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test: [Automatic] Constraints upgrades: imageio, napari, numpy, partsegcore-compiled-backend, pydantic, pygments, scipy, sentry-sdk, simpleitk, tifffile, xlsxwriter #1236

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merged 1 commit into from
Jan 27, 2025

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Czaki
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@Czaki Czaki commented Jan 13, 2025

This PR is automatically created and updated by PartSeg GitHub
action cron to keep bundle dependencies modules up to date.

The updated packages are:

  • attrs
  • cloudpickle
  • dask
  • debugpy
  • executing
  • imageio
  • importlib-metadata
  • napari
  • napari-svg
  • numpy
  • partsegcore-compiled-backend
  • prompt-toolkit
  • pydantic
  • pygments
  • pyinstaller-hooks-contrib
  • pyopengl
  • referencing
  • scikit-image
  • scipy
  • sentry-sdk
  • setuptools
  • simpleitk
  • tifffile
  • tomli-w
  • tzdata
  • wrapt
  • xlsxwriter

Summary by CodeRabbit

  • Dependencies
    • Updated multiple package versions across Python 3.9, 3.10, 3.11, and 3.12 constraint files
    • Minor version upgrades for libraries like numpy, scipy, napari, pydantic, and others
    • Incremental updates to improve package compatibility and potential bug fixes

@Czaki Czaki added the skip check PR title skip spellcheking PR title label Jan 13, 2025
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sourcery-ai bot commented Jan 13, 2025

Reviewer's Guide by Sourcery

This pull request updates the constraints files for various Python versions (3.9, 3.10, 3.11, and 3.12) and Pydantic versions. The updated packages include partsegcore-compiled-backend, pydantic, pygments, scipy, setuptools, tifffile, and wrapt.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change Details Files
Updated constraints for Python 3.9
  • Updated partsegcore-compiled-backend constraint.
  • Updated pydantic constraint.
  • Updated pygments constraint.
  • Updated scipy constraint.
  • Updated setuptools constraint.
  • Updated tifffile constraint.
  • Updated wrapt constraint.
requirements/constraints_py3.9.txt
requirements/constraints_py3.9_pydantic_1.txt
Updated constraints for Python 3.10
  • Updated partsegcore-compiled-backend constraint.
  • Updated pydantic constraint.
  • Updated pygments constraint.
  • Updated scipy constraint.
  • Updated setuptools constraint.
  • Updated tifffile constraint.
  • Updated wrapt constraint.
requirements/constraints_py3.10.txt
requirements/constraints_py3.10_pydantic_1.txt
Updated constraints for Python 3.11
  • Updated partsegcore-compiled-backend constraint.
  • Updated pydantic constraint.
  • Updated pygments constraint.
  • Updated scipy constraint.
  • Updated setuptools constraint.
  • Updated tifffile constraint.
  • Updated wrapt constraint.
requirements/constraints_py3.11.txt
requirements/constraints_py3.11_pydantic_1.txt
Updated constraints for Python 3.12
  • Updated partsegcore-compiled-backend constraint.
  • Updated pydantic constraint.
  • Updated pygments constraint.
  • Updated scipy constraint.
  • Updated setuptools constraint.
  • Updated tifffile constraint.
  • Updated wrapt constraint.
requirements/constraints_py3.12.txt
requirements/constraints_py3.12_docs.txt
requirements/constraints_py3.12_pydantic_1.txt

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coderabbitai bot commented Jan 13, 2025

Walkthrough

This pull request involves systematic updates to dependency versions across multiple Python version-specific constraint files. The changes are consistent across different Python version configurations (3.9, 3.10, 3.11, 3.12) and include both Pydantic version 1 and version 2 constraint files. The updates primarily involve minor version increments for packages like attrs, cloudpickle, dask, debugpy, executing, imageio, importlib-metadata, napari, napari-svg, numpy, partsegcore-compiled-backend, pydantic, pygments, pyinstaller-hooks-contrib, pyopengl, referencing, scikit-image, scipy, sentry-sdk, setuptools, simpleitk, tifffile, tomli-w, wrapt, and tzdata. Some Python 3.12 specific files also include updates to shiboken6.

Changes

File Changes
requirements/constraints_py3.9.txt
requirements/constraints_py3.9_pydantic_1.txt
requirements/constraints_py3.10.txt
requirements/constraints_py3.10_pydantic_1.txt
requirements/constraints_py3.11.txt
requirements/constraints_py3.11_pydantic_1.txt
requirements/constraints_py3.12.txt
requirements/constraints_py3.12_pydantic_1.txt
requirements/constraints_py3.12_docs.txt
Updated versions for multiple packages:
- attrs: 24.3.0 → 25.1.0
- cloudpickle: 3.1.0 → 3.1.1
- dask: 2024.12.1 → 2025.1.0
- debugpy: 1.8.11 → 1.8.12
- executing: 2.1.0 → 2.2.0
- imageio: 2.36.1 → 2.37.0
- importlib-metadata: 8.5.0 → 8.6.1
- napari: 0.5.5 → 0.5.6
- napari-svg: 0.2.0 → 0.2.1
- numpy: 2.2.1 → 2.2.2
- partsegcore-compiled-backend: 0.15.8 → 0.15.9
- pydantic: 1.10.19 → 1.10.21 (in Pydantic 1 files)
- pygments: 2.19.0 → 2.19.1
- pyinstaller-hooks-contrib: 2024.11 → 2025.0
- pyopengl: 3.1.7 → 3.1.9
- referencing: 0.35.1 → 0.36.2
- scikit-image: 0.25.0 → 0.25.1
- scipy: 1.15.0 → 1.15.1
- sentry-sdk: 2.19.2 → 2.20.0
- setuptools: 75.7.0 → 75.8.0
- shiboken6: 6.8.1 → 6.8.1.1 (in Python 3.12 files)
- simpleitk: 2.4.0 → 2.4.1
- tifffile: 2024.12.12 → 2025.1.10
- tomli-w: 1.1.0 → 1.2.0
- wrapt: 1.17.0 → 1.17.2
- tzdata: 2024.2 → 2025.1
- xlsxwriter: 3.2.0 → 3.2.1

Poem

🐰 Dependency Dance, a Rabbit's Delight
Versions bump up, oh so light
Packages twirl, a semantic flight
From 3.1.0 to 3.1.1 we go
Constraints updated, ready to grow! 🚀


📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 32935a5 and dea207a.

📒 Files selected for processing (9)
  • requirements/constraints_py3.10.txt (19 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (19 hunks)
  • requirements/constraints_py3.11.txt (18 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (18 hunks)
  • requirements/constraints_py3.12.txt (17 hunks)
  • requirements/constraints_py3.12_docs.txt (17 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (17 hunks)
  • requirements/constraints_py3.9.txt (18 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (18 hunks)
🚧 Files skipped from review as they are similar to previous changes (9)
  • requirements/constraints_py3.9.txt
  • requirements/constraints_py3.10.txt
  • requirements/constraints_py3.12_docs.txt
  • requirements/constraints_py3.12_pydantic_1.txt
  • requirements/constraints_py3.11.txt
  • requirements/constraints_py3.11_pydantic_1.txt
  • requirements/constraints_py3.9_pydantic_1.txt
  • requirements/constraints_py3.10_pydantic_1.txt
  • requirements/constraints_py3.12.txt
⏰ Context from checks skipped due to timeout of 300000ms (28)
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  • GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
  • GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
  • GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
  • GitHub Check: Base py3.12 / macos-14 py 3.12 latest PyQt6
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  • GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
  • GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
  • GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
  • GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
  • GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
  • GitHub Check: Test PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
  • GitHub Check: Test PartSeg conda
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  • GitHub Check: 4DNucleome.PartSeg (Documentation_check Notebook_check)
  • GitHub Check: 4DNucleome.PartSeg (formatting_check check_formating)
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Hey @Czaki - I've reviewed your changes and they look great!

Here's what I looked at during the review
  • 🟢 General issues: all looks good
  • 🟢 Security: all looks good
  • 🟢 Testing: all looks good
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good

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Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: partsegcore-compiled-backend, pydantic, pygments, scipy, tifffile test: [Automatic] Constraints upgrades: imageio, numpy, partsegcore-compiled-backend, pydantic, pygments, scipy, sentry-sdk, simpleitk, tifffile Jan 20, 2025
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from a697eea to 32935a5 Compare January 20, 2025 08:17
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codecov bot commented Jan 20, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.16%. Comparing base (a1c5879) to head (dea207a).
Report is 1 commits behind head on develop.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1236      +/-   ##
===========================================
+ Coverage    93.14%   93.16%   +0.01%     
===========================================
  Files          210      210              
  Lines        33268    33268              
===========================================
+ Hits         30989    30994       +5     
+ Misses        2279     2274       -5     

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

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, numpy, partsegcore-compiled-backend, pydantic, pygments, scipy, sentry-sdk, simpleitk, tifffile test: [Automatic] Constraints upgrades: imageio, napari, numpy, partsegcore-compiled-backend, pydantic, pygments, scipy, sentry-sdk, simpleitk, tifffile, xlsxwriter Jan 27, 2025
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 32935a5 to dea207a Compare January 27, 2025 08:17
@Czaki Czaki added this to the 0.16.1 milestone Jan 27, 2025
@Czaki Czaki merged commit cb68e74 into develop Jan 27, 2025
59 checks passed
@Czaki Czaki deleted the auto-dependency-upgrades branch January 27, 2025 08:48
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