Update to Python 3.10 and SLEAP v1.5.0

[eberrigan]

• In #1989 we fixed several segfaults and threading issues through better thread management and import ordering fixes.
• There is no GPU support on native-windows for TensorFlow >= 2.11.0 see tensorflow documentation

Old Description

• The conda package for Windows and Linux currently uses Python 3.7.12 which is at its end-of-life. We would like to use the latest Python version possible for our conda build.
• TensorFlow 2.7.0 is the current working version of TensorFlow in SLEAP for Windows and Linux. TensorFlow 2.7.0 is compatible with Python 3.7 - 3.9. TensorFlow 2.7.0 cannot be pip installed with Python 3.10.
• We are currently using PySide 2 in both the Windows/Linux and Mac conda packages. We would like to upgrade this to PySide 6.
• PySide 6 is dependent on SciPy which is dependent on numpy.
• The Mac conda package uses tensorflow-macos==2.9.2, is not compatible with Python 3.11 and 3.12.
• We will update the PyPI build dependencies as well.
• scikit-video is replaced with imageio.v2. Code will be refactored for VideoWriter and tests will be made for new VideoWriter using imageio.v2 in a new PR. #1900 ✅
• QtCharts is problematic. We are removing it and using matplotlib instead. Code will be refactored for LossViewer to use MplCanvas with added functionality for plotting and tests will be made in a future PR. The QT backend for matplotlib will be updated as well. #1899 ✅

Types of changes

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

Does this address any currently open issues?

• The Mac GUI is breaking in the latest pre-release #1803, #1802.
• This is following up many dependency updates in pre-release v1.4.1a1.

Outside contributors checklist

• [X] Review the guidelines for contributing to this repository
• [ ] Read and sign the CLA and add yourself to the authors list
• [X] 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!

:heart:

Summary by CodeRabbit

• New Features

  • Added a new channel sleap-deps for package management.
  • Enhanced lazy loading for OpenCV to improve performance.
  • Introduced a confirmation step for replacing missing file paths in dialogs.
  • Added new command-line arguments for training configuration.
  • Improved video management with additional assertions in tests.

• Bug Fixes

  • Improved handling of unsaved changes when closing the application.

• Documentation

  • Updated version numbers in installation instructions and documentation files.

• Refactor

  • Updated TensorFlow API usage for parallel processing across various classes.
  • Restructured instance and image management in the tracking process.

• Version Updates

  • Updated package version from 1.4.1a2 to 1.4.1a3.

[coderabbitai[bot]]

Walkthrough

This pull request updates multiple configuration and dependency files, GitHub workflows, environment activation/deactivation scripts, and tests. It revises dependency channels and version constraints, updates Python versions to 3.10, and refactors scripts to set and restore environment variables. Additionally, many modules now use lazy loading for libraries such as OpenCV, and several GUI control flows—such as close event handling—have been refined with added confirmation dialogs. Various test assertions were also updated for consistency.

Changes

File(s)	Change Summary
.conda_mac/condarc.yaml, .conda/condarc.yaml	Updated channel configuration: added sleap-deps, removed/re-ordered channels.
environment.yml, environment_mac.yml, environment_no_cuda.yml, .conda/meta.yaml, .conda_mac/meta.yaml, pypi_requirements.txt, dev_requirements.txt, requirements.txt	Revised dependency channels and version constraints; updated library versions (e.g., Python, TensorFlow, numpy, pyside); added new dependencies and adjusted formatting.
.github/workflows/*.yml (e.g. build_manual.yml, ci.yml, build.yml, build_pypi_ci.yml, website.yml)	Updated Python version to 3.10; restructured job steps, added dependency installation (e.g., OpenGL libraries, ffmpeg); expanded trigger paths and OS matrices.
.conda/sleap_activate.*, .conda/sleap_deactivate.*, .conda_mac/sleap_activate.sh, .conda_mac/sleap_deactivate.sh, .conda/bld.bat	Enhanced activation/deactivation scripts to set and restore environment variables (e.g., XLA_FLAGS, NO_ALBUMENTATIONS_UPDATE) and copy scripts for proper environment setup.
sleap/io/videowriter.py, sleap/gui/dialogs/importvideos.py, sleap/nn/tracking.py, sleap/io/video.py, tests/io/test_videowriter.py, tests/io/test_visuals.py	Replaced direct cv2 (and other module) imports with lazy loading via lazy_loader to defer heavy imports.
Various sleap/* modules (e.g., __init__.py, gui/app.py, gui/commands.py, gui/dialogs/missingfiles.py, gui/widgets/video.py, sleap/skeleton.py)	Reorganized import orders, enhanced control flows (e.g., confirmation dialogs on close events), and updated error handling and cleanup procedures.
Multiple files under sleap/nn/data/* (e.g., confidence_maps.py, dataset_ops.py, edge_maps.py, general.py, grouping.py, identity.py, inference.py, instance_centroids.py, instance_cropping.py, normalization.py, resizing.py)	Updated num_parallel_calls in tf.data.Dataset.map calls from tf.data.experimental.AUTOTUNE to tf.data.AUTOTUNE per TensorFlow API updates.
Test files under tests/* (e.g., test_skeleton.py, test_video.py, tests/gui/test_app.py)	Adjusted test assertions (e.g., replacing np.alltrue with np.all), updated lazy loading usage, and expanded test coverage for new GUI workflows.

Sequence Diagram(s)

sequenceDiagram
    participant U as User
    participant MW as MainWindow
    participant MB as QMessageBox
    U->>MW: Initiates close event
    MW->>MW: Check for unsaved changes
    alt Unsaved changes exist
        MW->>MB: Prompt user (Save / Discard / Cancel)
        MB-->>MW: User selection
        alt User selects Save
            MW->>MW: Save project
            MW->>MW: Proceed with cleanup
        else if User selects Discard
            MW->>MW: Proceed with cleanup
        else if User selects Cancel
            MW->>MW: Abort close event
        end
    else
        MW->>MW: Accept close event
    end
    MW->>MW: Call cleanup methods
    MW->>U: Close application

Suggested labels

MultiView Stack

Suggested reviewers

• roomrys
• talmo

Poem

Oh, how I hop with joyful code,
As channels shift in every node.
My lazy loads make modules glide,
In workflows where new steps reside.
With each refactor, bugs take flight –
A rabbit’s cheer in bytes so bright!
🐰 Happy coding through the night!

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• [ ] 📝 Generate Docstrings

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[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 75.62%. Comparing base (7ed1229) to head (c5e3ce8). Report is 56 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1841      +/-   ##
===========================================
+ Coverage    73.30%   75.62%   +2.31%     
===========================================
  Files          134      133       -1     
  Lines        24087    24626     +539     
===========================================
+ Hits         17658    18624     +966     
+ Misses        6429     6002     -427     

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