8000 test: [Automatic] Constraints upgrades: `imagecodecs`, `ipython`, `pydantic`, `sentry-sdk`, `superqt`, `tifffile` by Czaki · Pull Request #1255 · 4DNucleome/PartSeg · GitHub
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test: [Automatic] Constraints upgrades: imagecodecs, ipython, pydantic, sentry-sdk, superqt, tifffile #1255

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Merged
merged 2 commits into from
Apr 14, 2025

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Czaki
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@Czaki Czaki commented Mar 24, 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:

  • coverage
  • dask
  • debugpy
  • fsspec
  • imagecodecs
  • iniconfig
  • ipython
  • lxml
  • lxml-html-clean
  • pillow
  • platformdirs
  • pydantic
  • pydantic-core
  • pyinstaller-hooks-contrib
  • pyqt6
  • pyqt6-qt6
  • pytz
  • pyzmq
  • rich
  • rpds-py
  • sentry-sdk
  • setuptools
  • superqt
  • tifffile
  • typing-extensions
  • typing-inspection
  • tzdata
  • urllib3

Summary by CodeRabbit

  • Chores
    • Performed maintenance updates to numerous package dependencies across all supported configurations to help enhance stability, performance, and compatibility.
    • Introduced a new dependency to support improved type inspection.

@Czaki Czaki added the skip check PR title skip spellcheking PR title label Mar 24, 2025
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sourcery-ai bot commented Mar 24, 2025

Reviewer's Guide by Sourcery

This pull request updates constraint files for various Python versions and configurations, upgrading packages like coverage, dask, iniconfig, platformdirs, pyinstaller-hooks-contrib, sentry-sdk, setuptools, superqt, and tzdata to their latest compatible versions.

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

File-Level Changes

Change Details Files
Updates package versions in constraint files for Python 3.9 with and without Pydantic 1.
  • Updates package versions in constraints_py3.9.txt.
  • Updates package versions in constraints_py3.9_pydantic_1.txt.
requirements/constraints_py3.9.txt
requirements/constraints_py3.9_pydantic_1.txt
Updates package versions in constraint files for Python 3.10 with and without Pydantic 1.
  • Updates package versions in constraints_py3.10.txt.
  • Updates package versions in constraints_py3.10_pydantic_1.txt.
requirements/constraints_py3.10.txt
requirements/constraints_py3.10_pydantic_1.txt
Updates package versions in constraint files for Python 3.11 with and without Pydantic 1.
  • Updates package versions in constraints_py3.11.txt.
  • Updates package versions in constraints_py3.11_pydantic_1.txt.
requirements/constraints_py3.11.txt
requirements/constraints_py3.11_pydantic_1.txt
Updates package versions in constraint files for Python 3.12 with and without Pydantic 1, and for documentation.
  • Updates package versions in constraints_py3.12.txt.
  • Updates package versions in constraints_py3.12_docs.txt.
  • Updates package versions in constraints_py3.12_pydantic_1.txt.
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 Mar 24, 2025

Walkthrough

This pull request updates the version numbers of several dependencies across multiple requirements files for different Python versions. The updates cover files for standard, pydantic, and documentation configurations. Most files receive updates for packages such as coverage, dask, iniconfig, platformdirs, pyinstaller-hooks-contrib, sentry-sdk, setuptools, superqt, and tzdata, while a couple of files (e.g., for Python 3.9 and docs) have a subset of these updates. These changes serve as maintenance updates to keep the projects’ dependencies current.

Changes

Files Change Summary
requirements/constraints_py3.10(.txt, _pydantic_1.txt), requirements/constraints_py3.11(.txt, _pydantic_1.txt), requirements/constraints_py3.12(.txt, _pydantic_1.txt) Updated: coverage 7.7.0 → 7.8.0, dask 2025.2.0 → 2025.3.0, debugpy 1.8.13 → 1.8.14, fsspec 2025.3.0 → 2025.3.2, imagecodecs 2024.12.30 → 2025.3.30, iniconfig 2.0.0 → 2.1.0, ipython 8.34.0 → 8.35.0, lxml 5.3.1 → 5.3.2, lxml-html-clean 0.4.1 → 0.4.2, pillow 11.1.0 → 11.2.1, platformdirs 4.3.6 → 4.3.7, pydantic 2.10.6 → 2.11.3, pydantic-core 2.27.2 → 2.33.1, pyinstaller-hooks-contrib 2025.1 → 2025.2, pyqt6 6.8.1 → 6.9.0, pyqt6-qt6 6.8.2 → 6.9.0, pytz 2025.1 → 2025.2, pyzmq 26.3.0 → 26.4.0, rich 13.9.4 → 14.0.0, rpds-py 0.23.1 → 0.24.0, sentry-sdk 2.22.0 → 2.25.1, setuptools 76.0.0 → 78.1.0, superqt 0.7.1 → 0.7.3, tifffile 2025.3.13 → 2025.3.30, typing-extensions 4.12.2 → 4.13.2, tzdata 2025.1 → 2025.2, New: typing-inspection 0.4.0
requirements/constraints_py3.9(.txt, _pydantic_1.txt) Updated: coverage 7.7.0 → 7.8.0, debugpy 1.8.13 → 1.8.14, fsspec 2025.3.0 → 2025.3.2, iniconfig 2.0.0 → 2.1.0, lxml 5.3.1 → 5.3.2, lxml-html-clean 0.4.1 → 0.4.2, pillow 11.1.0 → 11.2.1, platformdirs 4.3.6 → 4.3.7, pydantic 2.10.6 → 2.11.3, pydantic-core 2.27.2 → 2.33.1, pyinstaller-hooks-contrib 2025.1 → 2025.2, pyqt6 6.8.1 → 6.9.0, pyqt6-qt6 6.8.2 → 6.9.0, pytz 2025.1 → 2025.2, pyzmq 26.3.0 → 26.4.0, rich 13.9.4 → 14.0.0, rpds-py 0.23.1 → 0.24.0, sentry-sdk 2.22.0 → 2.25.1, setuptools 76.0.0 → 78.1.0, superqt 0.7.1 → 0.7.3, typing-extensions 4.12.2 → 4.13.2, New: typing-inspection 0.4.0, tzdata 2025.1 → 2025.2
requirements/constraints_py3.12_docs.txt Updated: dask 2025.2.0 → 2025.3.0, debugpy 1.8.13 → 1.8.14, fsspec 2025.3.0 → 2025.3.2, imagecodecs 2024.12.30 → 2025.3.30, ipython 9.0.2 → 9.1.0, pillow 11.1.0 → 11.2.1, platformdirs 4.3.6 → 4.3.7, pydantic 2.10.6 → 2.11.3, pydantic-core 2.27.2 → 2.33.1, pyqt6 6.8.1 → 6.9.0, pyqt6-qt6 6.8.2 → 6.9.0, python-dotenv 1.0.1 → 1.1.0, pytz 2025.1 → 2025.2, pyzmq 26.3.0 → 26.4.0, rich 13.9.4 → 14.0.0, rpds-py 0.23.1 → 0.24.0, sentry-sdk 2.22.0 → 2.25.1, superqt 0.7.1 → 0.7.3, tifffile 2025.3.13 → 2025.3.30, typing-extensions 4.12.2 → 4.13.2, tzdata 2025.1 → 2025.2, New: typing-inspection 0.4.0

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I'm a bunny coder with a joyful heart,
Hopping through dependencies with a brand-new start.
My carrots (dependencies) now shine so bright,
With updates in versions, my code feels light.
Each package upgraded is a leap so grand—
A hop, a nibble, a dance, as I cheer in rabbit land!

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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 force-pushed the auto-dependency-upgrades branch from c37f640 to 5767104 Compare March 31, 2025 08:19
@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: sentry-sdk, superqt test: [Automatic] Constraints upgrades: imagecodecs, pydantic, sentry-sdk, superqt, tifffile Mar 31, 2025
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Actionable comments posted: 0

🧹 Nitpick comments (8)
requirements/constraints_py3.9.txt (2)

43-527: Dependency Version Bumps are Consistent
The updated versions for key packages such as “coverage”, “fsspec”, “iniconfig”, “platformdirs”, “pyinstaller-hooks-contrib”, “imagecodecs”, “sentry-sdk”, “setuptools”, “superqt”, “typing-extensions”, “tzdata”, and the addition of “typing-inspection==0.4.0” are in line with the coordinated maintenance update.

🧰 Tools
🪛 LanguageTool

[duplication] ~150-~150: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.1 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~287-~287: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~423-~423: Possible typo: you repeated a word.
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.4.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)


504-504: Duplicate 'typing-inspection' Entry Detected
Static analysis indicates that the dependency “typing-inspection==0.4.0” appears twice (e.g. “typing-inspection typing-inspection==0.4.0”) near the end of the file. Please review and remove any redundant occurrence to avoid confusion.

🧰 Tools
🪛 LanguageTool

[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt (2)

43-349: Upgraded Dependency Versions are Correct
The file updates several packages (for example, “dask” to 2025.3.0, “imagecodecs” to 2025.3.30, “iniconfig” to 2.1.0, “pydantic” to 2.11.1, “pydantic-core” to 2.33.0, etc.) in a manner consistent with other constraints files. These changes support compatibility across Python 3.11 environments.

🧰 Tools
🪛 LanguageTool

[duplication] ~142-~142: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.1 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~279-~279: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

(ENGLISH_WORD_REPEAT_RULE)


490-490: Possible Duplicate Text for 'typing-inspection'
A duplicate mention of “typing-inspection==0.4.0” appears to be present in the tail of the file. Please double-check if one instance should be removed.

🧰 Tools
🪛 LanguageTool

[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_docs.txt (1)

440-442: Recheck Duplicate 'typing-inspection' Entry
Static analysis flagged a duplicate entry for “typing-inspection==0.4.0.” Please inspect these lines (around ~441) in the autogenerated file and remove any unintentional repetition.

🧰 Tools
🪛 LanguageTool

[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10.txt (1)

490-492: Duplicate 'typing-inspection' Warning
A repeated occurrence of “typing-inspection==0.4.0” has been observed. Please verify whether the duplicate text is needed or if one instance should be removed.

requirements/constraints_py3.12.txt (2)

43-508: Comprehensive Version Bumps Across Dependencies
The file shows updates for many dependencies—including the important ones like “pydantic”, “pydantic-core”, “pyinstaller-hooks-contrib”, “pyside6” (now upgraded to 6.8.3), “tifffile”, and more—which are now in line with the latest available releases. Overall, the changes are consistent across the different constraint files.

🧰 Tools
🪛 LanguageTool

[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.1 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~277-~277: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~414-~414: Possible typo: you repeated a word.
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==8.2.3 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)


486-488: Address Duplicate Text for 'typing-inspection'
Static analysis hints at a potential duplicate line for “typing-inspection==0.4.0” (i.e. the word “typing-inspection” appears twice consecutively before the version spec). Please review and remove the redundant text if it is not intentional.

🧰 Tools
🪛 LanguageTool

[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

📜 Review details

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

📥 Commits

Reviewing files that changed from the base of the PR and between c37f640 and 5767104.

📒 Files selected for processing (9)
  • requirements/constraints_py3.10.txt (15 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (13 hunks)
  • requirements/constraints_py3.11.txt (15 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (13 hunks)
  • requirements/constraints_py3.12.txt (16 hunks)
  • requirements/constraints_py3.12_docs.txt (13 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (14 hunks)
  • requirements/constraints_py3.9.txt (13 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (11 hunks)
🚧 Files skipped from review as they are similar to previous changes (4)
  • 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_pydantic_1.txt
🧰 Additional context used
🪛 LanguageTool
requirements/constraints_py3.10.txt

[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt

[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt

[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_docs.txt

[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9.txt

[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

⏰ Context from checks skipped due to timeout of 300000ms (27)
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  • GitHub Check: 4DNucleome.PartSeg (Builds sdist)
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  • GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
  • GitHub Check: Base py3.11 / windows-latest py 3.11 latest PyQt5
  • GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
  • GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
  • GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
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  • GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
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  • GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
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  • 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
  • GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
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  • GitHub Check: 4DNucleome.PartSeg (Documentation_check help)
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🔇 Additional comments (2)
requirements/constraints_py3.12_docs.txt (1)

45-72: Documentation Constraints: Versions Updated Properly
All version bumps (including updates for “dask”, “fsspec”, “imagecodecs”, “platformdirs”, etc.) are updated to their latest releases. This helps ensure the docs build uses the current dependencies.

requirements/constraints_py3.10.txt (1)

43-104: Dependency Updates on Python 3.10 Constraints are Consistent
The version changes (e.g. “coverage” to 7.8.0, “dask” to 2025.3.0, “iniconfig” to 2.1.0, etc.) appear well coordinated with the other Python version constraints.

@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 5767104 to 91123be Compare April 7, 2025 08:19
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Actionable comments posted: 0

🧹 Nitpick comments (2)
requirements/constraints_py3.12_docs.txt (1)

440-443: Remove Duplicate Typing-Inspection Entry

Static analysis indicates that the dependency "typing-inspection==0.4.0" may be declared twice in this file. Please verify this occurrence and remove any duplicate to avoid redundancy.

🧰 Tools
🪛 LanguageTool

[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt (1)

480-488: Eliminate Duplicate Typing-Inspection Declaration

Static analysis highlights a potential duplicate occurrence of "typing-inspection==0.4.0". To maintain clarity and avoid redundancy in the constraints file, please confirm this entry and remove any duplicate if present.

🧰 Tools
🪛 LanguageTool

[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

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📒 Files selected for processing (9)
  • requirements/constraints_py3.10.txt (16 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (14 hunks)
  • requirements/constraints_py3.11.txt (16 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (14 hunks)
  • requirements/constraints_py3.12.txt (17 hunks)
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  • requirements/constraints_py3.9.txt (14 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (12 hunks)
🚧 Files skipped from review as they are similar to previous changes (4)
  • requirements/constraints_py3.9_pydantic_1.txt
  • requirements/constraints_py3.11_pydantic_1.txt
  • requirements/constraints_py3.10_pydantic_1.txt
  • requirements/constraints_py3.12_pydantic_1.txt
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🪛 LanguageTool
requirements/constraints_py3.10.txt

[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt

[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt

[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_docs.txt

[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9.txt

[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

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🔇 Additional comments (5)
requirements/constraints_py3.12_docs.txt (1)

40-50: Dependency Version Increments Consistency

All updated dependency versions—such as
• dask==2025.3.0,
• fsspec==2025.3.2,
• imagecodecs==2025.3.30,
• pydantic==2.11.2,
• pydantic-core==2.33.1,
• python-dotenv==1.1.0,
• pytz==2025.2,
• pyzmq==26.4.0,
• rich==14.0.0,
• rpds-py==0.24.0,
• sentry-sdk==2.25.1,
• superqt==0.7.3, and
• tifffile==2025.3.30
—have been upgraded in line with our dependency-maintenance objectives. Please double-check that these new versions are fully compatible with the rest of the project.

requirements/constraints_py3.9.txt (1)

42-50: Version Bump Review for Python 3.9 Constraints

The file now shows consistent dependency version updates—for example, coverage has been bumped to 7.8.0, fsspec to 2025.3.2, iniconfig to 2.1.0, and lxml to 5.3.2. These adjustments match the coordinated upgrade plan. Please ensure compatibility with other parts of the project.

requirements/constraints_py3.11.txt (1)

41-50: Dependencies Updates Consistency in Python 3.11

The updated versions for dependencies—including dask, fsspec, imagecodecs, pydantic, and others—are accurate and in line with our overall upgrade strategy. Confirm that these increments meet the compatibility requirements for the 3.11 environment.

requirements/constraints_py3.10.txt (1)

1-10: Coherent Dependency Updates for Python 3.10

This file reflects the coordinated version bumps (coverage, dask, fsspec, imagecodecs, iniconfig, etc.) seen across our constraint files. All changes appear coherent with the PR objectives.

requirements/constraints_py3.12.txt (1)

40-50: Comprehensive Version Upgrade Check for Python 3.12

The dependency updates in this file are consistent with our overall strategy. Notably, the upgrades for packages such as pyside6 (from 6.8.2.1 to 6.9.0) and shiboken6 (from 6.8.2.1 to 6.9.0) have been applied alongside the other coordinated version increments. Please verify that these new versions integrate smoothly with your project.

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imagecodecs, pydantic, sentry-sdk, superqt, tifffile test: [Automatic] Constraints upgrades: imagecodecs, ipython, pydantic, sentry-sdk, superqt, tifffile Apr 14, 2025
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 91123be to cfdda70 Compare April 14, 2025 08:19
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🧹 Nitpick comments (11)
requirements/constraints_py3.9_pydantic_1.txt (1)

147-147: Duplication Warning in Comment Block
Static analysis flagged a possible duplicate wording for the lxml-html-clean dependency (around line 147). Since this file is auto-generated, if this redundancy is expected from the tool, you may ignore it; otherwise, consider cleaning up the duplicated text for clarity.

requirements/constraints_py3.12_docs.txt (1)

441-441: Duplication in Typing-Inspection Entry
A static analysis warning indicates a potential duplicate of “typing-inspection” on or around line 441. If this duplication is an artifact of the auto-generation process, it may be safe to ignore; otherwise, consider removing the redundant text to improve readability.

🧰 Tools
🪛 LanguageTool

[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_pydantic_1.txt (1)

138-138: Duplicate Wording in Lxml-html-clean Entry
Static analysis notes a possible duplicate word in the comment associated with the lxml-html-clean dependency around line 138. Review this duplication and remove the extra wording if it isn’t intentional.

🧰 Tools
🪛 LanguageTool

[duplication] ~138-~138: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9.txt (2)

150-150: Duplication Alert: lxml-html-clean Entry
A static analysis warning shows a possible duplicate in the lxml-html-clean entry at line 150. Confirm whether this duplication is necessary due to auto-generation or if it should be manually cleaned up.

🧰 Tools
🪛 LanguageTool

[duplication] ~150-~150: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


504-504: Duplication Alert in Typing-Inspection Entry
The entry for typing-inspection appears to be duplicated at line 504. Please verify if this is intended by the auto-generation process or if it should be corrected.

🧰 Tools
🪛 LanguageTool

[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt (1)

490-490: Duplication in Typing-Inspection Entry
A static analysis warning indicates a repeated wording in the typing-inspection entry on line 490. Please review and adjust if this repetition is not intentional.

🧰 Tools
🪛 LanguageTool

[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10_pydantic_1.txt (1)

141-145: [Static Analysis] Possible Duplicate Comment for lxml-html-clean
A static analysis warning indicates a duplicate or redundant reference near the lxml-html-clean==0.4.2 declaration. This appears in the commented lines preceding the dependency. Please review whether the repeated phrase is an artifact of auto-generation and if it can be cleaned up for clarity.

🧰 Tools
🪛 LanguageTool

[duplication] ~144-~144: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11_pydantic_1.txt (1)

137-141: [Static Analysis] Possible Duplicate Comment in lxml-html-clean Section
Similar to the previous constraints file, there is a possible duplicate mention in the lxml/html-clean comments. As this file is auto-generated, consider verifying if the duplication can be suppressed or cleaned up to improve readability.

🧰 Tools
🪛 LanguageTool

[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10.txt (2)

146-146: [Static Analysis] Duplicate Comment in lxml-html-clean Section
Static analysis flagged a possible duplicate in the commentary preceding lxml-html-clean==0.4.2. Please review to see if this repetition can be tidied up even if it is auto-generated.

🧰 Tools
🪛 LanguageTool

[duplication] ~146-~146: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


500-500: [Static Analysis] Duplicate Expression in Typing-Inspection Section
There is a warning about a duplicated phrase near the typing-inspection declaration. It may be a false positive due to auto-generation; please verify and adjust if necessary for clarity.

🧰 Tools
🪛 LanguageTool

[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt (1)

486-486: [Static Analysis] Possible Duplicate Expression in Typing-Inspection Section
A static analysis warning flags a duplicate phrase near the typing-inspection block. Although auto-generated content can be noisy, please review whether this repetition should be addressed to improve clarity.

🧰 Tools
🪛 LanguageTool

[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

📜 Review details

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

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Reviewing files that changed from the base of the PR and between 91123be and cfdda70.

📒 Files selected for processing (9)
  • requirements/constraints_py3.10.txt (16 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (14 hunks)
  • requirements/constraints_py3.11.txt (16 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (14 hunks)
  • requirements/constraints_py3.12.txt (16 hunks)
  • requirements/constraints_py3.12_docs.txt (14 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (14 hunks)
  • requirements/constraints_py3.9.txt (14 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (12 hunks)
🧰 Additional context used
🪛 LanguageTool
requirements/constraints_py3.10.txt

[duplication] ~146-~146: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10_pydantic_1.txt

[duplication] ~144-~144: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt

[duplication] ~142-~142: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11_pydantic_1.txt

[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt

[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_docs.txt

[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_pydantic_1.txt

[duplication] ~138-~138: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9.txt

[duplication] ~150-~150: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)


[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~148-~148: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...

(ENGLISH_WORD_REPEAT_RULE)

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🔇 Additional comments (37)
requirements/constraints_py3.9_pydantic_1.txt (1)

41-47: Dependency Version Updates and Consistency Check
All dependency versions (e.g., coverage==7.8.0, debugpy==1.8.14, fsspec==2025.3.2, iniconfig==2.1.0) have been updated in accordance with the latest releases. Please verify that these updates do not introduce conflicts with other parts of the dependency graph.

Also applies to: 73-92

requirements/constraints_py3.12_docs.txt (1)

45-50: Dependency Updates and New Additions Verification
The dependency versions have been updated (for example, dask==2025.3.0, debugpy==1.8.14, fsspec==2025.3.2, and imagecodecs==2025.3.30). Also, note the update of python-dotenv to 1.1.0. These changes look consistent with similar updates in other constraint files. Please double-check that these versions are compatible with your docs build process.

Also applies to: 70-82

requirements/constraints_py3.12_pydantic_1.txt (1)

41-47: Pydantic Constraint File Update Verification
The file correctly updates key dependencies for the Pydantic 1 constraints (e.g., pydantic==2.11.3 and pydantic-core==2.33.1). Please ensure these constraints are compatible with downstream use as defined in requirements/pydantic_1.txt.

Also applies to: 65-75

requirements/constraints_py3.9.txt (1)

41-50: Python 3.9 Dependency Constraint Updates
The file now reflects up-to-date dependency versions (for instance, coverage==7.8.0, iniconfig==2.1.0, and pillow==11.2.1). These updates appear consistent with similar constraint files. Please just verify that the updated versions work harmoniously within your environment.

Also applies to: 73-80, 106-112

requirements/constraints_py3.11.txt (1)

41-50: Python 3.11 Dependency Constraint Updates
The dependency versions (e.g., coverage==7.8.0, dask==2025.3.0, debugpy==1.8.14, fsspec==2025.3.2, and others) have been updated consistently. This supports maintained compatibility across different Python versions. A quick integration test is recommended to ensure no unexpected conflicts arise.

Also applies to: 73-80, 95-102

requirements/constraints_py3.10_pydantic_1.txt (6)

41-41: [Dependency Update] Coverage Version Change
The file updates coverage from 7.7.0 to 7.8.0. Please verify that this new version is compatible with our existing tooling and that no unexpected breaking changes are introduced.


45-45: [Dependency Update] Dask Version Change
dask has been updated to 2025.3.0. Confirm that any functionality relying on Dask’s APIs remains stable after this update.


47-47: [Dependency Update] Debugpy Update
The update to debugpy==1.8.14 appears to be routine. Please check that debugging integrations (e.g. with ipykernel) are not adversely affected.


73-73: [Dependency Update] fsspec Version Update
The new version fsspec==2025.3.2 is now in use. It’s important to ensure that file system operations in Dask or related data workflows continue to operate correctly.


83-83: [Dependency Update] imagecodecs Updated
imagecodecs has been updated to 2025.3.30. Please verify this version provides the required performance and compatibility, especially if image processing bugs were previously reported.


100-100: [Dependency Update] iniconfig Version Change
The upgrade to iniconfig==2.1.0 seems standard. Confirm that configuration parsing in our tests (and any other tooling using this package) remains correct.

requirements/constraints_py3.11_pydantic_1.txt (7)

41-41: [Dependency Update] Coverage Version Update
The update to coverage==7.8.0 looks correct. Please double-check compatibility with our test suites and reporting integrations.


45-45: [Dependency Update] Dask Version Change
dask is now set to 2025.3.0. Ensure that any parallel or delayed computations relying on Dask are thoroughly tested with this newer release.


47-47: [Dependency Update] Debugpy Updated
debugpy has been updated to 1.8.14. Please confirm that remote debugging and breakpoint functionality continue to operate as expected.


70-70: [Dependency Update] fsspec Version Update
The upgrade to fsspec==2025.3.2 is reflected here too. Verify that file system abstraction layers behave properly with this change.


79-79: [Dependency Update] imagecodecs Update
imagecodecs is now updated to 2025.3.30. Please check for any regressions in image I/O functions if they are actively used in our workflows.


94-94: [Dependency Update] iniconfig Version Change
The new version iniconfig==2.1.0 is now in place. Verify that our testing and configuration scripts using this library continue to parse configuration files accurately.


101-101: [Dependency Update] ipython Version Update
ipython has been updated to 9.1.0. Please review that the interactive shell and any IPython-dependent features (e.g. notebooks and qtconsole) are not disrupted by this change.

requirements/constraints_py3.10.txt (10)

43-43: [Dependency Update] Coverage Version Change
The change to coverage==7.8.0 is noted. Make sure that the newer version does not alter our coverage thresholds or reporting outputs unexpectedly.


47-47: [Dependency Update] Dask Update
dask is updated to 2025.3.0. Confirm that scheduling and task graph optimizations with this release meet our performance expectations.


49-49: [Dependency Update] Debugpy Version Change
The file now lists debugpy==1.8.14. Please review that this update does not break our debugging integrations in development and CI environments.


75-75: [Dependency Update] fsspec Version Update
The update to fsspec==2025.3.2 should be verified against any custom file-handling logic, especially in our Dask workflows.


85-85: [Dependency Update] imagecodecs Version Change
imagecodecs has been updated to 2025.3.30. Please ensure that any image I/O operations in the project function correctly with this change.


102-102: [Dependency Update] iniconfig Version Change
The update to iniconfig==2.1.0 is applied here. A quick validation for configuration parsing processes might be beneficial.


109-109: [Dependency Update] ipython Updated
ipython is now updated to version 8.35.0. Please verify that interactive sessions and any Jupyter integrations operate as expected.


240-240: [Dependency Update] Pillow Update
The upgrade to pillow==11.2.1 is included. Ensure that any image processing pipelines or thumbnail generators continue to work without regression.


247-247: [Dependency Update] Platformdirs Version Change
platformdirs is updated to 4.3.7. Verify that any filesystem or platform-specific configurations continue to be resolved correctly.


498-502: [New Dependency Addition] Typing-Inspection and Related Updates
A new dependency typing-inspection==0.4.0 has been added along with updates to tzdata and urllib3. Please confirm that these additions are required for compatibility with the updated Pydantic and that no conflicts arise in environments using dependency pinning.

🧰 Tools
🪛 LanguageTool

[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt (9)

43-43: [Dependency Update] Coverage Update
coverage==7.8.0 is now specified. As with other constraint files, confirm that our coverage collection and reporting remain consistent with this change.


47-47: [Dependency Update] Dask Version Change
The file updates dask to 2025.3.0. Please ensure that task scheduling and distributed computing features work as expected with this new version.


49-49: [Dependency Update] Debugpy Version Update
With debugpy==1.8.14 now included, it is advisable to confirm that all debugging and live inspection features remain operational.


71-71: [Dependency Update] fsspec Update
The new version fsspec==2025.3.2 appears here as well. Please test that any file system abstractions used (for example in Dask or other I/O operations) remain fully functional.


81-81: [Dependency Update] imagecodecs Upgrade
Updated to imagecodecs==2025.3.30—ensure any image handling routines are validated with the new release.


94-94: [Dependency Update] iniconfig Version Change
The upgrade to iniconfig==2.1.0 has been applied. A brief verification that our configuration parsers continue to behave normally is recommended.


101-101: [Dependency Update] ipython Update
ipython==9.1.0 is specified now. Please ensure that any interactive features (e.g. notebooks or qtconsole) are tested against this version.


271-280: [Dependency Update Group] Pydantic and Related Packages
The updates for pydantic==2.11.3, pydantic-compat==0.1.2, and pydantic-core==2.33.1 have been applied. These are critical for type validation and data parsing. It is essential to run a full test suite to ensure that changes in these libraries do not break our data models or API contracts.

🧰 Tools
🪛 LanguageTool

[duplication] ~277-~277: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

(ENGLISH_WORD_REPEAT_RULE)


308-316: [Dependency Update] PyQt6 and Pyside6 Updates
The updates to pyqt6==6.9.0, pyqt6-qt6==6.9.0 and the Pyside6 packages (including pyside6==6.9.0, pyside6-addons==6.9.0, and pyside6-essentials==6.9.0) are now present. Verify that these UI framework updates do not introduce regression in our QT-based interfaces.

@Czaki Czaki added this to the 0.16.2 milestone Apr 14, 2025
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@Czaki Czaki merged commit cc5e9fb into develop Apr 14, 2025
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@Czaki Czaki deleted the auto-dependency-upgrades branch April 14, 2025 21:10
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