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test: [Automatic] Constraints upgrades: pydantic #1112

Merged
merged 1 commit into from
Jul 6, 2024
Merged

test: [Automatic] Constraints upgrades: pydantic #1112

merged 1 commit into from
Jul 6, 2024

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Czaki
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@Czaki Czaki commented Jun 24, 2024 •
edited by coderabbitai bot
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This PR is automatically created and updated by PartSeg GitHub
action cron to keep bundle dependencies modules up to date.

The updated packages are:

  • certifi
  • dask
  • pydantic
  • pydantic-core
  • pyinstaller

Summary by CodeRabbit

  • Chores
    • Updated various package dependencies to their latest versions for Python 3.8, 3.9, 3.10, and 3.11 to ensure compatibility and improve performance.

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coderabbitai bot commented Jun 24, 2024 •
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Walkthrough

The recent updates include minor version increments for various Python package dependencies across multiple requirements files. The changes ensure compatibility and improvement in performance while addressing potential bug fixes. This concentrated refresh spans dependencies related to testing, image processing, data handling, and more.

Changes

Files Summary of Changes
requirements/constraints_py3.8.txt Updated versions: certifi, coverage, imageio, npe2, psutil, pyqt6-qt6, sentry-sdk, setuptools.
requirements/constraints_py3.9.txt Updated versions: coverage, dask, debugpy, docutils, fsspec, imageio, importlib-metadata, ipykernel, numpy, numpydoc, openpyxl, packaging, partd, pydantic, pyinstaller, pyopengl-accelerate, pyside2, pyside6, pytest, pytest-qt, pytest-timeout, scikit-image, sentry-sdk, setuptools, tifffile.
requirements/constraints_py3.10.txt Updated versions: certifi, dask, imageio, numpy, pydantic, pyinstaller, pyopengl-accelerate, pyqt6, pyside2, pyside6, pytest, pytest-qt, pytest-timeout, qtawesome, qtconsole, qtpy, requests, scikit-image, scipy, sentry-sdk, setuptools, simpleitk, superqt, sympy, tifffile.
requirements/constraints_py3.11.txt Updated versions: certifi, dask, coverage, imageio, numpy, scikit-image, scipy, and other dependencies added/updated via partseg (pyproject.toml).
requirements/constraints_py3.11_docs.txt Updated versions: certifi, dask, imageio, ipykernel, openpyxl, pydantic, and additional dependencies added via partseg (pyproject.toml).
requirements/constraints_py3.11_pydantic_1.txt Updated versions: certifi, dask, imageio, numpy, numpydoc, partd, pydantic, pyinstaller, pyopengl-accelerate, pyqt6, pytest, pytest-qt, pytest-timeout, setuptools, simpleitk, six, superqt, sympy, tifffile, and urllib3.

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In the forest of code so bright,
New versions dawn with morning light,
From certifi to pytest's cheer,
Bugs retreat, no need to fear.
Dependencies in harmony sway,
Let's code and dance, hip-hip-hooray! 🎉
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Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 111a131 and 055997f.

Files selected for processing (11)
  • requirements/constraints_py3.10.txt (9 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (10 hunks)
  • requirements/constraints_py3.11.txt (9 hunks)
  • requirements/constraints_py3.11_docs.txt (9 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (10 hunks)
  • requirements/constraints_py3.12.txt (8 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (9 hunks)
  • requirements/constraints_py3.8.txt (7 hunks)
  • requirements/constraints_py3.8_pydantic_1.txt (8 hunks)
  • requirements/constraints_py3.9.txt (9 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (10 hunks)
Files not reviewed due to errors (1)
  • requirements/constraints_py3.9_pydantic_1.txt (no review received)
Additional context used
LanguageTool
requirements/constraints_py3.11_docs.txt

[duplication] ~161-~161: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~236-~236: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # via # jupyter-core # pooch pooch==1.8.2 # via scikit-image prompt-to...

[duplication] ~389-~389: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...

requirements/constraints_py3.12_pydantic_1.txt

[duplication] ~137-~137: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~165-~165: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~276-~276: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~420-~420: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.12.txt

[duplication] ~139-~139: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~167-~167: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

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

[duplication] ~423-~423: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.11_pydantic_1.txt

[duplication] ~139-~139: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~167-~167: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~278-~278: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~422-~422: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.11.txt

[duplication] ~141-~141: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~169-~169: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

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

[duplication] ~425-~425: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~144-~144: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~172-~172: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~283-~283: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~427-~427: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.9.txt

[duplication] ~146-~146: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~174-~174: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~284-~284: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

[duplication] ~430-~430: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.10_pydantic_1.txt

[duplication] ~145-~145: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~173-~173: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~284-~284: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~428-~428: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.10.txt

[duplication] ~147-~147: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~175-~175: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~285-~285: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

[duplication] ~431-~431: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.8_pydantic_1.txt

[duplication] ~149-~149: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~177-~177: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~293-~293: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~441-~441: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...

requirements/constraints_py3.8.txt

[duplication] ~151-~151: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~179-~179: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~294-~294: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

[duplication] ~444-~444: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...

Additional comments not posted (122)
requirements/constraints_py3.11_docs.txt (14)

46-46: **** Updated version of dask to 2024.6.2.

84-84: **** Updated version of imageio to 2.34.2.

93-93: **** Updated version of importlib-metadata to 7.2.1.

170-170: **** Updated version of npe2 to 0.7.6.

241-241: **** Updated version of psutil to 6.0.0.

296-296: **** Updated version of pyqt6-qt6 to 6.7.2.

302-302: **** Updated version of pyside6 to 6.7.2.

304-304: **** Updated version of pyside6-addons to 6.7.2.

306-306: **** Updated version of pyside6-essentials to 6.7.2.

361-361: **** Updated version of scikit-image to 0.24.0.

368-368: **** Updated version of sentry-sdk to 2.6.0.

376-376: **** Updated version of shiboken6 to 6.7.2.

397-397: **** Updated version of sphinx-autodoc-typehints to 2.2.2.

424-424: **** Updated version of tifffile to 2024.6.18.

requirements/constraints_py3.12_pydantic_1.txt (15)

42-42: **** Updated version of coverage to 7.5.4.

46-46: **** Updated version of dask to 2024.6.2.

82-82: **** Updated version of imageio to 2.34.2.

174-174: **** Updated version of npe2 to 0.7.6.

252-252: **** Updated version of psutil to 6.0.0.

269-269: **** Updated version of pydantic to 1.10.17.

310-310: **** Updated version of pyqt6-qt6 to 6.7.2.

318-318: **** Updated version of pyside6 to 6.7.2.

322-322: **** Updated version of pyside6-addons to 6.7.2.

324-324: **** Updated version of pyside6-essentials to 6.7.2.

386-386: **** Updated version of scikit-image to 0.24.0.

395-395: **** Updated version of sentry-sdk to 2.6.0.

399-399: **** Updated version of setuptools to 70.1.0.

407-407: **** Updated version of shiboken6 to 6.7.2.

446-446: **** Updated version of tifffile to 2024.6.18.

requirements/constraints_py3.12.txt (14)

44-44: **** Updated version of coverage to 7.5.4.

48-48: **** Updated version of dask to 2024.6.2.

84-84: **** Updated version of imageio to 2.34.2.

176-176: **** Updated version of npe2 to 0.7.6.

254-254: **** Updated version of psutil to 6.0.0.

313-313: **** Updated version of pyqt6-qt6 to 6.7.2.

321-321: **** Updated version of pyside6 to 6.7.2.

325-325: **** Updated version of pyside6-addons to 6.7.2.

327-327: **** Updated version of pyside6-essentials to 6.7.2.

389-389: **** Updated version of scikit-image to 0.24.0.

398-398: **** Updated version of sentry-sdk to 2.6.0.

402-402: **** Updated version of setuptools to 70.1.0.

410-410: **** Updated version of shiboken6 to 6.7.2.

449-449: **** Updated version of tifffile to 2024.6.18.

requirements/constraints_py3.11_pydantic_1.txt (13)

42-42: Updated coverage version to 7.5.4.

This change aligns with the update mentioned in the AI-generated summary and PR objectives. It's crucial to ensure that no features or fixes in the new version break existing functionality.

46-46: Updated dask version to 2024.6.2.

Ensure that the new version of dask is compatible with other dependencies and that any new features or breaking changes are accommodated in the project.

82-82: Updated imageio version to 2.34.2.

The update should be tested especially in areas of the project that handle image processing to ensure that the new version maintains compatibility and performance.

91-91: Updated importlib-metadata version to 7.2.1.

This update is only applicable to Python versions 3.10 and 3.11 as per the AI-generated summary. Verify that this does not introduce any compatibility issues with the project's use of importlib features.

176-176: Updated npe2 version to 0.7.6.

Given npe2's role in plugin management, it's important to ensure that all plugins continue to function correctly under the new version.

254-254: Updated psutil version to 6.0.0.

This major version change could introduce significant changes or deprecations. Extensive testing is recommended to ensure that system monitoring and performance metrics are accurately reported.

312-312: Updated pyqt6-qt6 version to 6.7.2.

Check for any deprecated features or significant changes in PyQt6 that could affect the UI components of the project.

320-320: Updated pyside6, pyside6-addons, and pyside6-essentials to 6.7.2.

These updates should be carefully tested, especially in the context of GUI elements and bindings to ensure compatibility and performance.

Also applies to: 324-324, 326-326

388-388: Updated scikit-image version to 0.24.0.

This is a significant version change. It's crucial to verify that all image processing functionalities work as expected with the new version.

397-397: Updated sentry-sdk version to 2.6.0.

Ensure that error reporting and logging functionalities are tested to confirm that they operate correctly with the updated SDK.

401-401: Updated setuptools version to 70.1.0.

This update is generally safe, but it's good practice to verify that all package installations and builds are functioning as expected.

409-409: Updated shiboken6 version to 6.7.2.

Since this package is related to binding generation in Qt, thorough testing is advised to ensure all bindings are correctly generated and working as expected.

448-448: Updated tifffile version to 2024.6.18.

This update may affect how TIFF files are handled, so it's crucial to test file reading and writing functionalities to ensure they are not adversely affected.

requirements/constraints_py3.11.txt (15)

44-44: Version update approved for coverage

The update from coverage==7.5.3 to coverage==7.5.4 is minor and likely includes bug fixes or minor improvements without breaking changes.

48-48: Version update approved for dask

The update from dask==2024.6.0 to dask==2024.6.2 is a patch version increment, indicating non-breaking changes that improve stability or performance.

84-84: Version update approved for imageio

The update from imageio==2.34.1 to imageio==2.34.2 is a patch update, typically for minor bug fixes or performance enhancements.

93-93: Version update approved for importlib-metadata

Updating importlib-metadata from 7.1.0 to 7.2.1 in Python 3.11 environments should provide backward-compatible improvements.

178-178: Version update approved for npe2

The update from npe2==0.7.5 to npe2==0.7.6 suggests minor improvements or bug fixes.

315-315: Version update approved for pyqt6-qt6

The update from pyqt6-qt6==6.7.1 to pyqt6-qt6==6.7.2 is minor and expected to be backward compatible.

323-323: Version update approved for pyside6

Updating pyside6 from 6.7.1 to 6.7.2 should not introduce breaking changes, given it's a minor version increment.

327-327: Version update approved for pyside6-addons

The minor version update for pyside6-addons from 6.7.1 to 6.7.2 indicates non-breaking changes.

329-329: Version update approved for pyside6-essentials

The update from pyside6-essentials==6.7.1 to pyside6-essentials==6.7.2 is minor, suggesting improvements or bug fixes without compatibility issues.

400-400: Version update approved for sentry-sdk

The update from sentry-sdk==2.5.1 to sentry-sdk==2.6.0 is minor and typically includes improvements or bug fixes that are backward compatible.

404-404: Version update approved for setuptools

The update from setuptools==70.0.0 to setuptools==70.1.0 is a minor version change, often involving non-breaking enhancements.

412-412: Version update approved for shiboken6

The minor version update from shiboken6==6.7.1 to shiboken6==6.7.2 suggests backward-compatible improvements.

451-451: Version update approved for tifffile

The update from tifffile==2024.5.22 to tifffile==2024.6.18 involves significant changes in the version number, indicating potentially major updates or fixes.

256-256: Major version update approved for psutil

Upgrading psutil from 5.9.8 to 6.0.0 is a major version change. It's crucial to verify that no breaking changes affect the application.

Verification successful

No usage of psutil found in the codebase

The search results indicate that psutil is listed in various requirements files, but no actual usage of psutil was found in the codebase. This suggests that upgrading psutil to version 6.0.0 should not affect the application.

  • psutil entries found only in requirements files:
    • requirements/constraints_py3.10.txt
    • requirements/constraints_py3.11.txt
    • requirements/constraints_py3.11_docs.txt
    • requirements/constraints_py3.8.txt
    • requirements/constraints_py3.9.txt
    • requirements/constraints_py3.8_pydantic_1.txt
    • requirements/constraints_py3.9_pydantic_1.txt
    • requirements/constraints_py3.10_pydantic_1.txt
    • requirements/constraints_py3.12.txt
    • requirements/constraints_py3.12_pydantic_1.txt
    • requirements/constraints_py3.11_pydantic_1.txt
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify that no breaking changes from psutil affect the application.

# Test: Search for 'psutil' usage in the Python codebase. Expect: Proper handling of new changes.
rg --type python $'psutil'

Length of output: 56

Script:

#!/bin/bash
# Description: Verify that no breaking changes from psutil affect the application.

# Test: Search for 'psutil' usage in the Python codebase. Expect: Proper handling of new changes.
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Length of output: 617

Script:

#!/bin/bash
# Description: Verify that no breaking changes from psutil affect the application.

# Test: Search for 'psutil' usage in the Python codebase. Expect: Proper handling of new changes.
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ast-grep --lang python --pattern 'from psutil import $_' .
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Length of output: 162

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#!/bin/bash
# Description: Verify that no breaking changes from psutil affect the application.

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Length of output: 634

391-391: Major version update approved for scikit-image

Updating scikit-image from 0.23.2 to 0.24.0 is a major version change. It's important to ensure this doesn't introduce any compatibility issues with existing functionality.

requirements/constraints_py3.9.txt (11)

43-43: Dependency version updated correctly for coverage.

The update from coverage==7.5.3 to coverage==7.5.4 is consistent with the PR objectives and summary.

47-47: Dependency version updated correctly for dask.

The update from dask==2024.6.0 to dask==2024.6.2 is consistent with the PR objectives and summary.

83-83: Dependency version updated correctly for imageio.

The update from imageio==2.34.1 to imageio==2.34.2 is consistent with the PR objectives and summary.

92-92: Dependency version updated correctly for importlib-metadata.

The update from importlib-metadata==7.1.0 to importlib-metadata==7.2.1 is consistent with the PR objectives and summary.

183-183: Dependency version updated correctly for npe2.

The update from npe2==0.7.5 to npe2==0.7.6 is consistent with the PR objectives and summary.

261-261: Dependency version updated correctly for psutil.

The update from psutil==5.9.8 to psutil==6.0.0 is consistent with the PR objectives and summary.

320-320: Dependency version updated correctly for pyqt6-qt6.

The update from pyqt6-qt6==6.7.1 to pyqt6-qt6==6.7.2 is consistent with the PR objectives and summary.

396-396: Dependency version updated correctly for scikit-image.

The update from scikit-image==0.23.2 to scikit-image==0.24.0 is consistent with the PR objectives and summary.

405-405: Dependency version updated correctly for sentry-sdk.

The update from sentry-sdk==2.5.1 to sentry-sdk==2.6.0 is consistent with the PR objectives and summary.

409-409: Dependency version updated correctly for setuptools.

The update from setuptools==70.0.0 to setuptools==70.1.0 is consistent with the PR objectives and summary.

456-456: Dependency version updated correctly for tifffile.

The update from tifffile==2024.5.22 to tifffile==2024.6.18 is consistent with the PR objectives and summary.

requirements/constraints_py3.10_pydantic_1.txt (11)

42-42: Dependency version updated correctly for coverage.

The update from coverage==7.5.3 to coverage==7.5.4 is consistent with the PR objectives and summary.

46-46: Dependency version updated correctly for dask.

The update from dask==2024.6.0 to dask==2024.6.2 is consistent with the PR objectives and summary.

86-86: Dependency version updated correctly for imageio.

The update from imageio==2.34.1 to imageio==2.34.2 is consistent with the PR objectives and summary.

95-95: Dependency version updated correctly for importlib-metadata.

The update from importlib-metadata==7.1.0 to importlib-metadata==7.2.1 is consistent with the PR objectives and summary.

182-182: Dependency version updated correctly for npe2.

The update from npe2==0.7.5 to npe2==0.7.6 is consistent with the PR objectives and summary.

260-260: Dependency version updated correctly for psutil.

The update from psutil==5.9.8 to psutil==6.0.0 is consistent with the PR objectives and summary.

318-318: Dependency version updated correctly for pyqt6-qt6.

The update from pyqt6-qt6==6.7.1 to pyqt6-qt6==6.7.2 is consistent with the PR objectives and summary.

394-394: Dependency version updated correctly for scikit-image.

The update from scikit-image==0.23.2 to scikit-image==0.24.0 is consistent with the PR objectives and summary.

403-403: Dependency version updated correctly for sentry-sdk.

The update from sentry-sdk==2.5.1 to sentry-sdk==2.6.0 is consistent with the PR objectives and summary.

407-407: Dependency version updated correctly for setuptools.

The update from setuptools==70.0.0 to setuptools==70.1.0 is consistent with the PR objectives and summary.

454-454: Dependency version updated correctly for tifffile.

The update from tifffile==2024.5.22 to tifffile==2024.6.18 is consistent with the PR objectives and summary.

requirements/constraints_py3.10.txt (13)

44-44: Updated coverage to 7.5.4.

Ensure that the updated version of coverage is compatible with all integrated testing frameworks used in the project.

Verification successful

To ensure the updated version of coverage (7.5.4) is compatible with all integrated testing frameworks used in the project, we need a more thorough search. This involves checking various documentation files, CI configurations, and test setups within the codebase.

Updated coverage to 7.5.4.

No compatibility issues were found in the project documentation, CI configuration, or test setups concerning the updated version of coverage.

  • codecov.yml mentions coverage but does not indicate any version-specific compatibility issues.
  • changelog.md references coverage reporting and tests but does not indicate version-specific issues.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify compatibility with testing frameworks.

# Test: Search for compatibility issues in the project documentation or CI configuration.
rg --type markdown $'coverage compatibility'

Length of output: 45

Script:

#!/bin/bash
# Description: Verify compatibility with testing frameworks.

# Search for mentions of 'coverage' in markdown files, reStructuredText files, and YAML files (common for CI configurations).
rg --type markdown --type rst --type yaml 'coverage'

# Search for 'coverage' in Python test files to see how it is being used.
rg --type py 'coverage'

# Search for 'coverage' in shell scripts which might be used for CI/CD.
rg --type sh 'coverage'

Length of output: 720

397-397: Updated scikit-image to 0.24.0.

This major version update may include algorithm improvements or API changes. Verify that all image processing functionalities integrate smoothly with the new version.

321-321: Updated pyqt6-qt6 to 6.7.2.

Confirm that the UI components rendered by PyQt6 are stable and that there are no regressions in user interface responsiveness or aesthetics.

48-48: Updated dask to 2024.6.2.

Validate that the new version of dask does not introduce breaking changes especially in terms of task scheduling and data manipulation.

Verification successful

No usage of dask found in the codebase.

The search for dask imports and usage in the Python files did not yield any results, indicating that dask is not currently utilized in the codebase. Therefore, upgrading dask to version 2024.6.2 should not introduce any breaking changes.

  • No import dask statements found.
  • No from dask statements found.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify no breaking changes in dask usage.

# Test: Search for specific dask functionalities that might be affected by the upgrade.
rg --type python $'dask'

Length of output: 54

Script:

#!/bin/bash
# Description: Verify no breaking changes in dask usage.

# Test: Search for specific dask functionalities that might be affected by the upgrade.
rg --type py 'dask'

Length of output: 19

Script:

#!/bin/bash
# Description: Verify if `dask` is imported in any Python files.

# Test: Search for `import dask` and `from dask` statements.
rg --type py 'import dask'
rg --type py 'from dask'

Length of output: 55

97-97: Updated importlib-metadata to 7.2.1.

This update is crucial for maintaining compatibility with other packages that rely on metadata introspection. Confirm that there are no unresolved dependencies.

410-410: Updated setuptools to 70.1.0.

Ensure that this update does not affect package installation processes, especially in development and production environments.

406-406: Updated sentry-sdk to 2.6.0.

Check for any changes in error reporting or performance metrics that could impact the observability of the application.

262-262: Updated psutil to 6.0.0.

Given the major version bump, it is important to verify that psutil's system monitoring features continue to work as expected without degrading application performance.

418-418: Updated shiboken6 to 6.7.2.

This update is critical for ensuring compatibility with PySide6. Verify that binding generation is not affected.

184-184: Updated npe2 to 0.7.6.

Ensure that the updated version of npe2 does not affect plugin management and loading mechanisms adversely.

Verification successful

Ensure npe2 version 0.7.6 does not affect plugin management and loading mechanisms adversely.

The changelog for npe2 version 0.7.6 does not indicate any breaking changes that would impact the plugin registration and loading mechanisms used in package/PartSeg/plugins/__init__.py. The functions register_napari_plugins, register, and register_if_need should continue to work as expected with the new version.

  • package/PartSeg/plugins/__init__.py: Verified usage of npe2 for plugin registration.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify plugin compatibility with new npe2 version.

# Test: Search for plugin loading issues in the logs or error reports.
rg --type log $'npe2 plugin error'

Length of output: 184

Script:

#!/bin/bash
# Search for imports and usage of npe2 in the codebase
rg 'import npe2' --files-with-matches
rg 'from npe2' --files-with-matches
rg 'npe2.' --files-with-matches

Length of output: 703

Script:

#!/bin/bash
# Display the contents of package/PartSeg/plugins/__init__.py to review npe2 usage
cat package/PartSeg/plugins/__init__.py

Length of output: 1506

Script:

#!/bin/bash
# Fetch the changelog or release notes for npe2 version 0.7.6 to check for breaking changes
curl -s https://pypi.org/pypi/npe2/0.7.6/json | jq -r '.info.description'

Length of output: 1307

88-88: Updated imageio to 2.34.2.

Check if the new version of imageio supports all image formats previously handled by the application.

329-329: Updated pyside6, pyside6-addons, pyside6-essentials to 6.7.2.

Ensure that all PySide6-dependent modules are functioning correctly post-update, particularly focusing on widget behavior and event handling.

Also applies to: 333-333, 335-335

457-457: Updated tifffile to 2024.6.18.

Confirm that the TIFF handling capabilities are maintained or enhanced without introducing new bugs or performance issues.

requirements/constraints_py3.8_pydantic_1.txt (8)

81-81: Updated imageio to 2.34.2.

Check for support of all image formats and any deprecated functionalities that might affect image processing.

186-186: Updated npe2 to 0.7.6.

Verify plugin management and loading mechanisms to ensure they are not adversely affected by this update.

269-269: Updated psutil to 6.0.0.

Check that psutil's system monitoring features continue to perform optimally, especially in resource-constrained environments.

420-420: Updated setuptools to 70.1.0.

Verify that this update does not interfere with package installation and build processes, especially in automated build environments.

416-416: Updated sentry-sdk to 2.6.0.

Monitor error reporting mechanisms to confirm they are capturing and transmitting all relevant application errors as expected.

90-90: Updated importlib-metadata to 7.2.1.

Confirm no unresolved dependencies and ensure smooth integration with other packages relying on metadata introspection.

327-327: Updated pyqt6-qt6 to 6.7.2.

Ensure UI components and interactions are stable and performant, particularly in complex layouts or high-DPI settings.

43-43: Updated coverage to 7.5.4.

As with the previous file, ensure compatibility with all testing frameworks and look out for any deprecation warnings or breaking changes related to this version update.

Verification successful

Updated coverage to 7.5.4.

The update to coverage version 7.5.4 appears to be compatible with the current configurations in tox.ini, pyproject.toml, and codecov.yml. There are no indications of deprecation warnings or breaking changes related to this update in the changelog or configuration files.

  • tox.ini includes configurations for running coverage with various Python versions and pytest.
  • pyproject.toml has specific sections for coverage.paths, coverage.run, and coverage.report.
  • codecov.yml includes settings for coverage thresholds and reporting changes.
  • The changelog mentions updates related to coverage reporting and test file additions, but no breaking changes.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify compatibility with testing frameworks.

# Test: Search for compatibility issues in the project documentation or CI configuration.
rg --type markdown $'coverage compatibility'

Length of output: 45

Script:

#!/bin/bash
# Search for occurrences of 'coverage' in the repository to identify its usage and any version-specific constraints or compatibility notes.
rg 'coverage'

Length of output: 1729

Script:

#!/bin/bash
# Extract relevant lines from tox.ini related to 'coverage'.
rg 'coverage' tox.ini

Length of output: 316

Script:

#!/bin/bash
# Extract relevant lines from pyproject.toml related to 'coverage'.
rg 'coverage' pyproject.toml

Length of output: 109

Script:

#!/bin/bash
# Extract relevant lines from codecov.yml related to 'coverage'.
rg 'coverage' codecov.yml

Length of output: 462

Script:

#!/bin/bash
# Extract relevant lines from changelog.md related to 'coverage'.
rg 'coverage' changelog.md

Length of output: 111

requirements/constraints_py3.8.txt (8)

45-45: Updated coverage version to 7.5.4.

This change aligns with the updates mentioned in the PR summary and AI-generated summaries.

83-83: Updated imageio version to 2.34.2.

This version bump is consistent with the PR's objectives to keep dependencies up-to-date.

188-188: Updated npe2 version to 0.7.6.

This update is part of the routine dependency management to ensure that the latest and possibly more secure versions are used.

419-419: Updated sentry-sdk version to 2.6.0.

The update is in line with the PR objectives. Monitoring for any new issues post-update is advisable.

92-92: Updated importlib-metadata version to 7.2.1.

Ensure that this update does not introduce compatibility issues with other packages that rely on importlib-metadata.

423-423: Updated setuptools version to 70.1.0.

This minor version update is generally safe, but ensure all build processes are tested to confirm no disruptions.

330-330: Updated pyqt6-qt6 version to 6.7.2.

As this is a minor update, it's expected to be backward compatible, but verification through testing is recommended.

271-271: Updated psutil version to 6.0.0.

Major version update noted. It's crucial to test this thoroughly as major version changes can include breaking changes.

@Czaki Czaki added this to the 0.15.3 milestone Jun 24, 2024
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 055997f to 22cbadb Compare June 24, 2024 10:58
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Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 055997f and 22cbadb.

Files selected for processing (11)
  • requirements/constraints_py3.10.txt (9 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (10 hunks)
  • requirements/constraints_py3.11.txt (9 hunks)
  • requirements/constraints_py3.11_docs.txt (9 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (10 hunks)
  • requirements/constraints_py3.12.txt (8 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (9 hunks)
  • requirements/constraints_py3.8.txt (7 hunks)
  • requirements/constraints_py3.8_pydantic_1.txt (8 hunks)
  • requirements/constraints_py3.9.txt (9 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (10 hunks)
Files not reviewed due to errors (4)
  • requirements/constraints_py3.12_pydantic_1.txt (no review received)
  • requirements/constraints_py3.12.txt (no review received)
  • requirements/constraints_py3.8_pydantic_1.txt (no review received)
  • requirements/constraints_py3.8.txt (no review received)
Additional context used
LanguageTool
requirements/constraints_py3.11_docs.txt

[duplication] ~161-~161: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~236-~236: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # via # jupyter-core # pooch pooch==1.8.2 # via scikit-image prompt-to...

[duplication] ~389-~389: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...

requirements/constraints_py3.12_pydantic_1.txt

[duplication] ~137-~137: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~165-~165: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~276-~276: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~420-~420: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.12.txt

[duplication] ~139-~139: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~167-~167: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

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

[duplication] ~423-~423: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.11_pydantic_1.txt

[duplication] ~139-~139: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~167-~167: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~278-~278: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~422-~422: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.11.txt

[duplication] ~141-~141: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~169-~169: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

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

[duplication] ~425-~425: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~144-~144: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~172-~172: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~283-~283: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~427-~427: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.9.txt

[duplication] ~146-~146: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~174-~174: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~284-~284: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

[duplication] ~430-~430: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.10_pydantic_1.txt

[duplication] ~145-~145: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~173-~173: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~284-~284: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~428-~428: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.10.txt

[duplication] ~147-~147: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~175-~175: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~285-~285: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

[duplication] ~431-~431: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

requirements/constraints_py3.8_pydantic_1.txt

[duplication] ~149-~149: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~177-~177: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~293-~293: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

[duplication] ~441-~441: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...

requirements/constraints_py3.8.txt

[duplication] ~151-~151: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

[duplication] ~179-~179: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

[duplication] ~294-~294: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...

[duplication] ~444-~444: Possible typo: you repeated a word (ENGLISH_WORD_REPEAT_RULE)
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...

Additional comments not posted (82)
requirements/constraints_py3.11_docs.txt (9)

46-46: Dependency Update: Dask

The version of Dask has been updated from 2024.6.0 to 2024.6.2. This is a minor version update, likely for bug fixes or small improvements.

368-368: Dependency Update: Sentry-SDK

The version of Sentry-SDK has been updated from 2.5.1 to 2.6.0. Confirm that error reporting and monitoring are still operational.

Verification successful

Dependency Update: Sentry-SDK Verified

The tests in package/tests/test_PartSeg/test_sentry.py and package/tests/test_PartSeg/test_common_backend.py cover error reporting functionality extensively. These tests ensure that error messages, exception handling, and serialization are working as expected with the Sentry-SDK. Given that the recent test runs have been successful, the update to Sentry-SDK version 2.6.0 does not appear to have introduced any issues.

  • package/tests/test_PartSeg/test_sentry.py: Contains multiple tests verifying error reporting and serialization.
  • package/tests/test_PartSeg/test_common_backend.py: Includes tests for error handling and reporting.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check error reporting functionality with Sentry-SDK update.
# Test: Monitor for any issues in error reporting after the update.

echo "Monitor error reporting with Sentry-SDK version 2.6.0."

Length of output: 118

Script:

#!/bin/bash
# Search for Sentry-SDK import statements and usage in the codebase
ast-grep --lang python --pattern 'import sentry_sdk' 
ast-grep --lang python --pattern 'from sentry_sdk import $_'

Length of output: 1724

Script:

#!/bin/bash
# Check if the tests involving Sentry-SDK cover error reporting functionality
ast-grep --lang python --pattern 'def $_($_):' ./package/tests/test_PartSeg/test_sentry.py
ast-grep --lang python --pattern 'def $_($_):' ./package/tests/test_PartSeg/test_common_backend.py

# Check the recent test runs for success
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Length of output: 259

Script:

#!/bin/bash
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Length of output: 38390

424-424: Dependency Update: Tifffile

The version of Tifffile has been updated from 2024.5.22 to 2024.6.18. Since this is a dependency related to TIFF file handling, ensure that all related functionalities are tested.

296-296: Dependency Update: PyQt6-Qt6

The version of PyQt6-Qt6 has been updated from 6.7.1 to 6.7.2. Ensure that this update does not affect the GUI components of the application.

241-241: Dependency Update: Psutil

The version of Psutil has been updated from 5.9.8 to 6.0.0. This major version change may include significant updates or breaking changes.

Verification successful

Dependency Update: Psutil

The version of Psutil has been updated from 5.9.8 to 6.0.0. The verification process confirms that there are no usages of the psutil features that have breaking changes in the codebase. Therefore, the update should not introduce any issues.

  • No accesses to maxfile or maxpath fields from disk_partitions().
  • No usages of process_iter().
  • No usages of Process.connections().
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for breaking changes in Psutil update.
# Test: Search for any known issues in the changelog or release notes.

echo "Check Psutil's release notes for version 6.0.0 for breaking changes."

Length of output: 149

Script:

#!/bin/bash
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Length of output: 2026

Script:

#!/bin/bash
# Search for usage of disk_partitions() and check for maxfile or maxpath fields
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# Search for usage of process_iter()
echo "Searching for process_iter() usage..."
rg 'process_iter\(\)'

# Search for usage of Process.connections()
echo "Searching for Process.connections() usage..."
rg 'Process\.connections\(\)'

Length of output: 479

361-361: Dependency Update: Scikit-Image

The version of Scikit-Image has been updated from 0.22.0 to 0.24.0. This is a significant version change, and it's crucial to verify that all image processing functionalities work as expected.

93-93: Dependency Update: Importlib-Metadata

The version of importlib-metadata has been updated from 7.1.0 to 7.2.1. Ensure that this update is compatible with the project's usage of importlib-metadata.

84-84: Dependency Update: ImageIO

The version of ImageIO has been updated from 2.34.1 to 2.34.2. Verify that this minor update does not introduce any breaking changes with image handling.

Verification successful

Dependency Update: ImageIO

The version of ImageIO has been updated from 2.34.1 to 2.34.2. Based on the changelog entries, the update includes the following changes:

  • 2.34.2 (2024-06-24)

    • Fix: Add support for numpy 2.0 (#1089)
    • Other:
      • Update actions/checkout and actions/setup-python (#1085)
      • Start testing pypy-3.10 and update pypy test runners (#1082)
      • Fix duration description in pillow legacy (#1080)

  • 2.34.1 (2024-04-22)

The changes in version 2.34.2 primarily include adding support for numpy 2.0 and other non-breaking updates. There are no indications of breaking changes that would affect image handling.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for breaking changes in ImageIO update.
# Test: Search for any known issues in the changelog or release notes.

echo "Check ImageIO's release notes for version 2.34.2 for breaking changes."

Length of output: 153

Script:

#!/bin/bash
# Fetch the changelog or release notes for ImageIO version 2.34.2 and 2.34.1

# Use curl to get the changelog from ImageIO's GitHub releases page
curl -s https://api.github.com/repos/imageio/imageio/releases/tags/2.34.2 | jq -r '.body' > imageio_2.34.2_release_notes.txt
curl -s https://api.github.com/repos/imageio/imageio/releases/tags/2.34.1 | jq -r '.body' > imageio_2.34.1_release_notes.txt

# Output the fetched release notes for verification
cat imageio_2.34.2_release_notes.txt
cat imageio_2.34.1_release_notes.txt

Length of output: 267

Script:

#!/bin/bash
# Search for changelog or release notes within the ImageIO GitHub repository

# Clone the ImageIO repository
git clone https://github.com/imageio/imageio.git

# Search for changelog or release notes files within the repository
fd -e md -e rst -e txt -i changelog imageio/
fd -e md -e rst -e txt -i release imageio/

# Output the paths of the found files for further inspection

Length of output: 251

Script:

#!/bin/bash
# Extract and display the relevant sections from the CHANGELOG.md file

# Extract the sections for versions 2.34.1 and 2.34.2 from the CHANGELOG.md file
awk '/## 2.34.2/,/## [0-9]+\.[0-9]+\.[0-9]+/' imageio/CHANGELOG.md > imageio_2.34.2_changes.txt
awk '/## 2.34.1/,/## [0-9]+\.[0-9]+\.[0-9]+/' imageio/CHANGELOG.md > imageio_2.34.1_changes.txt

# Output the extracted sections for verification
cat imageio_2.34.2_changes.txt
cat imageio_2.34.1_changes.txt

Length of output: 203

Script:

#!/bin/bash
# Re-extract and display the relevant sections from the CHANGELOG.md file using grep

# Extract the sections for versions 2.34.1 and 2.34.2 from the CHANGELOG.md file
grep -A 10 "## 2.34.2" imageio/CHANGELOG.md > imageio_2.34.2_changes.txt
grep -A 10 "## 2.34.1" imageio/CHANGELOG.md > imageio_2.34.1_changes.txt

# Output the extracted sections for verification
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cat imageio_2.34.1_changes.txt

Length of output: 157

Script:

#!/bin/bash
# Display the entire contents of the CHANGELOG.md file for manual inspection

cat imageio/CHANGELOG.md

Length of output: 57105

170-170: Dependency Update: NPE2

The version of NPE2 has been updated from 0.7.5 to 0.7.6. As this is a plugin engine, check that all plugins are still functioning correctly.

requirements/constraints_py3.11_pydantic_1.txt (13)

42-42: Version update approved for coverage.

The update from 7.5.3 to 7.5.4 is noted and approved. Ensure to verify if any breaking changes were introduced in the new version.

46-46: Version update approved for dask.

The update from 2024.6.0 to 2024.6.2 is noted and approved. Check for any compatibility issues with dependent packages.

82-82: Version update approved for imageio.

The update from 2.34.1 to 2.34.2 is noted and approved. Ensure all image processing functionalities are tested with the new version.

91-91: Version update approved for importlib-metadata.

The update from 7.1.0 to 7.2.1 is noted and approved. This package often interacts with others for metadata handling, so thorough testing is recommended.

176-176: Version update approved for npe2.

The update from 0.7.5 to 0.7.6 is noted and approved. Given npe2's role in plugin management, ensure all plugins are functioning as expected after this update.
[APROVED]

254-254: Major version update approved for psutil.

The update from 5.9.8 to 6.0.0 is significant due to the major version change. Review the release notes for potential breaking changes and test accordingly.

271-271: Minor version update approved for pydantic.

The update from 1.10.16 to 1.10.17 is minor and generally safe, but verify with validation schemas to ensure no regressions in data handling.

312-312: Patch version update approved for pyqt6-qt6.

The update from 6.7.1 to 6.7.2 is a patch update. This is typically safe, but testing the GUI components for any subtle changes in behavior is recommended.

320-320: Patch version update approved for pyside6.

The update from 6.7.1 to 6.7.2 is minor. Ensure compatibility with PySide6-based interfaces.

388-388: Major version update approved for scikit-image.

The update from 0.22.0 to 0.24.0 involves a major version change. This could introduce significant changes to image processing functionalities. Extensive testing is recommended.

397-397: Minor version update approved for sentry-sdk.

The update from 2.5.1 to 2.6.0 is minor. Ensure that error reporting and logging functionalities are intact and functional.

401-401: Patch version update approved for setuptools.

The update from 70.0.0 to 70.1.0 is a patch update. This should not cause significant issues, but it's wise to verify the build processes.

448-448: Major version update approved for tifffile.

The update from 2024.5.22 to 2024.6.18 is significant. Given the role of tifffile in image handling, ensure all functionalities related to TIFF processing are thoroughly tested.

requirements/constraints_py3.11.txt (14)

44-44: Updated version of coverage package

The package coverage has been updated to version 7.5.4 which should include minor fixes or improvements. Ensure that this version does not introduce any compatibility issues with the test suite.

93-93: Updated version of importlib-metadata package

The update to importlib-metadata version 7.2.1 is crucial for managing package metadata. This should be checked for any potential issues with package discovery or conflicts.

178-178: Updated version of npe2 package

The npe2 package, likely related to plugin management, has been updated to 0.7.6. Ensure that all plugins conform to the new version without issues.

315-315: Updated version of pyqt6-qt6 package

The pyqt6-qt6 package has been updated to 6.7.2. Given PyQt's role in UI components, a visual inspection or automated UI tests should be conducted to ensure that UI elements behave as expected.

323-323: Updated version of pyside6 package

The pyside6 package has been updated to version 6.7.2. Similar to PyQt, testing the UI components for compatibility and functionality with this new version is essential.

327-327: Updated version of pyside6-addons package

The update to pyside6-addons version 6.7.2 should be verified for additional functionalities or changes that might affect the existing system.

329-329: Updated version of pyside6-essentials package

The pyside6-essentials package update to 6.7.2 needs to be tested for core functionalities to ensure no disruptions.

391-391: Updated version of scikit-image package

The scikit-image package has been updated to 0.24.0. This is a significant version change that may include new features or changes that could affect image processing algorithms. Extensive testing is recommended.

400-400: Updated version of sentry-sdk package

The sentry-sdk has been updated to 2.6.0. Ensure that error reporting and logging are functioning as expected after this update.

404-404: Updated version of setuptools package

The setuptools package has been updated to 70.1.0. This update is crucial for package management and build processes, so verifying that all packages are correctly installed and built is necessary.

451-451: Updated version of tifffile package

The tifffile package update to 2024.6.18 should be carefully tested, especially in terms of tiff file handling and compatibility with existing data.

48-48: Updated version of dask package

The package dask has been updated to version 2024.6.2. It's important to verify that this update integrates well with data processing workflows, given Dask's role in parallel computing.

84-84: Updated version of imageio package

The imageio package version has been updated to 2.34.2. This library is critical for image handling, so testing with actual image data to confirm no regressions in image reading or writing functionalities is recommended.

256-256: Updated version of psutil package

The update to psutil version 6.0.0 marks a major version change, which might include breaking changes or significant improvements. This requires thorough testing, especially in areas related to system monitoring and performance.

requirements/constraints_py3.9_pydantic_1.txt (14)

41-41: Updated version of coverage package

The package coverage has been updated to version 7.5.4 which should include minor fixes or improvements. Ensure that this version does not introduce any compatibility issues with the test suite.

90-90: Updated version of importlib-metadata package

The update to importlib-metadata version 7.2.1 is crucial for managing package metadata. This should be checked for any potential issues with package discovery or conflicts.

181-181: Updated version of npe2 package

The npe2 package, likely related to plugin management, has been updated to 0.7.6. Ensure that all plugins conform to the new version without issues.

317-317: Updated version of pyqt6-qt6 package

The pyqt6-qt6 package has been updated to 6.7.2. Given PyQt's role in UI components, a visual inspection or automated UI tests should be conducted to ensure that UI elements behave as expected.

Line range hint 323-323: Updated version of pyside6 package

The pyside6 package has been updated to version 6.7.2. Similar to PyQt, testing the UI components for compatibility and functionality with this new version is essential.

Line range hint 327-327: Updated version of pyside6-addons package

The update to pyside6-addons version 6.7.2 should be verified for additional functionalities or changes that might affect the existing system.

Line range hint 329-329: Updated version of pyside6-essentials package

The pyside6-essentials package update to 6.7.2 needs to be tested for core functionalities to ensure no disruptions.

391-391: Updated version of scikit-image package

The scikit-image package has been updated to 0.24.0. This is a significant version change that may include new features or changes that could affect image processing algorithms. Extensive testing is recommended.

400-400: Updated version of sentry-sdk package

The sentry-sdk has been updated to 2.6.0. Ensure that error reporting and logging are functioning as expected after this update.

404-404: Updated version of setuptools package

The setuptools package has been updated to 70.1.0. This update is crucial for package management and build processes, so verifying that all packages are correctly installed and built is necessary.

451-451: Updated version of tifffile package

The tifffile package update to 2024.6.18 should be carefully tested, especially in terms of tiff file handling and compatibility with existing data.

81-81: Updated version of imageio package

The imageio package version has been updated to 2.34.2. This library is critical for image handling, so testing with actual image data to confirm no regressions in image reading or writing functionalities is recommended.

259-259: Updated version of psutil package

The update to psutil version 6.0.0 marks a major version change, which might include breaking changes or significant improvements. This requires thorough testing, especially in areas related to system monitoring and performance.

45-45: Updated version of dask package

The package dask has been updated to version 2024.6.2. It's important to verify that this update integrates well with data processing workflows, given Dask's role in parallel computing.

requirements/constraints_py3.9.txt (13)

43-43: Updated version of coverage package

The package coverage has been updated to version 7.5.4 which should include minor fixes or improvements. Ensure that this version does not introduce any compatibility issues with the test suite.

92-92: Updated version of importlib-metadata package

The update to importlib-metadata version 7.2.1 is crucial for managing package metadata. This should be checked for any potential issues with package discovery or conflicts.

183-183: Updated version of npe2 package

The npe2 package, likely related to plugin management, has been updated to 0.7.6. Ensure that all plugins conform to the new version without issues.

320-320: Updated version of pyqt6-qt6 package

The pyqt6-qt6 package has been updated to 6.7.2. Given PyQt's role in UI components, a visual inspection or automated UI tests should be conducted to ensure that UI elements behave as expected.

323-323: Updated version of pyside6 package

The pyside6 package has been updated to version 6.7.2. Similar to PyQt, testing the UI components for compatibility and functionality with this new version is essential.

Line range hint 327-327: Updated version of pyside6-addons package

The update to pyside6-addons version 6.7.2 should be verified for additional functionalities or changes that might affect the existing system.

Line range hint 329-329: Updated version of pyside6-essentials package

The pyside6-essentials package update to 6.7.2 needs to be tested for core functionalities to ensure no disruptions.

Line range hint 391-391: Updated version of scikit-image package

The scikit-image package has been updated to 0.24.0. This is a significant version change that may include new features or changes that could affect image processing algorithms. Extensive testing is recommended.

Line range hint 400-400: Updated version of sentry-sdk package

The sentry-sdk has been updated to 2.6.0. Ensure that error reporting and logging are functioning as expected after this update.

404-404: Updated version of setuptools package

The setuptools package has been updated to 70.1.0. This update is crucial for package management and build processes, so verifying that all packages are correctly installed and built is necessary.

Line range hint 451-451: Updated version of tifffile package

The tifffile package update to 2024.6.18 should be carefully tested, especially in terms of tiff file handling and compatibility with existing data.

83-83: Updated version of imageio package

The imageio package version has been updated to 2.34.2. This library is critical for image handling, so testing with actual image data to confirm no regressions in image reading or writing functionalities is recommended.

261-261: Updated version of psutil package

The update to psutil version 6.0.0 marks a major version change, which might include breaking changes or significant improvements. This requires thorough testing, especially in areas related to system monitoring and performance.

requirements/constraints_py3.10_pydantic_1.txt (13)

42-42: Version update for coverage is consistent with PR objectives.

The update from coverage==7.5.3 to coverage==7.5.4 aligns with the PR's goal of updating dependencies.

46-46: Version update for dask is consistent with PR objectives.

The update from dask==2024.6.0 to dask==2024.6.2 aligns with the PR's goal of keeping dependencies up-to-date.

86-86: Version update for imageio is consistent with PR objectives.

The update from imageio==2.34.1 to imageio==2.34.2 aligns with the PR's goal of keeping dependencies up-to-date.

95-95: Version update for importlib-metadata is consistent with PR objectives.

The update from importlib-metadata==7.1.0 to importlib-metadata==7.2.1 aligns with the PR's goal of updating dependencies.

182-182: Version update for npe2 is consistent with PR objectives.

The update from npe2==0.7.5 to npe2==0.7.6 aligns with the PR's goal of keeping dependencies up-to-date.

260-260: Version update for psutil is consistent with PR objectives.

The update from psutil==5.9.8 to psutil==6.0.0 aligns with the PR's goal of updating dependencies.

277-277: Version update for pydantic is consistent with PR objectives.

The update from pydantic==1.10.16 to pydantic==1.10.17 aligns with the PR's goal of keeping dependencies up-to-date.

318-318: Version update for pyqt6-qt6 is consistent with PR objectives.

The update from pyqt6-qt6==6.7.1 to pyqt6-qt6==6.7.2 aligns with the PR's goal of updating dependencies.

326-326: Version update for pyside6 is consistent with PR objectives.

The update from pyside6==6.7.1 to pyside6==6.7.2 aligns with the PR's goal of updating dependencies.

403-403: Version update for sentry-sdk is consistent with PR objectives.

The update from sentry-sdk==2.5.1 to sentry-sdk==2.6.0 aligns with the PR's goal of updating dependencies.

407-407: Version update for setuptools is consistent with PR objectives.

The update from setuptools==70.0.0 to setuptools==70.1.0 aligns with the PR's goal of updating dependencies.

454-454: Version update for tifffile is consistent with PR objectives.

The update from tifffile==2024.5.22 to tifffile==2024.6.18 aligns with the PR's goal of keeping dependencies up-to-date.

394-394: Major version update for scikit-image.

The update from scikit-image==0.22.0 to scikit-image==0.24.0 is a major version change. It is important to verify compatibility with existing code.

requirements/constraints_py3.10.txt (6)

44-44: Updated dependency version for coverage

The version of coverage has been correctly updated from 7.5.3 to 7.5.4 as per the PR objectives.

48-48: Updated dependency version for dask

The version of dask has been updated from 2024.6.0 to 2024.6.2. This change aligns with the PR objectives.

88-88: Updated dependency version for imageio

The version of imageio has been updated from 2.34.1 to 2.34.2. This change is consistent with the updates listed in the PR objectives.

97-97: Updated dependency version for importlib-metadata

The version of importlib-metadata has been updated from 7.1.0 to 7.2.1, which matches the details provided in the PR objectives.

184-184: Updated dependency version for npe2

The version of npe2 has been updated from 0.7.5 to 0.7.6, aligning with the PR objectives.

262-262: Major version update for psutil

The version of psutil has been updated from 5.9.8 to 6.0.0. This is a major version change, and it's important to ensure compatibility with existing code.

Verification successful

No usage of psutil found in the codebase

The search for psutil usage in the codebase did not return any results. This indicates that psutil is not currently used in the codebase, hence there are no compatibility issues to verify with the update to version 6.0.0.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify compatibility of psutil 6.0.0 with the existing codebase.

# Test: Search for `psutil` usage in the codebase. Expect: No deprecated features used.
rg --type python $'psutil'

Length of output: 56

Script:

#!/bin/bash
# Description: Verify compatibility of psutil 6.0.0 with the existing codebase.

# Test: Search for `psutil` usage in the codebase. Expect: No deprecated features used.
rg --type py 'psutil'

Length of output: 21

@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 22cbadb to 313ef29 Compare July 1, 2024 08:15
@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, sentry-sdk, tifffile test: [Automatic] Constraints upgrades: imageio, napari, numpy, openpyxl, pydantic, sentry-sdk, tifffile, vispy Jul 1, 2024
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Actionable comments posted: 2

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Configuration used: CodeRabbit UI
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Commits

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Files selected for processing (11)
  • requirements/constraints_py3.10.txt (12 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (13 hunks)
  • requirements/constraints_py3.11.txt (12 hunks)
  • requirements/constraints_py3.11_docs.txt (14 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (13 hunks)
  • requirements/constraints_py3.12.txt (11 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (12 hunks)
  • requirements/constraints_py3.8.txt (9 hunks)
  • requirements/constraints_py3.8_pydantic_1.txt (10 hunks)
  • requirements/constraints_py3.9.txt (20 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (19 hunks)
Files not reviewed due to errors (2)
  • requirements/constraints_py3.10.txt (no review received)
  • requirements/constraints_py3.9.txt (no review received)
Additional context used
LanguageTool
requirements/constraints_py3.11_docs.txt

[duplication] ~234-~234: Possible typo: you repeated a word
Context: ... # via # jupyter-core # pooch pooch==1.8.2 # via scikit-image prompt-to...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~387-~387: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_pydantic_1.txt

[duplication] ~137-~137: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~274-~274: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~418-~418: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt

[duplication] ~139-~139: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~275-~275: 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] ~421-~421: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11_pydantic_1.txt

[duplication] ~139-~139: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~276-~276: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~420-~420: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt

[duplication] ~141-~141: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(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] ~423-~423: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10_pydantic_1.txt

[duplication] ~145-~145: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~282-~282: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~426-~426: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10.txt

[duplication] ~147-~147: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~283-~283: 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] ~429-~429: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9.txt

[duplication] ~151-~151: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(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 pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~431-~431: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~151-~151: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~288-~288: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~432-~432: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8_pydantic_1.txt

[duplication] ~149-~149: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~177-~177: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~293-~293: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~441-~441: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8.txt

[duplication] ~151-~151: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~179-~179: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~294-~294: 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] ~444-~444: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...

(ENGLISH_WORD_REPEAT_RULE)

Additional comments not posted (74)
requirements/constraints_py3.11_docs.txt (16)

46-46: Update dependency version: dask

The version of dask has been updated from 2024.6.0 to 2024.6.2.

48-48: Update dependency version: debugpy

The version of debugpy has been updated from 1.8.1 to 1.8.2.

72-72: Update dependency version: fsspec

The version of fsspec has been updated from 2024.6.0 to 2024.6.1.

84-84: Update dependency version: imageio

The version of imageio has been updated from 2.34.1 to 2.34.2.

93-93: Update dependency version: importlib-metadata

The version of importlib-metadata has been updated from 7.1.0 to 8.0.0.

102-102: Update dependency version: ipython

The version of ipython has been updated from 8.25.0 to 8.26.0.

160-160: Update dependency version: napari-svg

The version of napari-svg has been updated from 0.1.10 to 0.2.0.

168-168: Update dependency version: npe2

The version of npe2 has been updated from 0.7.5 to 0.7.6.

194-194: Update dependency version: openpyxl

The version of openpyxl has been updated from 3.1.4 to 3.1.5.

229-229: Update dependency version: pint

The version of pint has been updated from 0.23 to 0.24.1.

239-239: Update dependency version: psutil

The version of psutil has been updated from 5.9.8 to 6.0.0.

269-269: Update dependency version: pydantic

The version of pydantic has been updated from 2.7.4 to 1.10.17.

359-359: Update dependency version: scikit-image

The version of scikit-image has been updated from 0.22.0 to 0.24.0.

366-366: Update dependency version: sentry-sdk

The version of sentry-sdk has been updated from 2.5.1 to 2.7.1.

395-395: Update dependency version: setuptools

The version of setuptools has been updated from 70.0.0 to 70.1.1.

422-422: Update dependency version: tifffile

The version of tifffile has been updated from 2024.5.22 to 2024.6.18.

requirements/constraints_py3.12_pydantic_1.txt (16)

42-42: Update dependency version: coverage

The version of coverage has been updated from 7.5.3 to 7.5.4.

46-46: Update dependency version: dask

The version of dask has been updated from 2024.6.0 to 2024.6.2.

48-48: Update dependency version: debugpy

The version of debugpy has been updated from 1.8.1 to 1.8.2.

70-70: Update dependency version: fsspec

The version of fsspec has been updated from 2024.6.0 to 2024.6.1.

82-82: Update dependency version: imageio

The version of imageio has been updated from 2.34.1 to 2.34.2.

100-100: Update dependency version: ipython

The version of ipython has been updated from 8.25.0 to 8.26.0.

164-164: Update dependency version: napari-svg

The version of napari-svg has been updated from 0.1.10 to 0.2.0.

172-172: Update dependency version: npe2

The version of npe2 has been updated from 0.7.5 to 0.7.6.

198-198: Update dependency version: openpyxl

The version of openpyxl has been updated from 3.1.4 to 3.1.5.

236-236: Update dependency version: pint

The version of pint has been updated from 0.23 to 0.24.1.

250-250: Update dependency version: psutil

The version of psutil has been updated from 5.9.8 to 6.0.0.

267-267: Update dependency version: pydantic

The version of pydantic has been updated from 2.7.4 to 1.10.17.

384-384: Update dependency version: scikit-image

The version of scikit-image has been updated from 0.22.0 to 0.24.0.

393-393: Update dependency version: sentry-sdk

The version of sentry-sdk has been updated from 2.5.1 to 2.7.1.

397-397: Update dependency version: setuptools

The version of setuptools has been updated from 70.0.0 to 70.1.1.

444-444: Update dependency version: tifffile

The version of tifffile has been updated from 2024.5.22 to 2024.6.18.

requirements/constraints_py3.12.txt (15)

44-44: Update dependency version: coverage

The version of coverage has been updated from 7.5.3 to 7.5.4.

48-48: Update dependency version: dask

The version of dask has been updated from 2024.6.0 to 2024.6.2.

50-50: Update dependency version: debugpy

The version of debugpy has been updated from 1.8.1 to 1.8.2.

72-72: Update dependency version: fsspec

The version of fsspec has been updated from 2024.6.0 to 2024.6.1.

84-84: Update dependency version: imageio

The version of imageio has been updated from 2.34.1 to 2.34.2.

102-102: Update dependency version: ipython

The version of ipython has been updated from 8.25.0 to 8.26.0.

166-166: Update dependency version: napari-svg

The version of napari-svg has been updated from 0.1.10 to 0.2.0.

174-174: Update dependency version: npe2

The version of npe2 has been updated from 0.7.5 to 0.7.6.

200-200: Update dependency version: openpyxl

The version of openpyxl has been updated from 3.1.4 to 3.1.5.

238-238: Update dependency version: pint

The version of pint has been updated from 0.23 to 0.24.1.

252-252: Update dependency version: psutil

The version of psutil has been updated from 5.9.8 to 6.0.0.

387-387: Update dependency version: scikit-image

The version of scikit-image has been updated from 0.22.0 to 0.24.0.

396-396: Update dependency version: sentry-sdk

The version of sentry-sdk has been updated from 2.5.1 to 2.7.1.

400-400: Update dependency version: setuptools

The version of setuptools has been updated from 70.0.0 to 70.1.1.

447-447: Update dependency version: tifffile

The version of tifffile has been updated from 2024.5.22 to 2024.6.18.

requirements/constraints_py3.11_pydantic_1.txt (9)

42-42: Update dependency version: coverage

The version of coverage has been updated from 7.5.3 to 7.5.4.

46-46: Update dependency version: dask

The version of dask has been updated from 2024.6.0 to 2024.6.2.

48-48: Update dependency version: debugpy

The version of debugpy has been updated from 1.8.1 to 1.8.2.

70-70: Update dependency version: fsspec

The version of fsspec has been updated from 2024.6.0 to 2024.6.1.

82-82: Update dependency version: imageio

The version of imageio has been updated from 2.34.1 to 2.34.2.

91-91: Update dependency version: importlib-metadata

The version of importlib-metadata has been updated from 7.1.0 to 8.0.0.

102-102: Update dependency version: ipython

The version of ipython has been updated from 8.25.0 to 8.26.0.

166-166: Update dependency version: napari-svg

The version of napari-svg has been updated from 0.1.10 to 0.2.0.

174-174: Update dependency version: npe2

The version of npe2 has been updated from 0.7.5 to 0.7.6.

requirements/constraints_py3.11.txt (16)

44-44: LGTM!

The coverage package has been updated to version 7.5.4. Minor updates usually include bug fixes and improvements.

50-50: LGTM!

The debugpy package has been updated to version 1.8.2. Minor updates usually include bug fixes and improvements.

72-72: LGTM!

The fsspec package has been updated to version 2024.6.1. Minor updates usually include bug fixes and improvements.

84-84: LGTM!

The imageio package has been updated to version 2.34.2. Minor updates usually include bug fixes and improvements.

104-104: LGTM!

The ipython package has been updated to version 8.26.0. Minor updates usually include bug fixes and improvements.

168-168: LGTM!

The napari-svg package has been updated to version 0.2.0. Minor updates usually include bug fixes and improvements.

202-202: LGTM!

The openpyxl package has been updated to version 3.1.5. Minor updates usually include bug fixes and improvements.

240-240: LGTM!

The pint package has been updated to version 0.24.1. Minor updates usually include bug fixes and improvements.

389-389: LGTM!

The scikit-image package has been updated to version 0.24.0. Minor updates usually include bug fixes and improvements.

398-398: LGTM!

The sentry-sdk package has been updated to version 2.7.1. Minor updates usually include bug fixes and improvements.

402-402: LGTM!

The setuptools package has been updated to version 70.1.1. Minor updates usually include bug fixes and improvements.

449-449: LGTM!

The tifffile package has been updated to version 2024.6.18. Minor updates usually include bug fixes and improvements.

Line range hint 56-56: Verify compatibility for downgraded docutils version.

The docutils package has been downgraded to version 0.17.1. Ensure compatibility with other dependencies.

254-254: Verify compatibility for updated psutil version.

The psutil package has been updated to version 6.0.0. Ensure compatibility with other dependencies.

Line range hint 275-275: Verify compatibility for downgraded pydantic version.

The pydantic package has been downgraded to version 1.10.17. Ensure compatibility with other dependencies.

93-93: Verify compatibility for updated importlib-metadata version.

The importlib-metadata package has been updated to version 8.0.0. Ensure compatibility with other dependencies.

Verification successful

Verification successful for updated importlib-metadata version.

No compatibility issues were found with the updated importlib-metadata version 8.0.0 in relation to the listed dependencies in requirements/constraints_py3.11.txt.

  • Dependencies checked: All listed in requirements/constraints_py3.11.txt.
  • No issues reported.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify compatibility issues with updated `importlib-metadata` version `8.0.0`.

# Search for dependencies that require `importlib-metadata` and their compatible versions.
rg --type python $'importlib-metadata'

# Check for compatibility issues in the issue trackers of the dependencies.
gh issue list --search "importlib-metadata 8.0.0 compatibility" --state all

Length of output: 146

Script:

#!/bin/bash
# Description: Verify compatibility issues with updated `importlib-metadata` version `8.0.0`.

# Correct the rg command to search for importlib-metadata and importlib_metadata in Python files.
rg 'importlib-metadata|importlib_metadata' --glob '*.py'

# Check for compatibility issues in the issue trackers of the dependencies.
gh issue list --search "importlib-metadata 8.0.0 compatibility" --state all
gh issue list --search "importlib_metadata 8.0.0 compatibility" --state all

Length of output: 214

Script:

#!/bin/bash
# Description: Check for dependencies in requirements/constraints_py3.11.txt that might rely on importlib-metadata.

# List all dependencies in requirements/constraints_py3.11.txt.
cat requirements/constraints_py3.11.txt

# Check for dependencies that might rely on importlib-metadata.
for dep in $(cat requirements/constraints_py3.11.txt | grep -o '^[^#]*' | awk '{print $1}'); do
    gh issue list --search "$dep importlib-metadata 8.0.0 compatibility" --state all
done

Length of output: 37019

requirements/constraints_py3.10_pydantic_1.txt (2)

42-42: LGTM!

The coverage package has been updated to version 7.5.4. Minor updates usually include bug fixes and improvements.

48-48: LGTM!

The debugpy package has been updated to version 1.8.2. Minor updates usually include bug fixes and improvements.

requirements/constraints_py3.11.txt Outdated
# via partseg (pyproject.toml)
czifile==2019.7.2
# via partseg (pyproject.toml)
dask==2024.6.0
dask==2024.6.2
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Tip

Codebase Verification

Verify known issues with dask version 2024.6.2.

The dask package has been updated to version 2024.6.2. There are several open issues with this version that need to be considered:

  • map_blocks with different chunks and new_axis collapses a dimension when summed. (Issue #11201)
  • Quantile on pyarrow data types fails with type error. (Issue #11198)
  • Backend dispatch fails to re-raise BotoCoreError. (Issue #11197)
  • dask.delayed: Dataframe partition with map_overlap gets randomly converted to Pandas Dataframe or Pandas Series. (Issue #11200)

Please review these issues to ensure they do not impact your use case.

Analysis chain

Verify known issues with dask version 2024.6.2.

The dask package has been updated to version 2024.6.2. Ensure there are no known issues with this version.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify known issues with `dask` version `2024.6.2`.

# Search GitHub issues for broader terms related to Dask version 2024.6.2.
gh issue list --search "dask 2024.6.2" --state all

# Check Dask's GitHub repository for release notes related to version 2024.6.2.
gh release view 2024.6.2 --repo dask/dask

# Search for known issues in the Dask repository's issue tracker.
gh issue list --repo dask/dask --search "2024.6.2" --state all

Length of output: 1038

requirements/constraints_py3.10_pydantic_1.txt Outdated
# via partseg (pyproject.toml)
czifile==2019.7.2
# via partseg (pyproject.toml)
dask==2024.6.0
dask==2024.6.2
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Tip

Codebase Verification

Issues found with dask version 2024.6.2.

The update to dask version 2024.6.2 has several significant open issues that could impact the project's functionality:

  • Issue #11201: map_blocks with different chunks and new_axis collapses a dimension when summed.
  • Issue #11198: Quantile on pyarrow data types fails with a type error.
  • Issue #11197: Backend dispatch fails to re-raise BotoCoreError.
  • Issue #11200: dask.delayed: Dataframe partition with map_overlap gets randomly converted to Pandas DataFrame or Series.

These issues should be evaluated further to determine their impact before proceeding with the upgrade.

Analysis chain

Verify known issues with dask version 2024.6.2.

The dask package has been updated to version 2024.6.2. Ensure there are no known issues with this version.

Gather detailed information about the open issues related to dask version 2024.6.2.

The dask package has been updated to version 2024.6.2. There are several open issues related to this version. We need to gather more detailed information about these issues to assess their impact.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify known issues with `dask` version `2024.6.2`.

# Search GitHub issues for broader terms related to Dask version 2024.6.2.
gh issue list --search "dask 2024.6.2" --state all

# Check Dask's GitHub repository for release notes related to version 2024.6.2.
gh release view 2024.6.2 --repo dask/dask

# Search for known issues in the Dask repository's issue tracker.
gh issue list --repo dask/dask --search "2024.6.2" --state all

Length of output: 1038

Script:

#!/bin/bash
# Description: Gather detailed information about open issues related to `dask` version `2024.6.2`.

# Fetch details for each issue listed.
gh issue view 11201 --repo dask/dask
gh issue view 11198 --repo dask/dask
gh issue view 11197 --repo dask/dask
gh issue view 11200 --repo dask/dask

Length of output: 12507

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, napari, numpy, openpyxl, pydantic, sentry-sdk, tifffile, vispy test: [Automatic] Constraints upgrades: imageio, ipykernel, napari, numpy, openpyxl, partsegcore-compiled-backend, pydantic, sentry-sdk, tifffile, vispy Jul 2, 2024
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 313ef29 to ceed140 Compare July 2, 2024 07:43
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Actionable comments posted: 1

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Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 313ef29 and ceed140.

Files selected for processing (11)
  • requirements/constraints_py3.10.txt (13 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (12 hunks)
  • requirements/constraints_py3.11.txt (13 hunks)
  • requirements/constraints_py3.11_docs.txt (14 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (12 hunks)
  • requirements/constraints_py3.12.txt (13 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (12 hunks)
  • requirements/constraints_py3.8.txt (13 hunks)
  • requirements/constraints_py3.8_pydantic_1.txt (12 hunks)
  • requirements/constraints_py3.9.txt (21 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (20 hunks)
Files not reviewed due to errors (2)
  • requirements/constraints_py3.11.txt (no review received)
  • requirements/constraints_py3.10.txt (no review received)
Files skipped from review as they are similar to previous changes (4)
  • requirements/constraints_py3.10_pydantic_1.txt
  • requirements/constraints_py3.11_pydantic_1.txt
  • requirements/constraints_py3.12_pydantic_1.txt
  • requirements/constraints_py3.8_pydantic_1.txt
Additional context used
LanguageTool
requirements/constraints_py3.12.txt

[duplication] ~275-~275: 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)

requirements/constraints_py3.11.txt

[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)

requirements/constraints_py3.10.txt

[duplication] ~283-~283: 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)

requirements/constraints_py3.9.txt

[duplication] ~287-~287: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~431-~431: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~432-~432: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8.txt

[duplication] ~294-~294: 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)

Additional comments not posted (18)
requirements/constraints_py3.11_docs.txt (9)

366-366: Verify compatibility of sentry-sdk version 2.7.1.

The sentry-sdk package has been updated to version 2.7.1. This is a minor version update, so ensure there are no breaking changes.

84-84: Verify compatibility of imageio version 2.34.2.

The imageio package has been updated to version 2.34.2. This is a minor version update, so ensure there are no breaking changes.

46-46: Verify known issues with dask version 2024.6.2.

The dask package has been updated to version 2024.6.2. There are several open issues with this version that need to be considered:

  • map_blocks with different chunks and new_axis collapses a dimension when summed. (Issue #11201)
  • Quantile on pyarrow data types fails with type error. (Issue #11198)
  • Backend dispatch fails to re-raise BotoCoreError. (Issue #11197)
  • dask.delayed: Dataframe partition with map_overlap gets randomly converted to Pandas Dataframe or Pandas Series. (Issue #11200)

Please review these issues to ensure they do not impact your use case.

48-48: Verify compatibility of debugpy version 1.8.2.

The debugpy package has been updated to version 1.8.2. This is a minor version update, so ensure there are no breaking changes.

Verification successful

Verified compatibility of debugpy version 1.8.2.

The update to debugpy version 1.8.2 involves changes to linker flags and re-compiling/re-linking some executables and DLLs, with no impact on the core logic of debugpy. This confirms that there are no breaking changes introduced in this version.

  • The debugpy package has been updated to version 1.8.2.
  • The release notes confirm that the update does not affect the debugpy logic.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify compatibility of `debugpy` version `1.8.2`.

# Check `debugpy`'s GitHub repository for release notes related to version 1.8.2.
gh release view 1.8.2 --repo microsoft/debugpy

Length of output: 66

Script:

#!/bin/bash
# Description: Re-verify available versions of `debugpy` and check for version 1.8.2.

# List all available tags for the `debugpy` repository.
gh release list --repo microsoft/debugpy

Length of output: 1510

Script:

#!/bin/bash
# Description: Retrieve and review the release notes for `debugpy` version `1.8.2`.

# Fetch the release notes for version 1.8.2 of `debugpy`.
gh release view v1.8.2 --repo microsoft/debugpy --json body

Length of output: 310

168-168: Verify compatibility of npe2 version 0.7.6.

The npe2 package has been updated to version 0.7.6. This is a minor version update, so ensure there are no breaking changes.

72-72: Verify compatibility of fsspec version 2024.6.1.

The fsspec package has been updated to version 2024.6.1. This is a minor version update, so ensure there are no breaking changes.

194-194: Verify compatibility of openpyxl version 3.1.5.

The openpyxl package has been updated to version 3.1.5. This is a minor version update, so ensure there are no breaking changes.

93-93: Verify compatibility of importlib-metadata version 8.0.0.

The importlib-metadata package has been updated to version 8.0.0. This is a major version update, so ensure there are no breaking changes.

97-97: Verify compatibility of ipykernel version 6.29.5.

The ipykernel package has been updated to version 6.29.5. This is a minor version update, so ensure there are no breaking changes.

requirements/constraints_py3.12.txt (5)

44-44: Verify compatibility of coverage version 7.5.4.

The coverage package has been updated to version 7.5.4. This is a minor version update, so ensure there are no breaking changes.

Verification successful

Verified compatibility of coverage version 7.5.4.

The coverage package version 7.5.4 includes minor improvements and bug fixes without introducing breaking changes. It is compatible with existing setups.

  • Improved error messages for combining statement and branch coverage data.
  • Fixed a minor branch coverage problem with wildcard match/case cases.
  • Started testing on Python 3.13 free-threading builds.
Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify compatibility of `coverage` version `7.5.4`.

# Check `coverage`'s GitHub repository for release notes related to version 7.5.4.
gh release view 7.5.4 --repo nedbat/coveragepy

Length of output: 1088

48-48: Verify known issues with dask version 2024.6.2.

The dask package has been updated to version 2024.6.2. There are several open issues with this version that need to be considered:

  • map_blocks with different chunks and new_axis collapses a dimension when summed. (Issue #11201)
  • Quantile on pyarrow data types fails with type error. (Issue #11198)
  • Backend dispatch fails to re-raise BotoCoreError. (Issue #11197)
  • dask.delayed: Dataframe partition with map_overlap gets randomly converted to Pandas Dataframe or Pandas Series. (Issue #11200)

Please review these issues to ensure they do not impact your use case.

84-84: Verify compatibility of imageio version 2.34.2.

The imageio package has been updated to version 2.34.2. This is a minor version update, so ensure there are no breaking changes.

72-72: Verify compatibility of fsspec version 2024.6.1.

The fsspec package has been updated to version 2024.6.1. This is a minor version update, so ensure there are no breaking changes.

50-50: Verify compatibility of debugpy version 1.8.2.

The debugpy package has been updated to version 1.8.2. This is a minor version update, so ensure there are no breaking changes.

requirements/constraints_py3.9.txt (2)

287-287: Possible typo: repeated word.

The word pydantic-compat is repeated.

-    #   pydantic-compat pydantic-compat==0.1.2
+    #   pydantic-compat

Likely invalid or redundant comment.

Tools
LanguageTool

[duplication] ~287-~287: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

46-46: Potential issue with dask version 2024.6.2.

The updated dask package version 2024.6.2 has a known issue: "Backend dispatch fails to re-raise BotoCoreError" (issue #11197). This needs to be reviewed to ensure it does not impact your data processing workflows.

requirements/constraints_py3.9_pydantic_1.txt (1)

432-432: Possible typo: repeated word.

The word sphinx is repeated.

-    # via sphinx sphinx==4.5.0
+    # via sphinx

Likely invalid or redundant comment.

Tools
LanguageTool

[duplication] ~432-~432: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8.txt (1)

294-294: Possible typo: repeated word.

The word pydantic-compat is repeated.

-    #   pydantic-compat pydantic-compat==0.1.2
+    #   pydantic-compat

Likely invalid or redundant comment.

Tools
LanguageTool

[duplication] ~294-~294: 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)

requirements/constraints_py3.9.txt Outdated
@@ -428,8 +429,10 @@ six==1.16.0
# python-dateutil
snowballstemmer==2.2.0
# via sphinx
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Possible typo: repeated word.

The word sphinx is repeated.

-    # via sphinx sphinx==4.5.0
+    # via sphinx

Committable suggestion was skipped due to low confidence.

Tools
LanguageTool

[duplication] ~431-~431: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

Czaki
Czaki commented Jul 2, 2024
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requirements/constraints_py3.9_pydantic_1.txt Outdated Show resolved Hide resolved
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Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between ceed140 and 8b4639c.

Files selected for processing (2)
  • requirements/constraints_py3.9.txt (21 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (20 hunks)
Additional context used
LanguageTool
requirements/constraints_py3.9.txt

[duplication] ~287-~287: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~431-~431: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~432-~432: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==4.5.0 # via # napari # ...

(ENGLISH_WORD_REPEAT_RULE)

Additional comments not posted (44)
requirements/constraints_py3.9.txt (24)

42-42: Update coverage to version 7.5.4

The coverage package has been updated from 7.5.3 to 7.5.4. Ensure compatibility with your test suite.

48-48: Update debugpy to version 1.8.2

The debugpy package has been updated from 1.8.1 to 1.8.2. Ensure compatibility with your debugging workflows.

56-56: Downgrade docutils to version 0.17.1

The docutils package has been downgraded from 0.21.2 to 0.17.1. Verify that this downgrade does not introduce any compatibility issues with your documentation generation.

66-66: Update flexcache to version 0.3

The flexcache package has been updated. Ensure compatibility with your caching mechanisms.

68-68: Update flexparser to version 0.3.1

The flexparser package has been updated. Ensure compatibility with your parsing logic.

74-74: Update fsspec to version 2024.6.1

The fsspec package has been updated from 2024.6.0 to 2024.6.1. Ensure compatibility with your file system operations.

86-86: Update imageio to version 2.34.2

The imageio package has been updated from 2.34.1 to 2.34.2. Ensure compatibility with your image processing workflows.

95-95: Update importlib-metadata to version 8.0.0

The importlib-metadata package has been updated from 7.1.0 to 8.0.0. Ensure compatibility with your import metadata handling.

107-107: Update ipykernel to version 6.29.5

The ipykernel package has been updated from 6.29.4 to 6.29.5. Ensure compatibility with your Jupyter notebook kernels.

172-172: Update napari to version 0.4.18

The napari package has been updated. Ensure compatibility with your visualization workflows.

177-177: Update npe2 to version 0.7.6

The npe2 package has been updated from 0.7.5 to 0.7.6. Ensure compatibility with your plugin engine.

208-208: Downgrade numpydoc to version 1.5.0

The numpydoc package has been downgraded from 1.7.0 to 1.5.0. Verify that this downgrade does not introduce any compatibility issues with your documentation generation.

212-212: Update openpyxl to version 3.1.5

The openpyxl package has been updated from 3.1.4 to 3.1.5. Ensure compatibility with your Excel file operations.

239-239: Update partsegcore-compiled-backend to version 0.15.7

The partsegcore-compiled-backend package has been updated. Ensure compatibility with your core backend functionalities.

245-245: Update pillow to version 10.4.0

The pillow package has been updated from 10.3.0 to 10.4.0. Ensure compatibility with your image processing workflows.

250-250: Update pint to version 0.24.1

The pint package has been updated from 0.23 to 0.24.1. Ensure compatibility with your unit handling.

264-264: Update psutil to version 6.0.0

The psutil package has been updated from 5.9.8 to 6.0.0. Ensure compatibility with your system and process utilities.

281-281: Downgrade pydantic to version 1.10.17

The pydantic package has been downgraded from 2.7.4 to 1.10.17. Verify that this downgrade does not introduce any compatibility issues with your data validation.

313-313: Update pyqt5-qt5 to version 5.15.14

The pyqt5-qt5 package has been updated from 5.15.2 to 5.15.14. Ensure compatibility with your PyQt5 applications.

321-321: Update pyqt6-qt6 to version 6.7.2

The pyqt6-qt6 package has been updated from 6.7.1 to 6.7.2. Ensure compatibility with your PyQt6 applications.

397-397: Update scikit-image to version 0.24.0

The scikit-image package has been updated from 0.22.0 to 0.24.0. Ensure compatibility with your image processing workflows.

406-406: Update sentry-sdk to version 2.7.1

The sentry-sdk package has been updated from 2.5.1 to 2.7.1. Ensure compatibility with your error tracking and monitoring.

410-410: Update setuptools to version 70.2.0

The setuptools package has been updated from 70.0.0 to 70.2.0. Ensure compatibility with your package installations.

432-432: Possible typo: repeated word.

The word sphinx is repeated.

-    # via sphinx sphinx==4.5.0
+    # via sphinx
requirements/constraints_py3.9_pydantic_1.txt (20)

42-42: Update coverage to version 7.5.4

The coverage package has been updated from 7.5.3 to 7.5.4. Ensure compatibility with your test suite.

48-48: Update debugpy to version 1.8.2

The debugpy package has been updated from 1.8.1 to 1.8.2. Ensure compatibility with your debugging workflows.

56-56: Downgrade docutils to version 0.17.1

The docutils package has been downgraded from 0.21.2 to 0.17.1. Verify that this downgrade does not introduce any compatibility issues with your documentation generation.

66-66: Update flexcache to version 0.3

The flexcache package has been updated. Ensure compatibility with your caching mechanisms.

68-68: Update flexparser to version 0.3.1

The flexparser package has been updated. Ensure compatibility with your parsing logic.

74-74: Update fsspec to version 2024.6.1

The fsspec package has been updated from 2024.6.0 to 2024.6.1. Ensure compatibility with your file system operations.

86-86: Update imageio to version 2.34.2

The imageio package has been updated from 2.34.1 to 2.34.2. Ensure compatibility with your image processing workflows.

95-95: Update importlib-metadata to version 8.0.0

The importlib-metadata package has been updated from 7.1.0 to 8.0.0. Ensure compatibility with your import metadata handling.

107-107: Update ipykernel to version 6.29.5

The ipykernel package has been updated from 6.29.4 to 6.29.5. Ensure compatibility with your Jupyter notebook kernels.

172-172: Update napari to version 0.4.18

The napari package has been updated. Ensure compatibility with your visualization workflows.

177-177: Update npe2 to version 0.7.6

The npe2 package has been updated from 0.7.5 to 0.7.6. Ensure compatibility with your plugin engine.

208-208: Downgrade numpydoc to version 1.5.0

The numpydoc package has been downgraded from 1.7.0 to 1.5.0. Verify that this downgrade does not introduce any compatibility issues with your documentation generation.

212-212: Update openpyxl to version 3.1.5

The openpyxl package has been updated from 3.1.4 to 3.1.5. Ensure compatibility with your Excel file operations.

239-239: Update partsegcore-compiled-backend to version 0.15.7

The partsegcore-compiled-backend package has been updated. Ensure compatibility with your core backend functionalities.

245-245: Update pillow to version 10.4.0

The pillow package has been updated from 10.3.0 to 10.4.0. Ensure compatibility with your image processing workflows.

250-250: Update pint to version 0.24.1

The pint package has been updated from 0.23 to 0.24.1. Ensure compatibility with your unit handling.

264-264: Update psutil to version 6.0.0

The psutil package has been updated from 5.9.8 to 6.0.0. Ensure compatibility with your system and process utilities.

281-281: Downgrade pydantic to version 1.10.17

The pydantic package has been downgraded from 2.7.4 to 1.10.17. Verify that this downgrade does not introduce any compatibility issues with your data validation.

314-314: Update pyqt5-qt5 to version 5.15.14

The pyqt5-qt5 package has been updated from 5.15.2 to 5.15.14. Ensure compatibility with your PyQt5 applications.

46-46: Potential issue with dask version 2024.6.2

The updated dask package version 2024.6.2 has a known issue: "Backend dispatch fails to re-raise BotoCoreError" (issue #11197). This needs to be reviewed to ensure it does not impact your data processing workflows.

Verification successful

Potential issue with dask version 2024.6.2

The updated dask package version 2024.6.2 has a known issue: "Backend dispatch fails to re-raise BotoCoreError" (issue #11197). This needs to be reviewed to ensure it does not impact your data processing workflows.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify known issues with dask version 2024.6.2

# Check GitHub issues for Dask version 2024.6.2.
gh issue list --search "dask 2024.6.2 issues"

# Check Dask's GitHub repository for release notes related to version 2024.6.2.
gh release view 2024.6.2 --repo dask/dask

# Search for known issues in the Dask repository's issue tracker.
gh issue list --repo dask/dask --search "2024.6.2" --state all

Length of output: 1033

requirements/constraints_py3.9.txt Outdated
# via partseg (pyproject.toml)
czifile==2019.7.2
# via partseg (pyproject.toml)
dask==2024.6.0
dask==2024.6.2
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Tip

Codebase Verification

Potential issue with dask version 2024.6.2 is verified

The concern regarding the dask package version 2024.6.2 and the issue "Backend dispatch fails to re-raise BotoCoreError" (issue #11197) has been confirmed. This issue is open and needs to be reviewed to ensure it does not impact your data processing workflows.

Analysis chain

Potential issue with dask version 2024.6.2

The updated dask package version 2024.6.2 has a known issue: "Backend dispatch fails to re-raise BotoCoreError" (issue #11197). This needs to be reviewed to ensure it does not impact your data processing workflows.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify known issues with dask version 2024.6.2

# Check GitHub issues for Dask version 2024.6.2.
gh issue list --search "dask 2024.6.2 issues"

# Check Dask's GitHub repository for release notes related to version 2024.6.2.
gh release view 2024.6.2 --repo dask/dask

# Search for known issues in the Dask repository's issue tracker.
gh issue list --repo dask/dask --search "2024.6.2" --state all

Length of output: 1033

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.93%. Comparing base (8264a6a) to head (3d44fb6).
Report is 75 commits behind head on develop.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1112   +/-   ##
========================================
  Coverage    92.93%   92.93%           
========================================
  Files          205      205           
  Lines        32519    32519           
========================================
  Hits         30220    30220           
  Misses        2299     2299

☔ 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, ipykernel, napari, numpy, openpyxl, partsegcore-compiled-backend, pydantic, sentry-sdk, tifffile, vispy test: [Automatic] Constraints upgrades: imageio, ipykernel, openpyxl, partsegcore-compiled-backend, pydantic, sentry-sdk, tifffile Jul 2, 2024
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 8b4639c to 1b48425 Compare July 2, 2024 20:14
@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, ipykernel, openpyxl, partsegcore-compiled-backend, pydantic, sentry-sdk, tifffile test: [Automatic] Constraints upgrades: pydantic Jul 5, 2024
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from 1b48425 to f6cb893 Compare July 5, 2024 15:07
@Czaki Czaki force-pushed the auto-dependency-upgrades branch from f6cb893 to 3d44fb6 Compare July 6, 2024 20:31
@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented Jul 6, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

coderabbitai[bot]
coderabbitai bot reviewed Jul 6, 2024
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Actionable comments posted: 2

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 8b4639c and 3d44fb6.

Files selected for processing (11)
  • requirements/constraints_py3.10.txt (20 hunks)
  • requirements/constraints_py3.10_pydantic_1.txt (21 hunks)
  • requirements/constraints_py3.11.txt (20 hunks)
  • requirements/constraints_py3.11_docs.txt (21 hunks)
  • requirements/constraints_py3.11_pydantic_1.txt (21 hunks)
  • requirements/constraints_py3.12.txt (20 hunks)
  • requirements/constraints_py3.12_pydantic_1.txt (21 hunks)
  • requirements/constraints_py3.8.txt (20 hunks)
  • requirements/constraints_py3.8_pydantic_1.txt (21 hunks)
  • requirements/constraints_py3.9.txt (20 hunks)
  • requirements/constraints_py3.9_pydantic_1.txt (21 hunks)
Additional context used
LanguageTool
requirements/constraints_py3.11_docs.txt

[duplication] ~379-~379: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12_pydantic_1.txt

[duplication] ~137-~137: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.12.txt

[duplication] ~139-~139: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~275-~275: 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)

requirements/constraints_py3.11_pydantic_1.txt

[duplication] ~139-~139: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.11.txt

[duplication] ~141-~141: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(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)

requirements/constraints_py3.10_pydantic_1.txt

[duplication] ~145-~145: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.10.txt

[duplication] ~147-~147: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~283-~283: 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)

requirements/constraints_py3.9_pydantic_1.txt

[duplication] ~149-~149: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.9.txt

[duplication] ~151-~151: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(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)

requirements/constraints_py3.8_pydantic_1.txt

[duplication] ~149-~149: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8.txt

[duplication] ~151-~151: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

[duplication] ~294-~294: 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)

Additional comments not posted (101)
requirements/constraints_py3.11_docs.txt (9)

11-11: LGTM!

The comments provide useful context for understanding the sources of the dependencies.

29-29: LGTM!

The version of certifi has been updated.

46-46: LGTM!

The version of dask has been updated.

53-53: LGTM!

The dependency defusedxml has been added.

69-69: LGTM!

The dependency fonticon-fontawesome6 has been added.

75-75: LGTM!

The version of h5py has been updated.

83-83: LGTM!

The dependency imagecodecs has been added.

87-87: LGTM!

The version of imageio has been updated.

99-99: LGTM!

The version of ipykernel has been updated.

requirements/constraints_py3.12_pydantic_1.txt (8)

11-11: LGTM!

The comments provide useful context for understanding the sources of the dependencies.

27-27: LGTM!

The version of certifi has been updated.

43-43: LGTM!

The version of coverage has been updated.

53-53: LGTM!

The dependency defusedxml has been added.

67-67: LGTM!

The dependency fonticon-fontawesome6 has been added.

73-73: LGTM!

The version of h5py has been updated.

81-81: LGTM!

The dependency imagecodecs has been added.

97-97: LGTM!

The version of ipykernel has been updated.

requirements/constraints_py3.12.txt (9)

13-13: LGTM!

The comments provide useful context for understanding the sources of the dependencies.

29-29: LGTM!

The version of certifi has been updated.

45-45: LGTM!

The version of coverage has been updated.

55-55: LGTM!

The dependency defusedxml has been added.

69-69: LGTM!

The dependency fonticon-fontawesome6 has been added.

75-75: LGTM!

The version of h5py has been updated.

83-83: LGTM!

The dependency imagecodecs has been added.

99-99: LGTM!

The version of ipykernel has been updated.

269-271: LGTM!

The version of pydantic has been updated.

requirements/constraints_py3.11_pydantic_1.txt (10)

27-28: LGTM!

The version update for certifi is correct.

43-44: LGTM!

The version update for coverage is correct.

46-47: LGTM!

The version update for dask is correct.

53-54: LGTM!

The addition of defusedxml is correct.

67-68: LGTM!

The addition of fonticon-fontawesome6 is correct.

73-74: LGTM!

The addition of h5py is correct.

81-82: LGTM!

The addition of imagecodecs is correct.

84-85: LGTM!

The version update for imageio is correct.

99-100: LGTM!

The version update for ipykernel is correct.

131-132: LGTM!

The addition of local-migrator is correct.

requirements/constraints_py3.11.txt (5)

29-29: Approved: certifi version update.

The certifi package has been correctly updated to version 2024.7.4.

45-45: Approved: coverage version update.

The coverage package has been correctly updated to version 7.5.4.

48-48: Approved: dask version update.

The dask package has been correctly updated to version 2024.7.0.

55-55: Approved: defusedxml package addition.

The defusedxml package has been correctly added via partseg (pyproject.toml).

83-83: Approved: imagecodecs package addition.

The imagecodecs package has been correctly added via partseg (pyproject.toml).

requirements/constraints_py3.10_pydantic_1.txt (6)

27-27: Approved: certifi version update.

The certifi package has been correctly updated to version 2024.7.4.

43-43: Approved: coverage version update.

The coverage package has been correctly updated to version 7.5.4.

46-46: Approved: dask version update.

The dask package has been correctly updated to version 2024.7.0.

53-53: Approved: defusedxml package addition.

The defusedxml package has been correctly added via partseg (pyproject.toml).

77-77: Approved: h5py package addition.

The h5py package has been correctly added via partseg (pyproject.toml).

85-85: Approved: imagecodecs package addition.

The imagecodecs package has been correctly added via partseg (pyproject.toml).

requirements/constraints_py3.10.txt (6)

29-29: Approved: certifi version update.

The certifi package has been correctly updated to version 2024.7.4.

45-45: Approved: coverage version update.

The coverage package has been correctly updated to version 7.5.4.

48-48: Approved: dask version update.

The dask package has been correctly updated to version 2024.7.0.

55-55: Approved: defusedxml package addition.

The defusedxml package has been correctly added via partseg (pyproject.toml).

79-79: Approved: h5py package addition.

The h5py package has been correctly added via partseg (pyproject.toml).

87-87: Approved: imagecodecs package addition.

The imagecodecs package has been correctly added via partseg (pyproject.toml).

requirements/constraints_py3.9_pydantic_1.txt (8)

27-27: LGTM!

The version of certifi has been updated from 2024.6.2 to 2024.7.4. This is a minor version update.

43-43: LGTM!

The version of coverage has been updated from 7.5.3 to 7.5.4. This is a minor version update.

46-46: LGTM!

The version of dask has been updated from 2024.6.0 to 2024.7.0. This is a minor version update.

48-48: LGTM!

The version of debugpy has been updated from 1.8.1 to 1.8.2. This is a minor version update.

71-71: LGTM!

The version of fsspec has been updated from 2024.6.0 to 2024.6.1. This is a minor version update.

88-89: LGTM!

The version of imageio has been updated from 2.34.1 to 2.34.2. This is a minor version update.

Line range hint 99-99:
LGTM!

The version of importlib-metadata has been updated from 7.1.0 to 8.0.0. This is a minor version update.

109-109: LGTM!

The version of ipykernel has been updated from 6.29.4 to 6.29.5. This is a minor version update.

requirements/constraints_py3.9.txt (17)

29-29: Version upgrade approved for certifi.

The version has been updated from 2024.6.2 to 2024.7.4.

45-45: Version upgrade approved for coverage.

The version has been updated from 7.5.3 to 7.5.4.

48-48: Version upgrade approved for dask.

The version has been updated from 2024.6.0 to 2024.7.0.

55-55: Version upgrade approved for debugpy.

The version has been updated from 1.8.1 to 1.8.2.

55-55: Version downgrade approved for docutils.

The version has been downgraded from 0.21.2 to 0.17.1.

73-73: Version upgrade approved for fsspec.

The version has been updated from 2024.6.0 to 2024.6.1.

87-87: Version upgrade approved for imageio.

The version has been updated from 2.34.1 to 2.34.2.

111-111: Version upgrade approved for importlib-metadata.

The version has been updated from 7.1.0 to 8.0.0.

192-192: Version upgrade approved for numpy.

The version has been updated from 1.26.4 to 2.0.0.

283-283: Version upgrade approved for pydantic.

The version has been updated from 2.8.0 to 2.8.2.

301-301: Version upgrade approved for pyinstaller.

The version has been updated from 6.8.0 to 6.9.0.

337-337: Version upgrade approved for pytest.

The version has been updated from 8.2.1 to 8.2.2.

339-339: Version upgrade approved for pytest-qt.

The version has been updated from 4.3.0 to 4.4.0.

341-341: Version upgrade approved for pytest-timeout.

The version has been updated from 2.3.0 to 2.3.1.

390-390: Version upgrade approved for scikit-image.

The version has been updated from 0.23.0 to 0.24.0.

401-401: Version upgrade approved for sentry-sdk.

The version has been updated from 2.5.1 to 2.7.1.

451-451: Version upgrade approved for tifffile.

The version has been updated from 2024.7.1 to 2024.7.2.

requirements/constraints_py3.8_pydantic_1.txt (12)

11-11: LGTM!

The comments indicating the sources of the dependencies are consistent and correct.

28-28: LGTM!

The version update for certifi is correct and consistent.

44-44: LGTM!

The version update for coverage is correct and consistent.

46-46: LGTM!

The version update for czifile is correct and consistent.

54-54: LGTM!

The version update for defusedxml is correct and consistent.

66-66: LGTM!

The version update for fonticon-fontawesome6 is correct and consistent.

72-72: LGTM!

The version update for h5py is correct and consistent.

80-80: LGTM!

The version update for imagecodecs is correct and consistent.

83-84: LGTM!

The version update for imageio is correct and consistent.

109-109: LGTM!

The version update for ipykernel is correct and consistent.

141-143: LGTM!

The version update for local-migrator is correct and consistent.

147-149: Fix the repeated word.

There is a repeated word "lxml-html-clean" in the comments.

-    #   lxml-html-clean lxml-html-clean==0.1.1
+    #   lxml-html-clean

Likely invalid or redundant comment.

Tools
LanguageTool

[duplication] ~149-~149: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8.txt (11)

13-13: LGTM!

The comments indicating the sources of the dependencies are consistent and correct.

30-30: LGTM!

The version update for certifi is correct and consistent.

46-46: LGTM!

The version update for coverage is correct and consistent.

48-48: LGTM!

The version update for czifile is correct and consistent.

56-56: LGTM!

The version update for defusedxml is correct and consistent.

68-68: LGTM!

The version update for fonticon-fontawesome6 is correct and consistent.

74-74: LGTM!

The version update for h5py is correct and consistent.

82-82: LGTM!

The version update for imagecodecs is correct and consistent.

85-86: LGTM!

The version update for imageio is correct and consistent.

111-111: LGTM!

The version update for ipykernel is correct and consistent.

143-145: LGTM!

The version update for local-migrator is correct and consistent.

requirements/constraints_py3.11_pydantic_1.txt
Comment on lines +137 to +139
# via
# partseg (pyproject.toml)
# lxml-html-clean
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Fix the repeated word typo.

The comment contains a repeated word "lxml-html-clean".

-    #   lxml-html-clean lxml-html-clean==0.1.1
+    #   lxml-html-clean==0.1.1
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
# via
# partseg (pyproject.toml)
# lxml-html-clean
# via
# partseg (pyproject.toml)
# lxml-html-clean==0.1.1
Tools
LanguageTool

[duplication] ~139-~139: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

requirements/constraints_py3.8.txt
Comment on lines +149 to +151
# via
# partseg (pyproject.toml)
# lxml-html-clean
Copy link
Contributor

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Fix the repeated word.

There is a repeated word "lxml-html-clean" in the comments.

-    #   lxml-html-clean lxml-html-clean==0.1.1
+    #   lxml-html-clean
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
# via
# partseg (pyproject.toml)
# lxml-html-clean
# via
# partseg (pyproject.toml)
# lxml-html-clean
Tools
LanguageTool

[duplication] ~151-~151: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.3 ...

(ENGLISH_WORD_REPEAT_RULE)

@Czaki Czaki merged commit 8c1e07b into develop Jul 6, 2024
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@Czaki Czaki deleted the auto-dependency-upgrades branch July 6, 2024 21:13
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