to v4 in website build

• update actions checkout and setup-python in ci

• update checkout action in ci to v4

• pip install lxml[html_clean] because of error message during action

• add error message to website to explain why pip install lxml[html_clean]

• remove my branch for pull request

• Bump to 1.4.1a1 (Bump to 1.4.1a1 #1791)

• bump versions to 1.4.1a1

• we can change the version on the installation page since this will be merged into the develop branch and not main

• Fix windows conda package upload and build ci (Fix windows conda package upload and build ci #1792)

• windows OS is 2022 not 2019 on runner

• upload windows conda build manually but not pypi build

• remove comment and run build ci

• change build manual back so that it doesn't upload

• remove branch from build manual

• update installation docs for 1.4.1a1

• Fix zmq inference (Fix zmq inference #1800)

• Ensure that we always pass in the zmq_port dict to LossViewer

• Ensure zmq_ports has correct keys inside LossViewer

• Use specified controller and publish ports for first attempted addresses

• Add test for ports being set in LossViewer

• Add max attempts to find unused port

• Fix find free port loop and add for controller port also

• Improve code readablility and reuse

• Improve error message when unable to find free port

• Set selected instance to None after removal (Set selected instance to None after removal #1808)

• Add test that selected instance set to None after removal

• Set selected instance to None after removal

• Add InstancesList class to handle backref to LabeledFrame (Add InstancesList class to handle backref to LabeledFrame #1807)

• Add InstancesList class to handle backref to LabeledFrame

• Register structure/unstructure hooks for InstancesList

• Add tests for the InstanceList class

• Handle case where instance are passed in but labeled_frame is None

• Add tests relevant methods in LabeledFrame

• Delegate setting frame to InstancesList

• Add test for PredictedInstance.frame after complex merge

• Add todo comment to not use Instance.frame

• Add rtest for InstasnceList.remove

• Use normal list for informative merged_instances

• Add test for copy and clear

• Add copy and clear methods, use normal lists in merge method

• Bump to v1.4.1a2 (Bump to v1.4.1a2 #1835)

bump to 1.4.1a2

• Updated trail length viewing options (Updated trail length viewing options #1822)

• updated trail length optptions

• Updated trail length options in the view menu

• Updated prefs to include length info from preferences.yaml

• Added trail length as method of MainWindow

• Updated trail length documentation

• black formatting

---

• Handle case when no frame selection for trail overlay (Handle case when no frame selection for trail overlay #1832)

• Menu option to open preferences directory and update to util functions to pathlib (Menu option to open preferences directory and update to util functions to pathlib #1843)

• Add menu to view preferences directory and update to pathlib

• text formatting

• Add Keep visualizations checkbox to training GUI (Add Keep visualizations checkbox to training GUI #1824)

• Renamed save_visualizations to view_visualizations for clarity

• Added Delete Visualizations button to the training pipeline gui, exposed del_viz_predictions config option to the user

• Reverted view_ back to save_ and changed new training checkbox to Keep visualization images after training.

• Fixed keep_viz config option state override bug and updated keep_viz doc description

• Added test case for reading training CLI argument correctly

• Removed unnecessary testing code

• Creating test case to check for viz folder

• Finished tests to check CLI argument reading and viz directory existence

• Use empty string instead of None in cli args test

• Use keep_viz_images false in most all test configs (except test to override config)

---

• Allowing inference on multiple videos via sleap-track (Allowing inference on multiple videos via sleap-track #1784)

• implementing proposed code changes from issue Allow inference on multiple individual videos via sleap-track #1777

• comments

• configuring output_path to support multiple video inputs

• fixing errors from preexisting test cases

• Test case / code fixes

• extending test cases for mp4 folders

• test case for output directory

• black and code rabbit fixes

• code rabbit fixes

• as_posix errors resolved

• syntax error

• adding test data

• black

• output error resolved

• edited for push to dev branch

• black

• errors fixed, test cases implemented

• invalid output test and invalid input test

• deleting debugging statements

• deleting print statements

• black

• deleting unnecessary test case

• implemented tmpdir

• deleting extraneous file

• fixing broken test case

• fixing test_sleap_track_invalid_output

• removing support for multiple slp files

• implementing talmo's comments

• adding comments

• Add object keypoint similarity method (Add object keypoint similarity method #1003)

• Add object keypoint similarity method

• fix max_tracking

• correct off-by-one error

• correct off-by-one error

• Generate suggestions using max point displacement threshold (Generate suggestions using max point displacement threshold #1862)

• create function max_point_displacement, _max_point_displacement_video. Add to yaml file. Create test for new function . . . will need to edit

• remove unnecessary for loop, calculate proper displacement, adjusted tests accordingly

• Increase range for displacement threshold

• Fix frames not found bug

• Return the latter frame index

• Lint

---

• Added Three Different Cases for Adding a New Instance (Added Three Different Cases for Adding a New Instance #1859)

• implemented paste with offset

• right click and then default will paste the new instance at the location of the cursor

• modified the logics for creating new instance

• refined the logic

• fixed the logic for right click

• refined logics for adding new instance at a specific location

• Remove print statements

• Comment code

• Ensure that we choose a non nan reference node

• Move OOB nodes to closest in-bounds position

---

• Allow csv and text file support on sleap track (Allow csv and text file support on sleap track #1875)

• initial changes

• csv support and test case

• increased code coverage

• Error fixing, black, deletion of (self-written) unused code

• final edits

• black

• documentation changes

• documentation changes

• Fix GUI crash on scroll (Fix GUI crash on scroll #1883)

• Only pass wheelEvent to children that can handle it

• Add test for wheelEvent

• Fix typo to allow rendering videos with mp4 (Mac) (Fix typo to allow rendering videos with mp4 (Mac) #1892)

Fix typo to allow rendering videos with mp4

• Do not apply offset when double clicking a PredictedInstance (Do not apply offset when double clicking a PredictedInstance #1888)

• Add offset argument to newInstance and AddInstance

• Apply offset of 10 for Add Instance menu button (Ctrl + I)

• Add offset for docks Add Instance button

• Make the QtVideoPlayer context menu unit-testable

• Add test for creating a new instance

• Add test for "New Instance" button in InstancesDock

• Fix typo in docstring

• Add docstrings and typehinting

• Remove unused imports and sort imports

• Refactor video writer to use imageio instead of skvideo (Refactor video writer to use imageio instead of skvideo #1900)

• modify VideoWriter to use imageio with ffmpeg backend

• check to see if ffmpeg is present

• use the new check for ffmpeg

• import imageio.v2

• add imageio-ffmpeg to environments to test

• using avi format for now

• remove SKvideo videowriter

• test VideoWriterImageio minimally

• add more documentation for ffmpeg

• default mp4 for ffmpeg should be mp4

• print using IMAGEIO when using ffmpeg

• mp4 for ffmpeg

• use mp4 ending in test

• test VideoWriterImageio with avi file extension

• test video with odd size

• remove redundant filter since imageio-ffmpeg resizes automatically

• black

• remove unused import

• use logging instead of print statement

• import cv2 is needed for resize

• remove logging

• Use Video.from_filename when structuring videos (Use Video.from_filename when structuring videos #1905)

• Use Video.from_filename when structuring videos

• Modify removal_test_labels to have extension in filename

• Use | instead of + in key commands (Use | instead of + in key commands #1907)

• Use | instead of + in key commands

• Lint

• Replace QtDesktop widget in preparation for PySide6 (Replace QtDesktop widget in preparation for PySide6 #1908)

• Replace to-be-depreciated QDesktopWidget

• Remove unused imports and sort remaining imports

• Remove unsupported |= operand to prepare for PySide6 (Remove unsupported |= operand to prepare for PySide6 #1910)

Fixes TypeError: unsupported operand type(s) for |=: 'int' and 'Option'

• Use positional argument for exception type (Use positional argument for exception type #1912)

traceback.format_exception has changed it's first positional argument's name from etype to exc in python 3.7 to 3.10

• Replace all Video structuring with Video.cattr() (Replace all Video structuring with Video.cattr() #1911)

• Remove unused AsyncVideo class (Remove unused AsyncVideo class #1917)

Remove unused AsyncVideo

• Refactor LossViewer to use matplotlib (Refactor LossViewer to use matplotlib #1899)

• use updated syntax for QtAgg backend of matplotlib

• start add features to MplCanvas to replace QtCharts features in LossViewer (untested)

• remove QtCharts imports and replace with MplCanvas

• remove QtCharts imports and replace with MplCanvas

• start using MplCanvas in LossViwer instead of QtCharts (untested)

• use updated syntax

• Uncomment all commented out QtChart

• Add debug code

• Refactor monitor to use LossViewer._init_series method

• Add monitor only debug code

• Add methods for setting up axes and legend

• Add the matplotlib canvas to the widget

• Resize axis with data (no log support yet)

• Try using PathCollection for "batch"

• Get "batch" plotting with ax.scatter (no log support yet)

• Add log support

• Add a _resize_axis method

• Modify init_series to work for ax.plot as well

• Use matplotlib to plot epoch_loss line

• Add method _add_data_to_scatter

• Add _add_data_to_plot method

• Add docstring to _resize_axes

• Add matplotlib plot for val_loss

• Add matplotlib scatter for val_loss_best

• Avoid errors with setting log scale before any positive values

• Add x and y axes labels

• Set title (removing html tags)

• Add legend

• Adjust positioning of plot

• Lint

• Leave MplCanvas unchanged

• Removed unused training_monitor.LossViewer

• Resize fonts

• Move legend outside of plot

• Add debug code for montitor aesthetics

• Use latex formatting to bold parts of title

• Make axes aesthetic

• Add midpoint grid lines

• Set initial limits on x and y axes to be 0+

• Ensure x axis minimum is always resized to 0+

• Adjust plot to account for plateau patience title

• Add debug code for plateau patience title line

• Lint

• Set thicker line width

• Remove unused import

• Set log axis on initialization

• Make tick labels smaller

• Move plot down a smidge

• Move ylabel left a bit

• Lint

• Add class LossPlot

• Refactor LossViewer to use LossPlot

• Remove QtCharts code

• Remove debug codes

• Allocate space for figure items based on item's size

• Refactor LossPlot to use underscores for internal methods

• Ensure y_min, y_max not equal Otherwise we get an unnecessary teminal message:
  UserWarning: Attempting to set identical bottom == top == 3.0 results in singular transformations; automatically expanding.
  self.axes.set_ylim(y_min, y_max)

---

• Refactor LossViewer to use underscores for internal method names (Refactor LossViewer to use underscores for internal method names #1919)

Refactor LossViewer to use underscores for internal method names

• Manually handle Instance.from_predicted structuring when not None (Manually handle Instance.from_predicted structuring when not None #1930)

• Use tf.math.mod instead of % (Use tf.math.mod instead of % #1931)

• Option for Max Stride to be 128 (Option for Max Stride to be 128 #1941)

• Add discussion comment workflow (Add discussion comment workflow #1945)

• Add a bot to autocomment on workflow

• Use github markdown warning syntax

• Add a multiline warning

• Change happy coding to happy SLEAPing

---

• Add comment on issue workflow (Add comment on issue workflow #1946)

• Add workflow to test conda packages (Add workflow to test conda packages #1935)

• Add missing imageio-ffmpeg to meta.ymls (Add missing imageio-ffmpeg to meta.ymls #1943)

• Update installation docs 1.4.1 (Update installation docs 1.4.1 #1810)

• [wip] Updated installation docs

• Add tabs for different OS installations

• Move installation methods to tabs

• Use tabs.css

• FIx styling error (line under last tab in terminal hint)

• Add installation instructions before TOC

• Replace mamba with conda

• Lint

• Find good light colors not switching when change dark/light themes

• Get color scheme switching with dark/light toggle button

• Upgrade website build dependencies

• Remove seemingly unneeded dependencies from workflow

• Add myst-nb>=0.16.0 lower bound

• Trigger dev website build

• Fix minor typo in css

• Add miniforge and one-liner installs for package managers

---

• Add imageio dependencies for pypi wheel (Add imageio dependencies for pypi wheel #1950)

Add imagio dependencies for pypi wheel

• Do not always color skeletons table black (Do not always color skeletons table black #1952)

• Remove no module named work error (Remove no module named work error #1956)

• Do not always color skeletons table black

• Remove offending (possibly unneeded) line that causes the no module named work error to print in terminal

• Remove offending (possibly unneeded) line that causes the no module named work error to print in terminal

• Remove accidentally added changes

• Add (failing) test to ensure menu-item updates with state change

• Reconnect callback for menu-item (using lambda)

• Add (failing) test to ensure menu-item updates with state change

Do not assume inital state

• Reconnect callback for menu-item (using lambda)

---

• Add normalized_instance_similarity method (Add normalized_instance_similarity method  #1939)

• Add normalize function

• Expose normalization function

• Fix tests

• Expose object keypoint sim function

• Fix tests

• Handle skeleton decoding internally (Handle skeleton decoding internally #1961)

• Reorganize (and add) imports

• Add (and reorganize) imports

• Modify decode_preview_image to return bytes if specified

• Implement (minimally tested) replace_jsonpickle_decode

• Add support for using idx_to_node map i.e. loading from Labels (slp file)

• Ignore None items in reduce_list

• Convert large function to SkeletonDecoder class

• Update SkeletonDecoder.decode docstring

• Move decode_preview_image to SkeletonDecoder

• Use SkeletonDecoder instead of jsonpickle in tests

• Remove unused imports

• Add test for decoding dict vs tuple pystates

• Handle skeleton encoding internally (Handle skeleton encoding internally #1970)

• start class SkeletonEncoder

• _encoded_objects need to be a dict to add to

• add notebook for testing

• format

• fix type in docstring

• finish classmethod for encoding Skeleton as a json string

• test encoded Skeleton as json string by decoding it

• add test for decoded encoded skeleton

• update jupyter notebook for easy testing

• constraining attrs in dev environment to make sure decode format is always the same locally

• encode links first then encode source then target then type

• save first enconding statically as an input to _get_or_assign_id so that we do not always get py/id

• save first encoding statically

• first encoding is passed to _get_or_assign_id

• use first_encoding variable to determine if we should assign a py/id

• add print statements for debugging

• update notebook for easy testing

• black

• remove comment

• adding attrs constraint to show this passes for certain attrs version only

• add import

• switch out jsonpickle.encode

• oops remove import

• can attrs be unconstrained?

• forgot comma

• pin attrs for testing

• test Skeleton from json, template, with symmetries, and template

• use SkeletonEncoder.encode

• black

• try removing None values in EdgeType reduced

• Handle case when nodes are replaced by integer indices from caller

• Remove prototyping notebook

• Remove attrs pins

• Remove sort keys (which flips the neccessary ordering of our py/ids)

• Do not add extra indents to encoded file

• Only append links after fully encoded (fat-finger)

• Remove outdated comment

• Lint

---

• Pin ndx-pose<0.2.0 (Pin ndx-pose<0.2.0 #1978)

• Pin ndx-pose<0.2.0

• Typo

• Sort encoded Skeleton dictionary for backwards compatibility (Sort encoded Skeleton dictionary for backwards compatibility  #1975)

• Add failing test to check that encoded Skeleton is sorted

• Sort Skeleton dictionary before encoding

• Remove unused import

• Disable comment bot for now

• Fix COCO Dataset Loading for Invisible Keypoints (Fix COCO Dataset Loading for Invisible Keypoints #2035)

Update coco.py

Fix COCO Dataset Loading for Invisible Keypoints

Issue

When loading COCO datasets, keypoints marked as invisible (flag=0) are currently skipped and later placed randomly within the instance's bounding box. However, in COCO format, these keypoints may still have valid coordinate information that should be preserved (see toy_dataset for expected vs. current behavior).

Changes

Modified the COCO dataset loading logic to:

• Check if invisible keypoints (flag=0) have non-zero coordinates
• If coordinates are (0,0), skip the point (existing behavior)
• If coordinates are not (0,0), create the point at those coordinates but mark it as not visible
• Maintain existing behavior for visible (flag=2) and labeled

• Lint

• Add tracking score as seekbar header options (Add tracking score as seekbar header options #2047)

• Add tracking_score as a constructor arg for PredictedInstance

• Add tracking_score to ID models

• Add fixture with tracking scores

• Add tracking score to seekbar header

• Add bonsai guide for sleap docs (Add bonsai guide for sleap docs #2050)

• [WIP] Add bonsai guide page

• Add more information to the guide with images

• add branch for website build

• Typos

• fix links

• Include suggestions

• Add more screenshots and refine the doc

• Remove branch from website workflow

• Completed documentation edits from PR made by reviewer + review bot.

---

• Don't mark complete on instance scaling (Don't mark complete on instance scaling #2049)

• Add check for instances with track assigned before training ID models (Add check for instances with track assigned before training ID models #2053)

• Add menu item for deleting instances beyond frame limit (Add menu item for deleting instances beyond frame limit #1797)

• Add menu item for deleting instances beyond frame limit

• Add test function to test the instances returned

• typos

• Update docstring

• Add frame range form

• Extend command to use frame range

---

• Highlight instance box on hover (Highlight instance box on hover #2055)

• Make node marker and label sizes configurable via preferences (Make node marker and label sizes configurable via preferences #2057)

• Make node marker and label sizes configurable via preferences

• Fix test

• Enable touchpad pinch to zoom (Enable touchpad pinch to zoom #2058)

• Fix import PySide2 -> qtpy (Fix import PySide2 -> qtpy #2065)

• Fix import PySide2 -> qtpy

• Remove unnecessary print statements.

• Add channels for pip conda env (Add channels for pip conda env #2067)

• Add channels for pypi conda env

• Trigger dev website build

• Separate the video name and its filepath columns in VideoTablesModel (Separate the video name and its filepath columns in VideoTablesModel #2052)

• add option to show video names with filepath

• add doc

• new feature added successfully

• delete unnecessary code

• remove attributes from video object

• Update dataviews.py

• remove all properties

• delete toggle option

• remove video show

• fix the order of the columns

• remove options

• Update sleap/gui/dataviews.py

• Update sleap/gui/dataviews.py

• use pathlib instead of substrings

• Update dataviews.py

• Use Path instead of pathlib.Path and sort imports and remove unused imports

• Use item.filename instead of getattr

---

• Make status bar dependent on UI mode (Make status bar dependent on UI mode #2063)

• remove bug for dark mode

• fix toggle case

---

• Bump version to 1.4.1 (Bump version to 1.4.1 #2062)

• Bump version to 1.4.1

• Trigger conda/pypi builds (no upload)

• Trigger website build

• Add dev channel to installation instructions

---

• Add -c sleap/label/dev channel for win/linux

• also trigger website build

---

Description

[describe your changes here]

Types of changes

• Bugfix
• New feature
• Refactor / Code style update (no logical changes)
• Build / CI changes
• Documentation Update
• Other (explain)

Does this address any currently open issues?

[list open issues here]

Outside contributors checklist

• Review the guidelines for contributing to this repository
• Read and sign the CLA and add yourself to the authors list
• Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
• Add tests that prove your fix is effective or that your feature works
• Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

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[codecov]

Codecov Report

Attention: Patch coverage is 77.29844% with 321 lines in your changes missing coverage. Please review.

Project coverage is 75.43%. Comparing base (a2092f0) to head (7991f14).
Report is 99 commits behind head on develop.

Files with missing lines	Patch %	Lines
sleap/gui/widgets/monitor.py	67.87%	106 Missing ⚠️
sleap/nn/inference.py	76.96%	38 Missing ⚠️
sleap/gui/widgets/video.py	54.00%	23 Missing ⚠️
sleap/gui/app.py	52.27%	21 Missing ⚠️
sleap/gui/commands.py	83.87%	20 Missing ⚠️
sleap/gui/dialogs/frame_range.py	28.57%	20 Missing ⚠️
sleap/gui/learning/runners.py	29.41%	12 Missing ⚠️
sleap/io/format/hdf5.py	61.53%	10 Missing ⚠️
sleap/nn/data/augmentation.py	28.57%	10 Missing ⚠️
sleap/nn/tracker/components.py	78.72%	10 Missing ⚠️
... and 17 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2069      +/-   ##
===========================================
+ Coverage    73.11%   75.43%   +2.32%     
===========================================
  Files          134      134              
  Lines        23963    24749     +786     
===========================================
+ Hits         17521    18670    +1149     
+ Misses        6442     6079     -363     

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