Update python versions and dependencies #1841

eberrigan · 2024-07-01T18:41:03Z

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.
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.

Types of changes

Does this address any currently open issues?

The Mac GUI is breaking in the latest pre-release No module named 'work' #1803, Scrolling to zoom crashing GUI in v1.4.1a1 #1802.
This is following up many dependency updates in pre-release v1.4.1a1.

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!

❤️

Summary by CodeRabbit

Dependency Updates
- Updated dependencies to support Python 3.10, including numpy, scipy, scikit-learn, and pyside6.
- Modified TensorFlow dependency to a newer version to reflect ongoing development changes.
- Added new dependencies for imageio and imageio-ffmpeg.
Environment Configuration
- Updated Conda environment files to ensure compatibility with Python 3.10 and the latest library versions. Added new channels, sleap-deps and sleap-deps/label/dev, for improved package management.
New Features
- Enhanced data visualization in the training monitor by switching from QtCharts to Matplotlib, improving user experience.

coderabbitai · 2024-07-01T18:41:10Z

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Walkthrough

The changes enhance the sleap project's compatibility with Python 3.10 across various configuration files. Key updates include modifying package versions, replacing pyside2 with pyside6, and introducing new dependencies like imageio. The addition of the sleap-deps channel improves package management and streamlines the development environment, promoting usability and functionality. Furthermore, the plotting mechanism has transitioned from QtCharts to Matplotlib for improved visualization.

Changes

File/Group	Change Summary
`.conda/...`, `.conda_mac/...`, `environment.yml`, `environment_mac.yml`, `environment_no_cuda.yml`, `.conda/meta.yaml`	Added `sleap-deps` channel; updated versions of `numpy`, `pyside6`, `scipy`, and `scikit-learn` for Python 3.10 compatibility. Included new dependencies like `imageio` and commented out outdated ones.
`.github/workflows/...`	Modified workflow triggers to include configuration files and updated Python version from 3.7/3.9 to 3.10 for compatibility across environments.
`sleap/gui/widgets/training_monitor.py`	Replaced QtCharts with Matplotlib for plotting, enhancing the visualization component of the application.
`sleap/io/videowriter.py`	Removed unnecessary import for `skvideo`, simplifying the `VideoWriterSkvideo` class.

Poem

In the meadow where code takes flight,
Python 3.10 gleams, oh what a sight!
With sleap-deps bringing new cheer,
Dependencies dance, our goals are clear.
Hoppy updates make our dreams come true,
A joyful journey, all thanks to you! 🐇✨

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codecov · 2024-07-11T00:54:32Z

Codecov Report

All modified and coverable lines are covered by tests ✅

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

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

In git we trust

…abeth/update-python-and-dependencies

Remove python version constraint (implicitly stated in environment yml)

PySide6 doesn't need this set and prints a warning message if it is set.

* Lower bound albumentation version to handle Nan keypoints * Reset tabwidth to 2 in environment ymls --------- Co-authored-by: Elizabeth <[email protected]>

eberrigan added 5 commits June 28, 2024 13:41

try python 3.12.x fpr mac conda build

5b080c7

try python 3.11.x for mac conda build

40c2802

trying 3.10.x for mac conda build

62bf16d

try python 3.11.x with scipy >=1.11.1

b4e5cf7

update windows dependencies python 3.9, pyside 6, scipy and numpy

0442139