test: [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy
#1107
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WalkthroughThe changes involve updating several Python package versions across different requirements files for better compatibility and performance. These updates mainly focus on enhancing security, fixing bugs, and improving existing functionalities. Additionally, a few new dependencies have been added to support various features and tools. Changes
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Actionable comments posted: 0
Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (11)
- requirements/constraints_py3.10.txt (4 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.11.txt (4 hunks)
- requirements/constraints_py3.11_docs.txt (2 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.12.txt (4 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.8.txt (4 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (4 hunks)
- requirements/constraints_py3.9.txt (4 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (4 hunks)
Files not reviewed due to errors (2)
- requirements/constraints_py3.8_pydantic_1.txt (no review received)
- requirements/constraints_py3.8.txt (no review received)
Additional Context Used
LanguageTool (43)
requirements/constraints_py3.10.txt (4)
Near line 127: Possible typo: you repeated a word
Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 151: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 248: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 363: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.10_pydantic_1.txt (4)
Near line 125: Possible typo: you repeated a word
Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 149: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 246: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 359: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11.txt (4)
Near line 121: Possible typo: you repeated a word
Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11_docs.txt (3)
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 203: Possible typo: you repeated a word
Context: ... # via # jupyter-core # pooch pooch==1.8.1 # via scikit-image prompt-to...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # autodoc-pydant...requirements/constraints_py3.11_pydantic_1.txt (4)
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Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12.txt (4)
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Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12_pydantic_1.txt (4)
Near line 117: Possible typo: you repeated a word
Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 141: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.8.txt (4)
Near line 136: Possible typo: you repeated a word
Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 160: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...requirements/constraints_py3.8_pydantic_1.txt (4)
Near line 134: Possible typo: you repeated a word
Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 158: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 377: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...requirements/constraints_py3.9.txt (4)
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Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 155: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 252: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.9_pydantic_1.txt (4)
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Context: ...0 # via partd lxml==5.2.2 # via lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 153: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 250: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 363: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Additional comments not posted (43)
requirements/constraints_py3.11_docs.txt (3)
7-7: Updatedapp-modelto0.2.7to align with the latest version.
359-359: Updatedsuperqtto0.6.6to keep up with the latest release.
366-366: Updatedtifffileto2024.5.10for enhanced features and bug fixes.requirements/constraints_py3.12_pydantic_1.txt (5)
7-7: Updatedapp-modelto0.2.7to align with the latest version.
116-116: Updatedlxmlto5.2.2to keep up with the latest release.
250-250: Updatedpyinstaller-hooks-contribto2024.6for enhanced features and bug fixes.
368-368: Updatedsuperqtto0.6.6to keep up with the latest release.
375-375: Updatedtifffileto2024.5.10for enhanced features and bug fixes.requirements/constraints_py3.12.txt (5)
9-9: Updatedapp-modelto0.2.7to align with the latest version.
118-118: Updatedlxmlto5.2.2to keep up with the latest release.
254-254: Updatedpyinstaller-hooks-contribto2024.6for enhanced features and bug fixes.
372-372: Updatedsuperqtto0.6.6to keep up with the latest release.
379-379: Updatedtifffileto2024.5.10for enhanced features and bug fixes.requirements/constraints_py3.11_pydantic_1.txt (5)
7-7: Updatedapp-modelto0.2.7to align with the latest version.
118-118: Updatedlxmlto5.2.2to keep up with the latest release.
252-252: Updatedpyinstaller-hooks-contribto2024.6for enhanced features and bug fixes.
370-370: Updatedsuperqtto0.6.6to keep up with the latest release.
377-377: Updatedtifffileto2024.5.10for enhanced features and bug fixes.requirements/constraints_py3.11.txt (5)
9-9: Updatedapp-modelto0.2.7as per PR objectives.
120-120: Updatedlxmlto5.2.2as per PR objectives.
256-256: Updatedpyinstaller-hooks-contribto2024.6as per PR objectives.
374-374: Updatedsuperqtto0.6.6as per PR objectives.
381-381: Updatedtifffileto2024.5.10as per PR objectives.requirements/constraints_py3.10_pydantic_1.txt (5)
7-7: Updatedapp-modelto0.2.7as per PR objectives.
124-124: Updatedlxmlto5.2.2as per PR objectives.
258-258: Updatedpyinstaller-hooks-contribto2024.6as per PR objectives.
376-376: Updatedsuperqtto0.6.6as per PR objectives.
383-383: Updatedtifffileto2024.5.10as per PR objectives.requirements/constraints_py3.10.txt (5)
9-9: Updatedapp-modelto0.2.7as per PR objectives.
126-126: Updatedlxmlto5.2.2as per PR objectives.
262-262: Updatedpyinstaller-hooks-contribto2024.6as per PR objectives.
380-380: Updatedsuperqtto0.6.6as per PR objectives.
387-387: Updatedtifffileto2024.5.10as per PR objectives.requirements/constraints_py3.9_pydantic_1.txt (5)
7-7: Updatedapp-modelto version0.2.7. This change aligns with the PR's objective to keep dependencies up-to-date.
128-128: Updatedlxmlto version5.2.2. This update is consistent with the PR's goal of maintaining current dependencies.
262-262: Updatedpyinstaller-hooks-contribto version2024.6. This change is part of the systematic updates across various Python versions.
380-380: Updatedsuperqtto version0.6.6. This update is part of the ongoing effort to ensure compatibility and stability across environments.
387-387: Updatedtifffileto version2024.5.10. This significant update is likely aimed at addressing new features or security patches.requirements/constraints_py3.9.txt (5)
9-9: Updatedapp-modelto0.2.7looks good.
130-130: Updatedlxmlto5.2.2looks good.
266-266: Updatedpyinstaller-hooks-contribto2024.6looks good.
384-384: Updatedsuperqtto0.6.6looks good.
391-391: Updatedtifffileto2024.5.10looks good.
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superqt, tifffilesentry-sdk, superqt, tifffile
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Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (11)
- requirements/constraints_py3.10.txt (20 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.11.txt (20 hunks)
- requirements/constraints_py3.11_docs.txt (22 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.12.txt (20 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.8.txt (20 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.9.txt (20 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (20 hunks)
Additional Context Used
LanguageTool (43)
requirements/constraints_py3.10.txt (4)
Near line 142: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 170: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 280: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 426: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.10_pydantic_1.txt (4)
Near line 140: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11.txt (4)
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Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11_docs.txt (3)
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ... # via # jupyter-core # pooch pooch==1.8.1 # via scikit-image prompt-to...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...requirements/constraints_py3.11_pydantic_1.txt (4)
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Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12.txt (4)
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Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12_pydantic_1.txt (4)
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Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.8.txt (4)
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Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...requirements/constraints_py3.8_pydantic_1.txt (4)
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Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...requirements/constraints_py3.9.txt (4)
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.9_pydantic_1.txt (4)
Near line 144: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
Near line 172: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Near line 283: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 427: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Additional comments not posted (77)
requirements/constraints_py3.11_docs.txt (5)
7-7: Updatedapp-modelto0.2.7aligns with the PR's objective to keep dependencies updated. Ensure that this version is compatible with other dependencies.
45-45: Updateddaskto2024.5.1. Verify that this version works well with the project's parallel computation requirements.Verification successful
The search results indicate that
daskis used in thelauncher.specfile, specifically for importing configurations and collecting data files. However, there were no issues found in the project's issue tracker related todask.Given this information, it seems that the update to
daskversion2024.5.1does not introduce any immediate compatibility issues based on the current codebase and issue tracker.
- File:
launcher.spec
- Lines:
from dask import configos.path.join(os.path.dirname(config.__file__), "dask.yaml")collect_data_files("dask")Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any reported issues with dask 2024.5.1 in relation to parallel computations. gh issue list --search "dask 2024.5.1 problems with parallel computation"Length of output: 75
Script:
#!/bin/bash # Search for `dask` usage in the codebase to identify potential compatibility issues rg 'dask' --glob '!requirements/*' # Check the project's issue tracker for any issues related to `dask` gh issue list --search "dask"Length of output: 241
482-482: Updatedzippto3.18.2. This package is often a transitive dependency; ensure no conflicts with direct dependencies.
67-67: Updatedfsspecto2024.5.0. This is crucial for handling file-system interfaces; please ensure it integrates smoothly withdask.
419-419: Updatedtifffileto2024.5.10. Given the significant version jump, confirm that there are no breaking changes affecting image processing functionalities.requirements/constraints_py3.12_pydantic_1.txt (5)
7-7: Updatedapp-modelto0.2.7is consistent with updates across other files. Good to maintain version consistency across environments.
45-45: Updateddaskto2024.5.1. As previously noted, ensure compatibility with parallel processing features.
65-65: Updatedfsspecto2024.5.0. As with other files, ensure it works well withdaskfor file handling.
441-441: Updatedtifffileto2024.5.10. As noted earlier, check for any potential breaking changes due to the version update.
323-323: Updatedpytestto8.2.1. Verify that all unit tests are compatible with this new version to avoid disruptions in CI pipelines.requirements/constraints_py3.12.txt (5)
9-9: Updatedapp-modelto0.2.7. Consistency across different Python versions is crucial for maintaining a stable build environment.
47-47: Updateddaskto2024.5.1. Consistent updates across files are good for maintaining compatibility.
67-67: Updatedfsspecto2024.5.0. Important for file system operations, especially in conjunction withdask.
444-444: Updatedtifffileto2024.5.10. Repeat the checks for breaking changes as noted in other files.
326-326: Updatedpytestto8.2.1. Ensure that this update does not introduce any issues with the project's testing framework.requirements/constraints_py3.11_pydantic_1.txt (9)
7-7: Updatedapp-modelto version0.2.7to keep dependencies up-to-date.
45-45: Updateddaskto version2024.5.1aligns with the latest available version, ensuring compatibility and performance improvements.
65-65: Updatedfsspecto version2024.5.0to maintain compatibility with the latestdaskversion.
131-131: Updatedlxmlto version5.2.2, enhancing XML processing capabilities with the latest security and performance improvements.
325-325: Updatedpytestto version8.2.1, ensuring compatibility with the latest Python features and improved testing capabilities.
392-392: Updatedsentry-sdkto version2.2.0, enhancing error tracking and performance monitoring capabilities.
434-434: Updatedsuperqtto version0.6.6, ensuring compatibility with the latest Qt features and performance improvements.
443-443: Updatedtifffileto version2024.5.10, enhancing TIFF file handling capabilities with the latest performance improvements.
134-134: Correct the repeated word in the comment.- # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml + # partseg (pyproject.toml) # lxml-html-clean==0.1.1 # via lxmlrequirements/constraints_py3.11.txt (9)
9-9: Updatedapp-modelto version0.2.7to keep dependencies up-to-date.
47-47: Updateddaskto version2024.5.1aligns with the latest available version, ensuring compatibility and performance improvements.
67-67: Updatedfsspecto version2024.5.0to maintain compatibility with the latestdaskversion.
133-133: Updatedlxmlto version5.2.2, enhancing XML processing capabilities with the latest security and performance improvements.
328-328: Updatedpytestto version8.2.1, ensuring compatibility with the latest Python features and improved testing capabilities.
395-395: Updatedsentry-sdkto version2.2.0, enhancing error tracking and performance monitoring capabilities.
437-437: Updatedsuperqtto version0.6.6, ensuring compatibility with the latest Qt features and performance improvements.
446-446: Updatedtifffileto version2024.5.10, enhancing TIFF file handling capabilities with the latest performance improvements.
136-136: Correct the repeated word in the comment.- # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml + # partseg (pyproject.toml) # lxml-html-clean==0.1.1 # via lxmlrequirements/constraints_py3.10_pydantic_1.txt (9)
7-7: Updatedapp-modelto version0.2.7to keep dependencies up-to-date.
45-45: Updateddaskto version2024.5.1aligns with the latest available version, ensuring compatibility and performance improvements.
69-69: Updatedfsspecto version2024.5.0to maintain compatibility with the latestdaskversion.
137-137: Updatedlxmlto version5.2.2, enhancing XML processing capabilities with the latest security and performance improvements.
331-331: Updatedpytestto version8.2.1, ensuring compatibility with the latest Python features and improved testing capabilities.
398-398: Updatedsentry-sdkto version2.2.0, enhancing error tracking and performance monitoring capabilities.
440-440: Updatedsuperqtto version0.6.6, ensuring compatibility with the latest Qt features and performance improvements.
449-449: Updatedtifffileto version2024.5.10, enhancing TIFF file handling capabilities with the latest performance improvements.
140-140: Correct the repeated word in the comment.- # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml + # partseg (pyproject.toml) # lxml-html-clean==0.1.1 # via lxmlrequirements/constraints_py3.10.txt (8)
9-9: Updatedapp-modelto0.2.7aligns with the PR's objective to keep dependencies updated.
47-47: Updateddaskto2024.5.1ensures compatibility with the latest features and fixes.
71-71: Updatedfsspecto2024.5.0to maintain compatibility withdask.
139-139: Updatedlxmlto5.2.2addresses potential security and performance improvements.
296-296: Updatedpyinstaller-hooks-contribto2024.6ensures that the latest hooks are available for PyInstaller.
443-443: Updatedsuperqtto0.6.6likely enhances UI components used in the project.
452-452: Updatedtifffileto2024.5.10ensures support for the latest image formats and fixes.
522-522: Updatedzippto3.18.2ensures better handling of zip files in Python environments.requirements/constraints_py3.9_pydantic_1.txt (8)
7-7: Updatedapp-modelto0.2.7aligns with the PR's objective to keep dependencies updated.
45-45: Updateddaskto2024.5.1ensures compatibility with the latest features and fixes.
69-69: Updatedfsspecto2024.5.0to maintain compatibility withdask.
141-141: Updatedlxmlto5.2.2addresses potential security and performance improvements.
297-297: Updatedpyinstaller-hooks-contribto2024.6ensures that the latest hooks are available for PyInstaller.
444-444: Updatedsuperqtto0.6.6likely enhances UI components used in the project.
453-453: Updatedtifffileto2024.5.10ensures support for the latest image formats and fixes.
522-522: Updatedzippto3.18.2ensures better handling of zip files in Python environments.requirements/constraints_py3.9.txt (7)
9-9: Updatedapp-modelto version0.2.7as per the PR objectives and AI-generated summary. This change is consistent and correctly documented.
47-47: Updateddaskto version2024.5.1. This change is consistent with the PR objectives to keep dependencies updated, although it is not explicitly mentioned in the AI-generated summary.
71-71: Updatedfsspecto version2024.5.0. This change aligns with the PR objectives to update dependencies, though not specifically highlighted in the AI-generated summary.
300-300: Updatedpyinstaller-hooks-contribto version2024.6. This change is consistent with the PR objectives and AI-generated summary.
447-447: Updatedsuperqtto version0.6.6. This change aligns with the PR objectives and AI-generated summary.
456-456: Updatedtifffileto version2024.5.10. This change is consistent with the PR objectives and AI-generated summary.
143-143: Updatedlxmlto version5.2.2. This update is consistent with the PR objectives and AI-generated summary. Ensure that all dependent packages are compatible with this new version.Also applies to: 145-145
requirements/constraints_py3.8_pydantic_1.txt (6)
7-7: Updatedapp-modelto version0.2.7as per the PR objectives and AI-generated summary. This change is consistent and correctly documented.
69-69: Updatedfsspecto version2024.5.0. This change aligns with the PR objectives to update dependencies, though not specifically highlighted in the AI-generated summary.
307-307: Updatedpyinstaller-hooks-contribto version2024.6. This change is consistent with the PR objectives and AI-generated summary.
458-458: Updatedsuperqtto version0.6.6. This change aligns with the PR objectives and AI-generated summary.
469-469: Updatedtifffileto version2023.7.10. This change is consistent with the PR objectives and AI-generated summary.
146-146: Updatedlxmlto version5.2.2. This update is consistent with the PR objectives and AI-generated summary. Ensure that all dependent packages are compatible with this new version.Also applies to: 148-148
Verification successful
The usage of
lxmlinpackage/tests/test_PartSegImage/test_image_writer.pyinvolves importingetreeand using it to create anXMLSchemaobject. This usage is standard and should be compatible withlxml==5.2.2.
package/tests/test_PartSegImage/test_image_writer.py:from lxml import etreeScripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `lxml==5.2.2` with dependent packages. # Test: Search for dependent packages in the project. Expect: No compatibility issues reported. rg --type python $'lxml==5.2.2'Length of output: 61
Script:
#!/bin/bash # Description: Verify compatibility of `lxml==5.2.2` with dependent packages. # Test: Search for dependent packages in the project. Expect: No compatibility issues reported. rg 'import lxml' --type py rg 'from lxml' --type pyLength of output: 140
Script:
#!/bin/bash # Description: Extract and review the usage of `lxml` in the identified file to ensure compatibility with version `5.2.2`. # Extract the relevant lines from the file rg 'from lxml import etree' -A 10 package/tests/test_PartSegImage/test_image_writer.pyLength of output: 416
requirements/constraints_py3.8.txt (6)
9-9: Updatedapp-modelto version0.2.7as per the PR objectives and AI-generated summary. This change is consistent and correctly documented.
71-71: Updatedfsspecto version2024.5.0. This change aligns with the PR objectives to update dependencies, though not specifically highlighted in the AI-generated summary.
310-310: Updatedpyinstaller-hooks-contribto version2024.6. This change is consistent with the PR objectives and AI-generated summary.
461-461: Updatedsuperqtto version0.6.6. This change aligns with the PR objectives and AI-generated summary.
472-472: Updatedtifffileto version2023.7.10. This change is consistent with the PR objectives and AI-generated summary.
148-148: Updatedlxmlto version5.2.2. This update is consistent with the PR objectives and AI-generated summary. Ensure that all dependent packages are compatible with this new version.Also applies to: 150-150
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1107 +/- ##
===========================================
- Coverage 92.95% 92.95% -0.01%
===========================================
Files 205 205
Lines 32480 32465 -15
===========================================
- Hits 30193 30178 -15
Misses 2287 2287 ☔ View full report in Codecov by Sentry. |
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Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (11)
- requirements/constraints_py3.10.txt (21 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (21 hunks)
- requirements/constraints_py3.11.txt (21 hunks)
- requirements/constraints_py3.11_docs.txt (23 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (21 hunks)
- requirements/constraints_py3.12.txt (21 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (21 hunks)
- requirements/constraints_py3.8.txt (22 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.9.txt (22 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (22 hunks)
Files not reviewed due to errors (1)
- requirements/constraints_py3.12_pydantic_1.txt (no review received)
Additional Context Used
LanguageTool (43)
requirements/constraints_py3.10.txt (4)
Near line 142: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
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Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
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Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.10_pydantic_1.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.11.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.11_docs.txt (3)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.11_pydantic_1.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.12.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.12_pydantic_1.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.8.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.8_pydantic_1.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.9.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.9_pydantic_1.txt (4)
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Rule ID: ENGLISH_WORD_REPEAT_RULE
Additional comments not posted (218)
requirements/constraints_py3.11_docs.txt (55)
5-5: Updatedannotated-typesto0.7.0to align with newer version requirements.
7-7: Updatedapp-modelto0.2.7to keep dependencies up-to-date.
44-44: Addedczifileversion2019.7.2as a new dependency.
45-45: Updateddaskto2024.5.1to ensure compatibility with other updated packages.
52-52: Addeddefusedxmlversion0.7.1as a new dependency.
64-64: Addedfonticon-fontawesome6version6.4.0as a new dependency.
67-67: Updatedfsspecto2024.5.0to align with the latest available version.
70-70: Addedh5pyversion3.11.0as a new dependency.
78-78: Addedimagecodecsversion2024.1.1as a new dependency.
81-82: Addedimageioversion2.34.1as a new dependency.
94-94: Addedipykernelversion6.29.4as a new dependency.
99-99: Addedipythonversion8.24.0as a new dependency.
110-110: Updatedjupyter-clientto8.6.2to ensure compatibility with other updated packages.
126-128: Addedlocal-migratorversion0.1.10as a new dependency.
132-134: Addedmagicguiversion0.8.2as a new dependency.
136-136: Addedmahotasversion1.4.15as a new dependency.
150-150: Addednapariversion0.4.19.post1as a new dependency.
164-164: Addednmeversion0.1.8as a new dependency.
166-168: Addednpe2version0.7.5as a new dependency.
171-171: Addednumpyversion1.26.4as a new dependency.
189-190: Updatedoiffileto2024.5.24to align with the latest available version.
192-192: Addedopenpyxlversion3.1.2as a new dependency.
195-195: Updatedpackagingto24.0to ensure compatibility with other updated packages.
208-210: Addedpandasversion2.2.2as a new dependency.
216-218: Addedpartsegcore-compiled-backendversion0.15.6as a new dependency.
228-228: Updatedplatformdirsto4.2.2to align with the latest available version.
242-242: Addedpsygnalversion0.11.1as a new dependency.
255-255: Addedpydanticversion2.7.1as a new dependency.
270-270: Addedpygmentsversion2.18.0as a new dependency.
282-282: Addedpyqt5version5.15.10as a new dependency.
286-288: Addedpyqt5-sipversion12.13.0as a new dependency.
290-290: Addedpyqt6version6.7.0as a new dependency.
296-297: Addedpyside2version5.13.2as a new dependency.
298-299: Addedpyside6version6.7.1as a new dependency.
301-301: Addedpyside6-addonsversion6.7.1as a new dependency.
324-324: Addedqtawesomeversion1.3.1as a new dependency.
326-328: Addedqtconsoleversion5.5.2as a new dependency.
331-331: Addedqtpyversion2.4.1as a new dependency.
342-344: Updatedrequeststo2.32.2to ensure compatibility with other updated packages.
358-360: Updatedscipyto1.13.1to align with the latest available version.
363-366: Updatedsentry-sdkto2.3.1to ensure compatibility with other updated packages.
371-371: Addedshiboken6version6.7.1as a new dependency.
377-377: Addedsimpleitkversion2.3.1as a new dependency.
380-380: Addedsixversion1.16.0as a new dependency.
387-387: Addedsphinxversion7.3.7as a new dependency.
393-395: Addedsphinx-qt-documentationversion0.4.1as a new dependency.
410-412: Updatedsuperqtto0.6.6to align with the latest available version.
416-416: Addedsympyversion1.12as a new dependency.
419-419: Addedtabulateversion0.9.0as a new dependency.
421-421: Updatedtifffileto2024.5.22to ensure compatibility with other updated packages.
440-440: Addedtraceback-with-variablesversion2.0.4as a new dependency.
452-452: Updatedtyping-extensionsto4.12.0to align with the latest available version.
471-471: Addedvispyversion0.14.2as a new dependency.
479-479: Addedxlrdversion2.0.1as a new dependency.
481-482: Addedxlsxwriterversion3.2.0as a new dependency.requirements/constraints_py3.12.txt (14)
7-7: Updatedannotated-typesto0.7.0aligns with the PR objectives to keep dependencies up to date.
9-9: Updatedapp-modelto0.2.7is consistent with the PR's update list.
43-44: Updatedcoverageto7.5.2as specified in the PR's objectives.
47-47: Updateddaskto2024.5.1matches the intended updates listed in the PR.
67-67: Updatedfsspecto2024.5.0correctly reflects the changes intended by the PR.
110-110: Updatedjupyter-clientto8.6.2is in line with the updates mentioned in the PR summary.
195-196: Updatedoiffileto2024.5.24is correctly listed in the PR's update objectives.
237-237: Updatedplatformdirsto4.2.2is part of the updates as per the PR description.
370-370: Updatedrequeststo2.32.2correctly reflects the intended updates in the PR.
388-389: Updatedscipyto1.13.1aligns with the updates listed in the PR.
393-394: Updatedsentry-sdkto2.3.1matches the updates intended in the PR.
435-435: Updatedsuperqtto0.6.6is consistent with the updates listed in the PR.
444-444: Updatedtifffileto2024.5.22correctly reflects the changes intended by the PR.
477-477: Updatedtyping-extensionsto4.12.0is part of the updates as per the PR description.requirements/constraints_py3.11_pydantic_1.txt (13)
7-7: Updatedapp-modelto0.2.7aligns with the PR objectives to keep dependencies up to date.
41-42: Updatedcoverageto7.5.2as specified in the PR's objectives.
45-45: Updateddaskto2024.5.1matches the intended updates listed in the PR.
65-65: Updatedfsspecto2024.5.0correctly reflects the changes intended by the PR.
110-110: Updatedjupyter-clientto8.6.2is in line with the updates mentioned in the PR summary.
195-196: Updatedoiffileto2024.5.24is correctly listed in the PR's update objectives.
237-237: Updatedplatformdirsto4.2.2is part of the updates as per the PR description.
369-370: Updatedrequeststo2.32.2correctly reflects the intended updates in the PR.
388-389: Updatedscipyto1.13.1aligns with the updates listed in the PR.
393-394: Updatedsentry-sdkto2.3.1matches the updates intended in the PR.
434-435: Updatedsuperqtto0.6.6is consistent with the updates listed in the PR.
443-444: Updatedtifffileto2024.5.22correctly reflects the changes intended by the PR.
476-477: Updatedtyping-extensionsto4.12.0is part of the updates as per the PR description.requirements/constraints_py3.11.txt (13)
7-7: Updatedannotated-typesto0.7.0as per PR objectives.
9-9: Updatedapp-modelto0.2.7as per PR objectives.
43-44: Updatedcoverageto7.5.2as per PR objectives.
47-47: Updateddaskto2024.5.1as per PR objectives.
67-67: Updatedfsspecto2024.5.0as per PR objectives.
112-112: Updatedjupyter-clientto8.6.2as per PR objectives.
197-198: Updatedoiffileto2024.5.24as per PR objectives.
328-328: Updatedpytestto8.2.1as per PR objectives.
372-372: Updatedrequeststo2.32.2as per PR objectives.
395-396: Updatedsentry-sdkto2.3.1as per PR objectives.
437-437: Updatedsuperqtto0.6.6as per PR objectives.
446-446: Updatedtifffileto2024.5.22as per PR objectives.
479-479: Updatedtyping-extensionsto4.12.0as per PR objectives.requirements/constraints_py3.10_pydantic_1.txt (12)
7-7: Updatedapp-modelto0.2.7as per PR objectives.
41-42: Updatedcoverageto7.5.2as per PR objectives.
45-45: Updateddaskto2024.5.1as per PR objectives.
69-69: Updatedfsspecto2024.5.0as per PR objectives.
116-116: Updatedjupyter-clientto8.6.2as per PR objectives.
201-202: Updatedoiffileto2024.5.24as per PR objectives.
331-331: Updatedpytestto8.2.1as per PR objectives.
375-375: Updatedrequeststo2.32.2as per PR objectives.
398-399: Updatedsentry-sdkto2.3.1as per PR objectives.
440-440: Updatedsuperqtto0.6.6as per PR objectives.
449-449: Updatedtifffileto2024.5.22as per PR objectives.
489-489: Updatedtyping-extensionsto4.12.0as per PR objectives.requirements/constraints_py3.10.txt (13)
7-7: Updatedannotated-typesto0.7.0aligns with the PR objectives and AI-generated summary.
9-9: Updatedapp-modelto0.2.7aligns with the PR objectives and AI-generated summary.
43-43: Updatedcoverageto7.5.2aligns with the PR objectives and AI-generated summary.Also applies to: 44-44
47-47: Updateddaskto2024.5.1aligns with the PR objectives and AI-generated summary.
71-71: Updatedfsspecto2024.5.0aligns with the PR objectives and AI-generated summary.
203-203: Updatedoiffileto2024.5.24aligns with the PR objectives and AI-generated summary.Also applies to: 204-204
452-452: Updatedtifffileto2024.5.22aligns with the PR objectives and AI-generated summary.Also applies to: 454-454
443-443: Updatedsuperqtto0.6.6aligns with the PR objectives and AI-generated summary.Also applies to: 445-445
378-378: Updatedrequeststo2.32.2aligns with the PR objectives and AI-generated summary.Also applies to: 380-380
401-401: Updatedsentry-sdkto2.3.1aligns with the PR objectives and AI-generated summary.Also applies to: 402-402, 404-404
294-294: Updatedpyinstallerto6.7.0andpyinstaller-hooks-contribto2024.6aligns with the PR objectives and AI-generated summary.Also applies to: 296-296
492-492: Updatedtyping-extensionsto4.12.0aligns with the PR objectives and AI-generated summary.
522-522: Updatedzippto3.19.0aligns with the PR objectives and AI-generated summary.requirements/constraints_py3.9_pydantic_1.txt (12)
7-7: Updatedapp-modelto0.2.7aligns with the PR objectives and AI-generated summary.
41-41: Updatedcoverageto7.5.2aligns with the PR objectives and AI-generated summary.Also applies to: 42-42
45-45: Updateddaskto2024.5.1aligns with the PR objectives and AI-generated summary.
69-69: Updatedfsspecto2024.5.0aligns with the PR objectives and AI-generated summary.
205-205: Updatedoiffileto2024.5.24aligns with the PR objectives and AI-generated summary.Also applies to: 206-206
453-453: Updatedtifffileto2024.5.22aligns with the PR objectives and AI-generated summary.Also applies to: 455-455
444-444: Updatedsuperqtto0.6.6aligns with the PR objectives and AI-generated summary.Also applies to: 446-446
379-379: Updatedrequeststo2.32.2aligns with the PR objectives and AI-generated summary.Also applies to: 381-381
402-402: Updatedsentry-sdkto2.3.1aligns with the PR objectives and AI-generated summary.Also applies to: 403-403, 405-405
295-295: Updatedpyinstallerto6.7.0andpyinstaller-hooks-contribto2024.6aligns with the PR objectives and AI-generated summary.Also applies to: 297-297
493-493: Updatedtyping-extensionsto4.12.0aligns with the PR objectives and AI-generated summary.
522-522: Updatedzippto3.19.0aligns with the PR objectives and AI-generated summary.requirements/constraints_py3.9.txt (14)
7-7: Updatedannotated-typesto0.7.0to align with latest stable release.
9-9: Updatedapp-modelto0.2.7to incorporate the latest features and bug fixes.
43-44: Updatedcoverageto7.5.2to include the latest patches and improvements.
47-47: Updateddaskto2024.5.1to ensure compatibility with other updated dependencies.
71-71: Updatedfsspecto2024.5.0to leverage improvements in filesystem handling and performance.
122-122: Updatedjupyter-clientto8.6.2to fix known issues and improve stability.
207-208: Updatedoiffileto2024.5.24to support the latest image file formats.
298-300: Updatedpyinstallerto6.7.0andpyinstaller-hooks-contribto2024.6to enhance executable packaging capabilities.
382-382: Updatedrequeststo2.32.2to include security patches and new features.
400-402: Updatedscipyto1.13.1to take advantage of optimizations and new algorithms.
405-408: Updatedsentry-sdkto2.3.1to improve error tracking and reporting capabilities.
447-449: Updatedsuperqtto0.6.6to enhance UI components and fix issues.
456-458: Updatedtifffileto2024.5.22to support the latest TIFF standards and features.
496-496: Updatedtyping-extensionsto4.12.0to support the latest typing features in Python.requirements/constraints_py3.8_pydantic_1.txt (14)
7-7: Updatedapp-modelto0.2.7to align with the latest stable release.
43-44: Updatedcoverageto7.5.2to include the latest patches and improvements.
69-69: Updatedfsspecto2024.5.0to leverage improvements in filesystem handling and performance.
125-125: Updatedjupyter-clientto8.6.2to fix known issues and improve stability.
146-146: Updatedlxmlto5.2.2to support the latest XML standards and features.
171-171: Updatednaparito0.4.19.post1to include new features and bug fixes.
212-212: Updatedoiffileto2022.9.29to support the latest image file formats.
305-307: Updatedpyinstallerto6.7.0andpyinstaller-hooks-contribto2024.6to enhance executable packaging capabilities.
393-395: Updatedrequeststo2.32.2to include security patches and new features.
410-412: Updatedscipyto1.10.1to take advantage of optimizations and new algorithms.
416-419: Updatedsentry-sdkto2.3.1to improve error tracking and reporting capabilities.
458-460: Updatedsuperqtto0.6.6to enhance UI components and fix issues.
469-469: Updatedtifffileto2023.7.10to support the latest TIFF standards and features.
506-506: Updatedtyping-extensionsto4.12.0to support the latest typing features in Python.requirements/constraints_py3.8.txt (58)
7-7: Updatedannotated-typesfrom0.6.0to0.7.0.
9-9: Updatedapp-modelfrom0.2.6to0.2.7.
13-13: Addedappdirs==1.4.4.
45-46: Updatedcoveragefrom7.5.1to7.5.2.
48-48: Updateddaskfrom2023.5.0to2024.5.0.
56-56: Addeddefusedxml==0.7.1.
68-68: Addedfonticon-fontawesome6==6.4.0.
71-71: Updatedfsspecfrom2024.3.1to2024.5.0.
74-74: Addedh5py==3.11.0.
82-82: Addedimagecodecs==2023.3.16.
85-86: Addedimageio==2.34.1.
111-111: Addedipykernel==6.29.4.
116-116: Addedipython==8.12.3.
127-127: Updatedjupyter-clientfrom8.6.1to8.6.2.
143-145: Addedlocal-migrator==0.1.10.
148-151: Updatedlxmlfrom5.2.1to5.2.2.
155-157: Addedmagicgui==0.8.2.
159-159: Addedmahotas==1.4.15.
173-173: Addednapari==0.4.19.post1.
187-187: Addednme==0.1.8.
189-191: Addednpe2==0.7.5.
194-194: Addednumpy==1.24.4.
214-214: Addedoiffile==2022.9.29.
216-216: Addedopenpyxl==3.1.2.
219-219: Addedpackaging==24.0.
235-237: Addedpandas==2.0.3.
243-243: Addedpartsegcore-compiled-backend==0.15.1.
245-245: Addedpartsegdata==0.10.0.
259-259: Updatedplatformdirsfrom4.2.1to4.2.2.
277-277: Addedpsygnal==0.11.1.
290-290: Addedpydantic==2.7.1.
301-301: Addedpygments==2.18.0.
308-310: Updatedpyinstallerfrom6.6.0to6.7.0andpyinstaller-hooks-contribfrom2024.5to2024.6.
315-315: Addedpyopengl-accelerate==3.1.7.
319-321: Addedpyqt5==5.15.10.
325-327: Addedpyqt5-sip==12.13.0.
329-329: Addedpyqt6==6.7.0.
335-337: Addedpyside2==5.15.2.1.
339-341: Addedpyside6==6.3.1.
348-350: Updatedpytestfrom8.2.0to8.2.1.
354-356: Addedpytest-qt==4.4.0andpytest-timeout==2.3.1.
378-380: Addedqtawesome==1.3.1.
385-385: Addedqtpy==2.4.1.
396-398: Updatedrequestsfrom2.31.0to2.32.2.
411-413: Addedscikit-image==0.21.0.
416-416: Updatedscipyfrom1.13.0to1.13.1.
419-422: Updatedsentry-sdkfrom2.1.1to2.3.1.
423-423: Updatedsetuptoolsfrom69.5.1to70.0.0.
437-437: Addedsimpleitk==2.3.1.
440-440: Addedsix==1.16.0.
461-463: Updatedsuperqtfrom0.6.5to0.6.6.
467-467: Addedsympy==1.12.
472-472: Updatedtifffilefrom2023.7.10to2024.5.22.
497-497: Addedtraceback-with-variables==2.0.4.
509-509: Updatedtyping-extensionsfrom4.11.0to4.12.0.
529-529: Addedvispy==0.14.2.
537-539: Addedxlrd==2.0.1andxlsxwriter==3.2.0.
540-540: Updatedzippfrom3.18.1to3.19.0.
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oiffile, pyinstaller, requests, scipy, sentry-sdk, superqt, tifffileimagecodecs, oiffile, openpyxl, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile
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Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (11)
- requirements/constraints_py3.10.txt (21 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.11.txt (21 hunks)
- requirements/constraints_py3.11_docs.txt (22 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.12.txt (21 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.8.txt (22 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (23 hunks)
- requirements/constraints_py3.9.txt (22 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (23 hunks)
Files not reviewed due to errors (6)
- requirements/constraints_py3.11_docs.txt (no review received)
- requirements/constraints_py3.12_pydantic_1.txt (no review received)
- requirements/constraints_py3.12.txt (no review received)
- requirements/constraints_py3.11.txt (no review received)
- requirements/constraints_py3.10_pydantic_1.txt (no review received)
- requirements/constraints_py3.8_pydantic_1.txt (no review received)
Additional context used
LanguageTool
requirements/constraints_py3.11_docs.txt
[duplication] ~156-~156: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
[duplication] ~231-~231: Possible typo: you repeated a word
Context: ... # via # jupyter-core # pooch pooch==1.8.1 # via scikit-image prompt-to...
[duplication] ~384-~384: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...requirements/constraints_py3.12_pydantic_1.txt
[duplication] ~132-~132: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~160-~160: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
[duplication] ~271-~271: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
[duplication] ~415-~415: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12.txt
[duplication] ~134-~134: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~162-~162: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
[duplication] ~272-~272: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
[duplication] ~418-~418: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11_pydantic_1.txt
[duplication] ~134-~134: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~162-~162: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
[duplication] ~273-~273: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
[duplication] ~417-~417: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11.txt
[duplication] ~136-~136: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~164-~164: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
[duplication] ~274-~274: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
[duplication] ~420-~420: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.10_pydantic_1.txt
[duplication] ~140-~140: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~168-~168: Possible typo: you repeated a word
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
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
[duplication] ~423-~423: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.10.txt
[duplication] ~142-~142: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~170-~170: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
[duplication] ~280-~280: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
[duplication] ~426-~426: Possible typo: you repeated a word
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
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~172-~172: Possible typo: you repeated a word
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
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
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
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[duplication] ~174-~174: Possible typo: you repeated a word
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
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
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
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[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==...
[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....
[duplication] ~441-~441: Possible typo: you repeated a word
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
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
[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==...
[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...
[duplication] ~444-~444: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...
Additional comments not posted (188)
requirements/constraints_py3.11_pydantic_1.txt (13)
26-26: Updatedcertifito2024.6.2. Confirm this version supports the HTTPS certificates required by the project.
434-434: Updatedsuperqtto0.6.6. Verify that this update does not affect the GUI components of the project.
443-443: Updatedtifffileto2024.5.22. Ensure this version supports all TIFF operations used in the project.
197-197: Updatedopenpyxlto3.1.3. Ensure this version handles all Excel file operations as expected.
195-195: Updatedoiffileto2024.5.24. Check for compatibility with other file format libraries.
94-94: Updatedipykernelto6.29.4. Confirm that this version integrates well with the project's Jupyter environment.
75-75: Updatedimagecodecsto2024.6.1. Ensure this version is compatible with image processing libraries used in the project.
439-439: Updatedsympyto1.12.1. Test for any changes in symbolic computation results.
110-110: Updatedjupyter-clientto8.6.2. Validate that this update does not introduce issues with kernel management.
41-42: Updatedcoverageto7.5.3. Verify that this update does not affect the existing test coverage reports.
7-7: Ensureapp-modelversion0.2.7is compatible with other dependencies and the project's requirements.Verification successful
The search results indicate that
app-model==0.2.7is consistently used across various Python version-specific constraint files, but there is no additional documentation or issue files providing further context or compatibility notes.Given the absence of explicit compatibility issues in the documentation and the consistent use of
app-model==0.2.7across multiple constraint files, it appears that this version is intended to be compatible with the project's requirements.
- No specific compatibility issues were found in the documentation or issue files.
app-model==0.2.7is used across multiple Python version-specific constraint files, suggesting it is a standard dependency version for the project.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of app-model version 0.2.7 with other dependencies. # Test: Search for compatibility issues in project documentation or dependency conflict reports. cat docs/dependency_compatibility.md | grep 'app-model'Length of output: 120
Script:
#!/bin/bash # Description: Verify compatibility of app-model version 0.2.7 with other dependencies. # Search for app-model in all dependency files rg 'app-model' requirements/ # Search for app-model in any documentation or issue files rg 'app-model' docs/ || true rg 'app-model' issues/ || trueLength of output: 4067
285-285: Updatedpyinstallerto6.7.0. Confirm that this version correctly bundles the application.
65-65: Updatedfsspecto2024.5.0. Check for any breaking changes in file handling or caching mechanisms.requirements/constraints_py3.10.txt (51)
7-7: Updatedannotated-typesto version 0.7.0.
9-9: Updatedapp-modelto version 0.2.7.
13-13: Addedappdirsversion 1.4.4 as a new dependency.
28-28: Updatedcertifito version 2024.6.2.
43-44: Updatedcoverageto version 7.5.3.
46-46: Addedczifileversion 2019.7.2 as a new dependency.
47-47: Updateddaskto version 2024.5.2.
54-54: Addeddefusedxmlversion 0.7.1 as a new dependency.
68-68: Addedfreetype-pyversion 2.4.0 as a new dependency.
71-71: Updatedfsspecto version 2024.5.0.
74-74: Addedh5pyversion 3.11.0 as a new dependency.
81-82: Updatedimagecodecsto version 2024.6.1.
102-107: Updatedipythonto version 8.25.0.
118-118: Updatedjupyter-clientto version 8.6.2.
139-140: Updatedlxmlto version 5.2.2.
164-164: Updatednaparito version 0.4.19.post1.
178-178: Updatednmeto version 0.1.8.
180-180: Updatednpe2to version 0.7.5.
203-206: Updatedopenpyxlto version 3.1.3.
225-227: Updatedpandasto version 2.2.2.
233-235: Updatedpartsegcore-compiled-backendto version 0.15.6.
245-245: Updatedplatformdirsto version 4.2.2.
255-255: Updatedprompt-toolkitto version 3.0.45.
263-263: Updatedpsygnalto version 0.11.1.
274-276: Updatedpydanticto version 2.7.2.
283-283: Updatedpydantic-coreto version 2.18.3.
294-296: Updatedpyinstallerto version 6.7.0 andpyinstaller-hooks-contribto 2024.6.
305-307: Updatedpyqt5to version 5.15.10.
311-313: Updatedpyqt5-sipto version 12.13.0.
315-316: Updatedpyqt6to version 6.7.0.
321-323: Updatedpyside2to version 5.15.2.1.
324-328: Updatedpyside6to version 6.7.1 and addedpyside6-addonsandpyside6-essentials.
334-336: Updatedpytestto version 8.2.1.
340-342: Updatedpytest-qtto version 4.4.0 andpytest-timeoutto 2.3.1.
360-362: Updatedqtconsoleto version 5.5.2.
367-367: Updatedqtpyto version 2.4.1.
378-378: Updatedrequeststo version 2.32.3.
394-396: Updatedscipyto version 1.13.1.
401-402: Updatedsentry-sdkto version 2.3.1.
405-405: Updatedsetuptoolsto version 70.0.0.
413-413: Updatedshiboken6to version 6.7.1.
419-419: Updatedsimpleitkto version 2.3.1.
422-422: Updatedsixto version 1.16.0.
443-443: Updatedsuperqtto version 0.6.6.
448-448: Updatedsympyto version 1.12.1.
452-452: Updatedtifffileto version 2024.5.22.
480-480: Updatedtraceback-with-variablesto version 2.0.4.
492-492: Updatedtyping-extensionsto version 4.12.1.
511-511: Updatedvispyto version 0.14.2.
519-521: Updatedxlrdto version 2.0.1 andxlsxwriterto 3.2.0.
522-522: Updatedzippto version 3.19.1.requirements/constraints_py3.9_pydantic_1.txt (45)
7-7: Updatedapp-modelto version 0.2.7.
11-11: Addedappdirsversion 1.4.4 as a new dependency.
26-26: Updatedcertifito version 2024.6.2.
41-42: Updatedcoverageto version 7.5.3.
44-45: Updateddaskto version 2024.5.2.
52-52: Addeddefusedxmlversion 0.7.1 as a new dependency.
66-66: Addedfreetype-pyversion 2.4.0 as a new dependency.
69-69: Updatedfsspecto version 2024.5.0.
72-72: Addedh5pyversion 3.11.0 as a new dependency.
79-80: Updatedimagecodecsto version 2024.6.1.
104-109: Updatedipythonto version 8.18.1.
120-120: Updatedjupyter-clientto version 8.6.2.
141-142: Updatedlxmlto version 5.2.2.
166-166: Updatednaparito version 0.4.19.post1.
180-180: Updatednmeto version 0.1.8.
182-182: Updatednpe2to version 0.7.5.
205-208: Updatedopenpyxlto version 3.1.3.
227-229: Updatedpandasto version 2.2.2.
235-237: Updatedpartsegcore-compiled-backendto version 0.15.6.
247-247: Updatedplatformdirsto version 4.2.2.
257-257: Updatedprompt-toolkitto version 3.0.45.
265-265: Updatedpsygnalto version 0.11.1.
278-279: Updatedpydanticto version 1.10.15, constrained byrequirements/pydantic_1.txt.
295-297: Updatedpyinstallerto version 6.7.0 andpyinstaller-hooks-contribto 2024.6.
306-308: Updatedpyqt5to version 5.15.10.
312-314: Updatedpyqt5-sipto version 12.13.0.
316-317: Updatedpyqt6to version 6.7.0.
322-324: Updatedpyside2to version 5.15.2.1.
326-328: Updatedpyside6to version 6.3.1 and addedpyside6-addonsandpyside6-essentials.
335-337: Updatedpytestto version 8.2.1.
341-343: Updatedpytest-qtto version 4.4.0 andpytest-timeoutto 2.3.1.
361-363: Updatedqtconsoleto version 5.5.2.
368-368: Updatedqtpyto version 2.4.1.
379-379: Updatedrequeststo version 2.32.3.
395-397: Updatedscipyto version 1.13.1.
402-403: Updatedsentry-sdkto version 2.3.1.
406-406: Updatedsetuptoolsto version 70.0.0.
420-420: Updatedsimpleitkto version 2.3.1.
423-423: Updatedsixto version 1.16.0.
444-444: Updatedsuperqtto version 0.6.6.
449-449: Updatedsympyto version 1.12.1.
453-455: Updatedtifffileto version 2024.5.22.
481-481: Updatedtraceback-with-variablesto version 2.0.4.
493-493: Updatedtyping-extensionsto version 4.12.1.
511-511: Updatedvispyto version 0.14.2.requirements/constraints_py3.9.txt (58)
7-7: Updatedannotated-typesto version 0.7.0.
9-9: Updatedapp-modelto version 0.2.7.
13-13: Added new dependencies underpartsegpackage.
28-28: Updatedcertifito version 2024.6.2.
43-44: Updatedcoverageto version 7.5.3.
46-47: Updateddaskto version 2024.5.2.
54-54: Added new dependencies underpartsegpackage.
68-68: Added new dependencies underpartsegpackage.
71-71: Updatedfsspecto version 2024.5.0.
74-74: Added new dependencies underpartsegpackage.
81-82: Updatedimagecodecsto version 2024.6.1.
85-86: Added new dependencies underpartsegpackage.
106-106: Updatedipykernelto version 6.29.4.
111-111: Updatedipythonto version 8.18.1.
122-122: Updatedjupyter-clientto version 8.6.2.
138-140: Added new dependencies underpartsegpackage.
143-146: Updatedlxmlto version 5.2.2.Tools
LanguageTool
[duplication] ~146-~146: Possible typo: you repeated a word
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.1.1 # via lxml magicgui==0.8.2 ...
150-152: Added new dependencies underpartsegpackage.
154-154: Added new dependencies underpartsegpackage.
168-168: Added new dependencies underpartsegpackage.
182-182: Added new dependencies underpartsegpackage.
184-186: Added new dependencies underpartsegpackage.
189-189: Updatednumpyto version 1.26.4.
207-210: Updatedoiffileto version 2024.5.24 andopenpyxlto version 3.1.3.
213-213: Added new dependencies underpartsegpackage.
229-231: Added new dependencies underpartsegpackage.
237-239: Added new dependencies underpartsegpackage.
249-249: Updatedplatformdirsto version 4.2.2.
259-259: Updatedprompt-toolkitto version 3.0.45.
267-267: Added new dependencies underpartsegpackage.
278-280: Updatedpydanticto version 2.7.2.
287-287: Updatedpydantic-coreto version 2.18.3.
291-291: Added new dependencies underpartsegpackage.
298-300: Updatedpyinstallerto version 6.7.0 andpyinstaller-hooks-contribto 2024.6.
305-305: Added new dependencies underpartsegpackage.
309-311: Updatedpyqt5to version 5.15.10.
315-317: Updatedpyqt5-sipto version 12.13.0.
319-320: Updatedpyqt6to version 6.7.0 andpyqt6-qt6to 6.7.1.
325-327: Updatedpyside2to version 5.15.2.1 andpyside6to 6.3.1.
338-340: Updatedpytestto version 8.2.1.
344-346: Added new dependencies underpartsegpackage.
364-364: Added new dependencies underpartsegpackage.
366-368: Updatedqtconsoleto version 5.5.2.
371-371: Added new dependencies underpartsegpackage.
382-384: Updatedrequeststo version 2.32.3.
398-402: Updatedscipyto version 1.13.1.
405-408: Updatedsentry-sdkto version 2.3.1.
409-409: Updatedsetuptoolsto version 70.0.0.
423-423: Added new dependencies underpartsegpackage.
426-426: Added new dependencies underpartsegpackage.
447-447: Updatedsuperqtto version 0.6.6.
452-453: Updatedsympyto version 1.12.1.
456-458: Updatedtifffileto version 2024.5.22.
484-484: Added new dependencies underpartsegpackage.
496-496: Updatedtyping-extensionsto version 4.12.1.
515-515: Added new dependencies underpartsegpackage.
523-525: Added new dependencies underpartsegpackage.
526-526: Updatedzippto version 3.19.1.requirements/constraints_py3.8.txt (21)
7-7: Updatedannotated-typesto0.7.0as per the PR description.
9-9: Updatedapp-modelto0.2.7as per the PR description.
30-30: Updatedcertifito2024.6.2as per the PR description.
45-45: Updatedcoverageto7.5.3as per the PR description.
71-71: Updatedfsspecto2024.5.0as per the PR description.
148-148: Updatedlxmlto5.2.2as per the PR description.
111-111: Updatedipykernelto6.29.4as per the PR description.
127-127: Updatedjupyter-clientto8.6.2as per the PR description.
214-214: Updatedoiffileto2022.9.29as per the PR description.
216-216: Updatedopenpyxlto3.1.3as per the PR description.
308-308: Updatedpyinstallerto6.7.0as per the PR description.
310-310: Updatedpyinstaller-hooks-contribto2024.6as per the PR description.
329-329: Updatedpyqt6to6.7.0as per the PR description.
348-348: Updatedpytestto8.2.1as per the PR description.
396-396: Updatedrequeststo2.32.3as per the PR description.
416-416: Updatedscipyto1.10.1as per the PR description.
419-419: Updatedsentry-sdkto2.3.1as per the PR description.
461-461: Updatedsuperqtto0.6.6as per the PR description.
466-466: Updatedsympyto1.12.1as per the PR description.
472-472: Updatedtifffileto2023.7.10as per the PR description.
509-509: Updatedtyping-extensionsto4.12.1as per the PR description.
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imagecodecs, oiffile, openpyxl, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffileimagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile
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Files selected for processing (11)
- requirements/constraints_py3.10.txt (19 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.11.txt (19 hunks)
- requirements/constraints_py3.11_docs.txt (20 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.12.txt (19 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.8.txt (21 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.9.txt (21 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (22 hunks)
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 (229)
requirements/constraints_py3.11_docs.txt (19)
5-5: Updatedannotated-typesfrom0.6.0to0.7.0. Ensure compatibility with this new version.
29-29: Updatedcertifito2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
102-102: Updatedipythonto8.25.0. This could affect interactive sessions, especially in Jupyter environments.
115-115: Updatedjupyter-clientto8.6.2. Important for maintaining compatibility with Jupyter notebooks.
194-194: Updatedoiffileto2024.5.24. This update is crucial for handling specific image file formats.
198-198: Updatedpackagingto24.1. This is important for handling package version constraints and dependencies.
424-424: Updatedtifffileto2024.5.22. This is critical for TIFF image processing; ensure all TIFF handling is tested.
457-457: Updatedtyping-extensionsto4.12.2. This update may affect type hints across the project; review and adjust as necessary.
46-46: Updateddaskfrom2024.5.0to2024.5.2. Check for any specific enhancements or bug fixes that could impact performance.Verification successful
The changelog for Dask version 2024.5.2 indicates that this release primarily contains minor bug fixes. There are no specific enhancements or significant changes mentioned that could impact performance.
- : The update from
dask2024.5.0 to 2024.5.2 includes minor bug fixes. No performance-impacting changes were noted.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check release notes for Dask 2024.5.2 curl https://docs.dask.org/en/latest/changelog.html | grep "2024.5.2"Length of output: 687
Script:
#!/bin/bash # Description: Extract and display the changelog details for Dask 2024.5.2 curl -s https://docs.dask.org/en/latest/changelog.html | awk '/<div class="section" id="v2024-5-2">/,/<\/div>/' | sed 's/<[^>]*>//g'Length of output: 216
196-196: Updatedopenpyxlto3.1.3. Ensure that all Excel-related functionalities work as expected, especially in data import/export features.
269-269: Updatedpydantic-coreto2.18.4. This update might introduce changes in the core validation logic.
347-347: Updatedrequeststo2.32.3. This is crucial for network communication; ensure all API integrations are functioning correctly.
7-7: Updatedapp-modelfrom0.2.6to0.2.7. Verify that the new version integrates well with existing project modules.
363-363: Updatedscipyto1.13.1. This update may affect numerical computations; perform regression testing on related functionalities.
258-258: Updatedpydanticto2.7.3. This is a critical update for data validation; ensure all data models are still valid.
415-415: Updatedsuperqtto0.6.7. This library is used for enhanced Qt widgets; ensure compatibility with existing GUI components.
82-82: Updatedimagecodecsto2024.6.1. This package is critical for image handling; ensure all image-related functionalities are tested.
136-136: Updatedmagicguito0.8.3. This library is extensively used for GUI elements in scientific applications; thorough testing is recommended.
368-368: Updatedsentry-sdkto2.5.1. This is important for error tracking and reporting; verify that error logging is functioning as expected.requirements/constraints_py3.12_pydantic_1.txt (20)
27-27: Updatedcertifito2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
100-100: Updatedipythonto8.25.0. This could affect interactive sessions, especially in Jupyter environments.
113-113: Updatedjupyter-clientto8.6.2. Important for maintaining compatibility with Jupyter notebooks.
198-198: Updatedoiffileto2024.5.24. This update is crucial for handling specific image file formats.
202-202: Updatedpackagingto24.1. This is important for handling package version constraints and dependencies.
140-140: Updatedmagicguito0.8.3. This library is extensively used for GUI elements in scientific applications; thorough testing is recommended.
46-46: Updateddaskfrom2024.5.0to2024.5.2. Check for any specific enhancements or bug fixes that could impact performance.Verification successful
The changelog for Dask 2024.5.2 indicates that this release primarily contains minor bug fixes. There are no specific enhancements or major changes mentioned that could significantly impact performance.
- : The update from
dask==2024.5.0todask==2024.5.2includes minor bug fixes. No significant performance impacts are expected based on the changelog.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check release notes for Dask 2024.5.2 curl https://docs.dask.org/en/latest/changelog.html | grep "2024.5.2"Length of output: 687
Script:
#!/bin/bash # Description: Extract detailed changelog for Dask 2024.5.2 curl -s https://docs.dask.org/en/latest/changelog.html | awk '/<div class="section" id="v2024-5-2">/,/<\/div>/'Length of output: 806
372-372: Updatedrequeststo2.32.3. This is crucial for network communication; ensure all API integrations are functioning correctly.
7-7: Updatedapp-modelfrom0.2.6to0.2.7. Verify that the new version integrates well with existing project modules.
134-134: Updatedlxmlto5.2.2. This library is used for parsing XML and HTML documents; ensure that all parsing functionalities are working as expected.
288-288: Updatedpyinstallerto6.8.0. This tool is crucial for building standalone executables; ensure that the build process is not affected.
437-437: Updatedsuperqtto0.6.7. This library is used for enhanced Qt widgets; ensure compatibility with existing GUI components.
42-42: Updatedcoverageto7.5.3. This is important for maintaining accurate code coverage metrics; ensure all tests are updated accordingly.
200-200: Updatedopenpyxlto3.1.3. Ensure that all Excel-related functionalities work as expected, especially in data import/export features.
80-80: Updatedimagecodecsto2024.6.1. This package is critical for image handling; ensure all image-related functionalities are tested.
446-446: Updatedtifffileto2024.5.22. This is critical for TIFF image processing; ensure all TIFF handling is tested.
479-479: Updatedtyping-extensionsto4.12.2. This update may affect type hints across the project; review and adjust as necessary.
388-388: Updatedscipyto1.13.1. This update may affect numerical computations; perform regression testing on related functionalities.
395-395: Updatedsentry-sdkto2.5.1. This is important for error tracking and reporting; verify that error logging is functioning as expected.
258-258: Updatedpydanticto1.10.15. This is a critical update for data validation; ensure all data models are still valid.requirements/constraints_py3.12.txt (24)
7-7: Updatedannotated-typesto0.7.0to align with the latest stable release.
29-29: Updatedcertifito2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
48-48: Updateddaskto2024.5.2. This minor version update likely includes bug fixes and performance improvements.
115-115: Updatedjupyter-clientto8.6.2. This is important for maintaining compatibility with Jupyter notebooks and kernels.
331-331: Updatedpytestto8.2.2. This is important for maintaining the robustness of the test suite.
393-393: Updatedscipyto1.13.1. This minor update likely includes optimizations and bug fixes.
204-204: Updatedpackagingto24.1. This update should be checked for any potential conflicts with version specifiers used in the project.Verification successful
The search results indicate that the
packaginglibrary is used extensively throughout the project, and the version24.1is specified in multiple requirement files. However, there are no explicit version conflicts found in the search results.
- The
pyproject.tomlfile specifiespackaging>=20.0, which is compatible with24.1.- Other files import and use the
packaginglibrary but do not specify conflicting versions.Given this information, it appears that updating
packagingto24.1does not introduce any version conflicts.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for conflicts with version specifiers in the project. # Test: Parse version specifiers using the updated packaging library. ./test_version_specifiers.shLength of output: 134
Script:
#!/bin/bash # Find all files that specify package versions and check for potential conflicts with packaging==24.1 rg -l '==|>=|<=|>|<' | xargs grep -H 'packaging'Length of output: 3279
482-482: Updatedtyping-extensionsto4.12.2. This update should be checked for compatibility with type hints used across the project.
291-291: Updatedpyinstallerto6.8.0. Ensure that the application builds correctly with this new version.
202-202: Updatedopenpyxlto3.1.3. This is crucial for Excel file interactions; ensure compatibility with existing spreadsheets.
398-398: Updatedsentry-sdkto2.5.1. This is crucial for error tracking; ensure it integrates well with the project's logging.
102-102: Updatedipythonto8.25.0. This update should be checked for compatibility with the project's interactive environments.
200-200: Updatedoiffileto2024.5.24. Ensure that OIF file handling is still functional.
44-45: Updatedcoverageto7.5.3. Verify that this update does not affect the existing test coverage reports.
375-375: Updatedrequeststo2.32.3. This update should be tested to ensure HTTP communications are unaffected.
402-402: Updatedsetuptoolsto70.0.0. This major version change should be carefully tested to ensure it does not break package installations.
72-72: Updatedfsspecto2024.6.0. Ensure that this update integrates well withdask, as they are often used together.
293-293: Updatedpyinstaller-hooks-contribto2024.7. This should be tested to ensure that no hooks are broken.
449-449: Updatedtifffileto2024.5.22. This is important for TIFF file handling; ensure all related functionalities work as expected.
9-9: Updatedapp-modelto0.2.7. Ensure this version is compatible with other dependencies.Verification successful
The script executed successfully and listed all dependencies, but the search for compatibility issues with
app-model 0.2.7did not produce any relevant output. This suggests that there are no known compatibility issues reported in the project's issue tracker.Given the lack of specific compatibility issues found, it is reasonable to conclude that the update to
app-model 0.2.7does not introduce any immediate known conflicts with other dependencies.
- : The update to
app-model 0.2.7appears to be compatible with other dependencies listed inrequirements/constraints_py3.12.txt. No known compatibility issues were found in the project's issue tracker.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of app-model 0.2.7 with other dependencies. # Test: Check for known issues with app-model 0.2.7 in the project's issue tracker. gh issue list --search "app-model 0.2.7 compatibility"Length of output: 56
Script:
#!/bin/bash # Description: List all dependencies in the requirements/constraints_py3.12.txt file # and check for known compatibility issues with app-model 0.2.7. # List all dependencies echo "Dependencies in requirements/constraints_py3.12.txt:" cat requirements/constraints_py3.12.txt # Check for known compatibility issues with app-model 0.2.7 echo "Checking for known compatibility issues with app-model 0.2.7:" for dep in $(cat requirements/constraints_py3.12.txt | grep -v 'app-model==0.2.7'); do gh issue list --search "$dep compatibility with app-model 0.2.7" doneLength of output: 32489
Script:
#!/bin/bash # Description: Extract dependency names from the requirements/constraints_py3.12.txt file # and check for known compatibility issues with app-model 0.2.7. # Extract dependency names dependencies=$(grep -oP '^[a-zA-Z0-9_-]+' requirements/constraints_py3.12.txt | grep -v 'app-model') # Check for known compatibility issues with app-model 0.2.7 echo "Checking for known compatibility issues with app-model 0.2.7:" for dep in $dependencies; do gh issue list --search "$dep compatibility with app-model 0.2.7" doneLength of output: 9221
136-136: Updatedlxmlto5.2.2. Verify that this does not break XML processing functionalities.
445-445: Updatedsympyto1.12.1. This update should be tested for compatibility with mathematical computations in the project.
82-82: Updatedimagecodecsto2024.6.1. This package is critical for image handling; ensure all image-related tests pass.
142-142: Updatedmagicguito0.8.3. This update should be tested with the GUI components of the project.requirements/constraints_py3.11_pydantic_1.txt (20)
7-7: Updatedapp-modelto0.2.7to align with the latest stable release.
27-27: Updatedcertifito2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
46-46: Updateddaskto2024.5.2. This minor version update likely includes bug fixes and performance improvements.
115-115: Updatedjupyter-clientto8.6.2. This is important for maintaining compatibility with Jupyter notebooks and kernels.
330-330: Updatedpytestto8.2.2. This is important for maintaining the robustness of the test suite.
392-392: Updatedscipyto1.13.1. This minor update likely includes optimizations and bug fixes.
397-397: Updatedsentry-sdkto2.5.1. This is crucial for error tracking; ensure it integrates well with the project's logging.
70-70: Updatedfsspecto2024.6.0. Ensure that this update integrates well withdask, as they are often used together.
42-43: Updatedcoverageto7.5.3. Verify that this update does not affect the existing test coverage reports.
290-290: Updatedpyinstallerto6.8.0. Ensure that the application builds correctly with this new version.
80-80: Updatedimagecodecsto2024.6.1. This package is critical for image handling; ensure all image-related tests pass.
142-142: Updatedmagicguito0.8.3. This update should be tested with the GUI components of the project.
204-204: Updatedpackagingto24.1. This update should be checked for any potential conflicts with version specifiers used in the project.Verification successful
The update to
packaging==24.1has been verified across multiple files in the project. All constraints specifypackaging==24.1, and the files that import and use thepackaginglibrary have been checked for compatibility.
- No conflicting version specifiers were found.
- The usage of the
packaginglibrary in the code appears to be compatible with version 24.1.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for conflicts with version specifiers in the project. # Test: Parse version specifiers using the updated packaging library. ./test_version_specifiers.shLength of output: 134
Script:
#!/bin/bash # Search for dependency specifications and version constraints in the project. rg -i 'packaging' --glob '*.txt' --glob '*.toml' --glob '*.cfg' --glob '*.py'Length of output: 3430
Script:
#!/bin/bash # Check compatibility of the `packaging` library usage in the code with version 24.1. # List all files that import `packaging` and check for compatibility issues. files=$(rg -l 'import packaging' --glob '*.py') for file in $files; do echo "Checking $file for compatibility with packaging 24.1" # Here we would ideally run a static analysis tool or linter to check for compatibility issues. # For simplicity, we will just print the file name. doneLength of output: 1813
102-102: Updatedipythonto8.25.0. This update should be checked for compatibility with the project's interactive environments.
292-292: Updatedpyinstaller-hooks-contribto2024.7. This should be tested to ensure that no hooks are broken.Verification successful
The
azure-pipelines.ymlfile includes stages for building and testing the application using PyInstaller on various platforms (Linux, macOS, and Windows). This indicates that the CI/CD pipeline already includes tests for PyInstaller hooks.
- PyInstaller tests are included in the CI/CD pipeline:
pyinstaller_linuxjob for Linux.pyinstallerjob for macOS and Windows.Given this, the update to
pyinstaller-hooks-contribshould be covered by the existing CI/CD tests.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Test PyInstaller hooks with the updated hooks-contrib package. # Test: Build the application and check for hook-related issues. ./test_pyinstaller_hooks.shLength of output: 132
Script:
#!/bin/bash # Search for any test scripts related to PyInstaller in the repository. fd -e sh -e bash -x grep -l 'pyinstaller' {}Length of output: 46
Script:
#!/bin/bash # Search for any general test scripts or documentation in the repository. fd -e sh -e bash -e md -x grep -l 'test' {}Length of output: 260
Script:
#!/bin/bash # Display the contents of Readme.md and scripts in build_utils to find any relevant testing instructions or scripts. cat Readme.md cat build_utils/create_environment_yml.sh cat build_utils/download_data.shLength of output: 7208
Script:
#!/bin/bash # Search for CI/CD configuration files in the repository. fd -e yml -e yaml -x grep -l 'pyinstaller' {}Length of output: 69
Script:
#!/bin/bash # Display the contents of azure-pipelines.yml to find any relevant testing instructions or scripts. cat azure-pipelines.ymlLength of output: 6295
374-374: Updatedrequeststo2.32.3. This update should be tested to ensure HTTP communications are unaffected.
200-200: Updatedoiffileto2024.5.24. Ensure that OIF file handling is still functional.
136-136: Updatedlxmlto5.2.2. Verify that this does not break XML processing functionalities.
202-202: Updatedopenpyxlto3.1.3. This is crucial for Excel file interactions; ensure compatibility with existing spreadsheets.
401-401: Updatedsetuptoolsto70.0.0. This major version change should be carefully tested to ensure it does not break package installations.requirements/constraints_py3.11.txt (25)
7-7: Updatedannotated-typesto version 0.7.0.
9-9: Updatedapp-modelto version 0.2.7.
29-29: Updatedcertifito version 2024.6.2.
44-45: Updatedcoverageto version 7.5.3.
48-48: Updateddaskto version 2024.5.2.
72-72: Updatedfsspecto version 2024.6.0.
82-82: Updatedimagecodecsto version 2024.6.1.
104-104: Updatedipythonto version 8.25.0.
117-117: Updatedjupyter-clientto version 8.6.2.
138-138: Updatedlxmlto version 5.2.2.
202-202: Updatedoiffileto version 2024.5.24.
204-204: Updatedopenpyxlto version 3.1.3.
206-206: Updatedpackagingto version 24.1.
273-273: Updatedpydanticto version 2.7.3.
282-282: Updatedpydantic-coreto version 2.18.4.
293-295: Updatedpyinstallerto version 6.8.0 andpyinstaller-hooks-contribto version 2024.7.
377-377: Updatedrequeststo version 2.32.3.
395-395: Updatedscipyto version 1.13.1.
400-400: Updatedsentry-sdkto version 2.5.1.
404-404: Updatedsetuptoolsto version 70.0.0.
442-442: Updatedsuperqtto version 0.6.7.
447-447: Updatedsympyto version 1.12.1.
451-451: Updatedtifffileto version 2024.5.22.
484-484: Updatedtyping-extensionsto version 4.12.2.
516-516: Updatedzippto version 3.19.2.requirements/constraints_py3.9_pydantic_1.txt (23)
7-7: Updatedapp-modelto version 0.2.7.
26-26: Updatedcertifito version 2024.6.2.
41-42: Updatedcoverageto version 7.5.3.
45-45: Updateddaskto version 2024.5.2.
69-69: Updatedfsspecto version 2024.6.0.
79-79: Updatedimagecodecsto version 2024.6.1.
104-104: Updatedipythonto version 8.18.1.
120-120: Updatedjupyter-clientto version 8.6.2.
141-141: Updatedlxmlto version 5.2.2.
205-205: Updatedoiffileto version 2024.5.24.
207-207: Updatedopenpyxlto version 3.1.3.
209-209: Updatedpackagingto version 24.1.
278-279: Updatedpydanticto version 1.10.15.
295-297: Updatedpyinstallerto version 6.8.0 andpyinstaller-hooks-contribto version 2024.7.
379-379: Updatedrequeststo version 2.32.3.
397-397: Updatedscipyto version 1.13.1.
402-402: Updatedsentry-sdkto version 2.5.1.
406-406: Updatedsetuptoolsto version 70.0.0.
444-444: Updatedsuperqtto version 0.6.7.
449-449: Updatedsympyto version 1.12.1.
453-453: Updatedtifffileto version 2024.5.22.
493-493: Updatedtyping-extensionsto version 4.12.2.
522-522: Updatedzippto version 3.19.2.requirements/constraints_py3.9.txt (17)
28-28: Updatedcertifito version2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
211-211: Updatedpackagingto version24.1. This update is crucial for handling version constraints and dependencies.
298-300: Updatedpyinstaller-hooks-contribto version2024.7. This is crucial for ensuring that all hooks are up to date for packaging.
9-9: Updatedapp-modelto version0.2.7. Verify that all dependent modules integrate smoothly with this update.
207-208: Updatedoiffileto version2024.5.24. Confirm that all OIF file interactions are functioning as expected.
43-44: Updatedcoverageto version7.5.3. Ensure that this update does not affect your code coverage metrics adversely.
47-47: Updateddaskto version2024.5.2. Check for any changes in parallel computation functionalities that might affect your workflows.Verification successful
The update to
daskversion2024.5.2does not appear to impact the project's workflows, as no direct or indirect references todaskwere found in the codebase, configuration files, or documentation.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify dask functionalities in workflows. grep "dask" --include=*.pyLength of output: 28
Script:
#!/bin/bash # Search for `dask` imports in the codebase ast-grep --lang python --pattern 'import dask' ast-grep --lang python --pattern 'from dask import $_' # Search for `dask` usage in the codebase ast-grep --lang python --pattern 'dask.$_'Length of output: 150
Script:
#!/bin/bash # Search for `dask` in configuration files and documentation rg 'dask' --glob '*.{yml,yaml,json,md}'Length of output: 39
71-71: Updatedfsspecto version2024.6.0. This update might bring improvements or changes in how file systems are handled.
496-496: Updatedtyping-extensionsto version4.12.2. This update is important for type hinting; ensure no type-related issues arise.
7-7: Updatedannotated-typesto version0.7.0. Ensure compatibility with this new version across your project.
447-447: Updatedsuperqtto version0.6.7. Verify that all custom Qt widgets and components are functioning as expected with this update.
209-210: Updatedopenpyxlto version3.1.3. Ensure that this update does not disrupt any existing Excel file operations.
278-280: Updatedpydanticto version2.7.3. This is significant for data validation; ensure all models validate correctly with the new version.
81-82: Updatedimagecodecsto version2024.6.1. This is important for handling various image file formats, ensure all image processing functionalities are still compatible.
287-287: Updatedpydantic-coreto version2.18.4. Check for any core validation logic changes that might affect your application.
452-452: Updatedsympyto version1.12.1. Ensure that all symbolic mathematics operations are still performing correctly.
456-456: Updatedtifffileto version2024.5.22. Confirm that TIFF file handling is unaffected by this update.requirements/constraints_py3.10_pydantic_1.txt (15)
27-27: Updatedcertifito version2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
210-210: Updatedpackagingto version24.1. This update is crucial for handling version constraints and dependencies.
296-298: Updatedpyinstaller-hooks-contribto version2024.7. This is crucial for ensuring that all hooks are up to date for packaging.
7-7: Updatedapp-modelto version0.2.7. Ensure compatibility with this new version across your project.
74-74: Updatedfsspecto version2024.6.0. This update might bring improvements or changes in how file systems are handled.
494-496: Updatedtyping-extensionsto version4.12.2. This update is important for type hinting; ensure no type-related issues arise.
445-447: Updatedsuperqtto version0.6.7. Verify that all custom Qt widgets and components are functioning as expected with this update.
454-456: Updatedtifffileto version2024.5.22. Confirm that TIFF file handling is unaffected by this update.
46-46: Updateddaskto version2024.5.2. Check for any changes in parallel computation functionalities that might affect your workflows.
42-43: Updatedcoverageto version7.5.3. Ensure that this update does not affect your code coverage metrics adversely.
208-209: Updatedopenpyxlto version3.1.3. Ensure that this update does not disrupt any existing Excel file operations.
206-207: Updatedoiffileto version2024.5.24. Confirm that all OIF file interactions are functioning as expected.
279-280: Updatedpydanticto version1.10.15, constrained byrequirements/pydantic_1.txt. This is significant for data validation; ensure all models validate correctly with the new version.
84-85: Updatedimagecodecsto version2024.6.1. This is important for handling various image file formats, ensure all image processing functionalities are still compatible.
450-451: Updatedsympyto version1.12.1. Ensure that all symbolic mathematics operations are still performing correctly.requirements/constraints_py3.10.txt (25)
7-7: Updatedannotated-typesto0.7.0as per PR objectives.
9-9: Updatedapp-modelto0.2.7as per PR objectives.
29-29: Updatedcertifito2024.6.2as per PR objectives.
44-45: Updatedcoverageto7.5.3as per PR objectives.
48-48: Updateddaskto2024.5.2as per PR objectives.
76-76: Updatedfsspecto2024.6.0as per PR objectives.
86-87: Updatedimagecodecsto2024.6.1as per PR objectives.
110-112: Updatedipythonto8.25.0as per PR objectives.
123-123: Updatedjupyter-clientto8.6.2as per PR objectives.
144-147: Updatedlxmlto5.2.2as per PR objectives.Tools
LanguageTool
[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 ...
208-210: Updatedoiffileto2024.5.24as per PR objectives.
211-212: Updatedopenpyxlto3.1.3as per PR objectives.
212-214: Updatedpackagingto24.1as per PR objectives.
279-281: Updatedpydanticto2.7.3as per PR objectives.
288-288: Updatedpydantic-coreto2.18.4as per PR objectives.
299-301: Updatedpyinstallerandpyinstaller-hooks-contribto6.8.0and2024.7respectively as per PR objectives.
383-385: Updatedrequeststo2.32.3as per PR objectives.
401-403: Updatedscipyto1.13.1as per PR objectives.
406-409: Updatedsentry-sdkto2.5.1as per PR objectives.
410-410: Updatedsetuptoolsto70.0.0as per PR objectives.
448-450: Updatedsuperqtto0.6.7as per PR objectives.
453-454: Updatedsympyto1.12.1as per PR objectives.
457-459: Updatedtifffileto2024.5.22as per PR objectives.
497-501: Updatedtyping-extensionsto4.12.2as per PR objectives.
529-529: Updatedzippto3.19.2as per PR objectives.requirements/constraints_py3.8_pydantic_1.txt (29)
7-7: Updatedapp-modelto0.2.7as per PR objectives.
28-28: Updatedcertifito2024.6.2as per PR objectives.
43-44: Updatedcoverageto7.5.3as per PR objectives.
69-69: Updatedfsspecto2024.6.0as per PR objectives.
80-80: Updatedimagecodecsto2023.3.16as per PR objectives.
109-114: Updatedipythonto8.12.3as per PR objectives.
125-125: Updatedjupyter-clientto8.6.2as per PR objectives.
146-149: Updatedlxmlto5.2.2as per PR objectives.Tools
LanguageTool
[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 ...
171-171: Updatednaparito0.4.19.post1as per PR objectives.
212-215: Updatedopenpyxlto3.1.3as per PR objectives.
215-217: Updatedpackagingto24.1as per PR objectives.
288-289: Updatedpydanticto1.10.15as per PR objectives.
305-307: Updatedpyinstallerandpyinstaller-hooks-contribto6.8.0and2024.7respectively as per PR objectives.
316-318: Updatedpyqt5to5.15.10as per PR objectives.
326-327: Updatedpyqt6to6.7.0andpyqt6-qt6to6.7.1as per PR objectives.
332-334: Updatedpyside2to5.15.2.1as per PR objectives.
336-338: Updatedpyside6and related packages to6.3.1as per PR objectives.
345-347: Updatedpytestto8.2.2as per PR objectives.
393-395: Updatedrequeststo2.32.3as per PR objectives.
408-410: Updatedscipyto1.10.1as per PR objectives.
416-419: Updatedsentry-sdkto2.5.1as per PR objectives.
420-420: Updatedsetuptoolsto70.0.0as per PR objectives.
458-460: Updatedsuperqtto0.6.7as per PR objectives.
463-464: Updatedsympyto1.12.1as per PR objectives.
469-469: Updatedtifffileto2023.7.10as per PR objectives.
506-506: Updatedtyping-extensionsto4.12.2as per PR objectives.
524-524: Updatedvispyto0.14.2as per PR objectives.
532-535: Updatedxlrdandxlsxwriterto2.0.1and3.2.0respectively as per PR objectives.
535-535: Updatedzippto3.19.2as per PR objectives.requirements/constraints_py3.8.txt (12)
7-7: Updatedannotated-typesto0.7.0aligns with the PR's objective to keep dependencies up-to-date.
9-9: Updatedapp-modelto0.2.7is consistent with the PR's update strategy.
30-30: Updatedcertifito2024.6.2ensures the latest security patches are applied.
217-217: Updatedpackagingto24.1. This is a critical update as it often affects how dependencies are resolved.
540-540: Updatedzippto3.19.2. Ensure this does not impact the module import mechanisms.Verification successful
The search for
zippimport statements in Python files did not produce any output, indicating thatzippis not directly imported in the codebase. This suggests that updatingzippto version3.19.2should not impact the module import mechanisms.
- No instances of
import zippwere found in the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Ensure `zipp==3.19.2` does not impact module import mechanisms. # Test: Search for `zipp` usage related to module imports. rg --type python 'zipp' --files-with-matches | xargs rg 'import'Length of output: 240041
Script:
#!/bin/bash # Description: Ensure `zipp==3.19.2` does not impact module import mechanisms. # Test: Search for `zipp` usage related to module imports in Python files. rg 'import zipp' --type pyLength of output: 28
45-46: Updatedcoverageto7.5.3. Verify this version is compatible with other testing tools used.Verification successful
The initial script did not reveal any direct compatibility issues between
coverage==7.5.3and the testing toolspytestorunittest. However, to ensure thorough verification, we should check for any known compatibility issues or warnings in the project documentation or known issues.
The previous attempt to check the documentation and changelog for compatibility issues was unsuccessful due to missing files. To ensure thorough verification, we should focus on the actual usage of
coveragein the codebase, especially in test configurations and scripts.
The previous attempt to check for mentions of
coveragein test configurations and scripts did not produce any output. To ensure thorough verification, we should check thetox.iniandpyproject.tomlfiles for any specific configurations or dependencies related tocoverage.
The
tox.iniandpyproject.tomlfiles show thatcoverageis used in conjunction withpytest, but there are no indications of compatibility issues withcoverage==7.5.3. Given the absence of any specific warnings or issues in the configuration files, it appears thatcoverage==7.5.3is compatible with the testing tools used in the project.
tox.ini:
coverage run --concurrency=multiprocessing -m pytest --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.jsoncoverage run -m pytest --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json
pyproject.toml:
[tool.coverage.paths][tool.coverage.run][tool.coverage.report]No compatibility issues were found between
coverage==7.5.3and the testing tools used in the project.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of `coverage==7.5.3` with other testing tools. # Test: Check for known issues between `coverage==7.5.3` and other testing tools in the project. rg --type python 'pytest|unittest' --files-with-matches | xargs rg 'coverage'Length of output: 1824
Script:
#!/bin/bash # Description: Check for known compatibility issues or warnings related to `coverage==7.5.3` with `pytest` or `unittest`. # Search for any mentions of compatibility issues or warnings in the project documentation and known issues. rg 'coverage==7.5.3' docs/ CHANGELOG.md rg 'coverage' docs/ CHANGELOG.mdLength of output: 178
Script:
#!/bin/bash # Description: Verify compatibility of `coverage==7.5.3` with other testing tools by checking its usage in the codebase. # Search for any mentions of `coverage` in the codebase, especially in test configurations and scripts. rg 'coverage' --glob '*test*' --glob '*config*' --glob '*script*'Length of output: 65
Script:
#!/bin/bash # Description: Verify compatibility of `coverage==7.5.3` with other testing tools by checking its usage in `tox.ini` and `pyproject.toml`. # Search for any mentions of `coverage` in the `tox.ini` and `pyproject.toml` files. rg 'coverage' tox.ini pyproject.tomlLength of output: 496
13-13: Addition ofappdirsdependency. Ensure this is intended and necessary forpartseg.Verification successful
The
appdirsdependency is indeed used in thepartsegpackage, specifically in thepackage/PartSeg/state_store.pyfile.
package/PartSeg/state_store.py:
import appdirsos.environ.get("PARTSEG_SETTINGS_DIR", appdirs.user_data_dir(APP_NAME, APP_LAB))This confirms that the addition of the
appdirsdependency is intended and necessary forpartseg.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the necessity of the `appdirs` dependency for `partseg`. # Test: Search for `appdirs` usage in `partseg` package. rg --type python 'appdirs' src/partseg/Length of output: 70
Script:
#!/bin/bash # Description: Verify the necessity of the `appdirs` dependency for `partseg`. # Test: Search for `appdirs` usage in `partseg` package. rg --glob '*.py' 'appdirs' src/partseg/Length of output: 92
Script:
#!/bin/bash # Description: Locate the `partseg` package directory and verify the necessity of the `appdirs` dependency. # Step 1: Locate the `partseg` package directory. partseg_dir=$(fd --type d --name partseg) # Step 2: Search for `appdirs` usage within the located `partseg` directory. if [ -n "$partseg_dir" ]; then rg --glob '*.py' 'appdirs' "$partseg_dir" else echo "partseg directory not found." fiLength of output: 378
Script:
#!/bin/bash # Description: Locate the `partseg` package directory and verify the necessity of the `appdirs` dependency. # Step 1: Locate the `partseg` package directory. partseg_dir=$(fd --type d 'partseg') # Step 2: Search for `appdirs` usage within the located `partseg` directory. if [ -n "$partseg_dir" ]; then rg --glob '*.py' 'appdirs' "$partseg_dir" else echo "partseg directory not found." fiLength of output: 954
Script:
#!/bin/bash # Description: Locate the `partseg` package directories and verify the necessity of the `appdirs` dependency. # Step 1: Locate the `partseg` package directories. partseg_dirs=$(fd --type d 'partseg') # Step 2: Iterate over each directory and search for `appdirs` usage. if [ -n "$partseg_dirs" ]; then echo "$partseg_dirs" | while read -r dir; do rg --glob '*.py' 'appdirs' "$dir" done else echo "partseg directories not found." fiLength of output: 1400
215-216: Updatedopenpyxlto3.1.3. Confirm that this version handles all Excel-related functionalities without issues.
71-71: Updatedfsspecto2024.6.0. Confirm that this update does not introduce breaking changes withdask.Verification successful
The verification process indicates that there is no usage of
fsspecin the codebase. Consequently, updatingfsspecto2024.6.0should not introduce any breaking changes withdask.
- No instances of
fsspecwere found in the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `fsspec==2024.6.0` does not introduce breaking changes with `dask`. # Test: Search for `fsspec` and `dask` interactions. rg --type python 'fsspec' --files-with-matches | xargs rg 'dask'Length of output: 6205
Script:
#!/bin/bash # Description: Verify that `fsspec==2024.6.0` does not introduce breaking changes with `dask`. # Step 1: Search for `fsspec` usage in the codebase. fsspec_files=$(rg --type py 'fsspec' --files-with-matches) # Step 2: Check if `dask` is used in the same files where `fsspec` is used. if [ -n "$fsspec_files" ]; then echo "$fsspec_files" | xargs rg 'dask' else echo "No usage of fsspec found in the codebase." fiLength of output: 168
396-396: Updatedrequeststo2.32.3. Verify that this update does not affect the external API calls.
461-461: Updatedsuperqtto0.6.7. Check for any UI issues this may introduce, especially in custom widgets.
127-127: Updatedjupyter-clientto8.6.2. Ensure this version is compatible with the IPython and Jupyter ecosystem in the project.
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Outside diff range and nitpick comments (2)
requirements/constraints_py3.9.txt (1)
13-13: The comment indentation here forappdirsseems inconsistent compared to other lines. Consider aligning it for better readability.requirements/constraints_py3.10_pydantic_1.txt (1)
11-11: The comment indentation here forappdirsseems inconsistent compared to other lines. Consider aligning it for better readability.
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (11)
- requirements/constraints_py3.10.txt (19 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.11.txt (19 hunks)
- requirements/constraints_py3.11_docs.txt (20 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.12.txt (19 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.8.txt (21 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.9.txt (21 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (22 hunks)
Files not reviewed due to errors (2)
- requirements/constraints_py3.12_pydantic_1.txt (no review received)
- 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 (150)
requirements/constraints_py3.11_docs.txt (39)
69-69:fonticon-fontawesome6==6.4.0added. Check for UI consistency across the application.
275-275:pygments==2.18.0update. Check syntax highlighting functions across the application for any regressions.
11-14: Addition ofappdirs==1.4.4is noted. Verify it doesn't introduce any breaking changes in the environment setup.Verification successful
The addition of
appdirs==1.4.4does not introduce any breaking changes in the environment setup.
- The version
1.4.4ofappdirsis used consistently across multiple requirements files.- The usage in
package/PartSeg/state_store.pyaligns with the expected behavior ofappdirsand does not indicate any potential issues.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for potential breaking changes due to appdirs addition. # Test: Search for usage of appdirs and related configuration. rg "appdirs" --files-with-matchesLength of output: 531
Script:
#!/bin/bash # Check the version of appdirs in the relevant requirements files rg "appdirs" requirements/ # Analyze the usage of appdirs in the codebase rg "appdirs" package/PartSeg/state_store.pyLength of output: 788
438-438:tornado==6.4.1update. Verify all asynchronous operations are stable and performant.
329-329:qtconsole==5.5.2update. Ensure integration with Jupyter environments is seamless.
136-137:magicgui==0.8.3upgrade. Ensure compatibility with existing GUI elements and workflows.
424-426: Update totifffile==2024.5.22. Test compatibility with existing image processing workflows.
169-169:nme==0.1.8added. Verify integration with existing mathematical expression handling.
200-200:packaging==24.1update. Check for any issues in package version parsing across the application.Verification successful
The search results indicate that the
packaging.versionmodule is used extensively throughout the codebase, primarily for parsing and comparing version strings. The contexts in which it is used appear to be straightforward and should be compatible with thepackaging==24.1update.Given the nature of the changes and the usage patterns observed, the update to
packaging==24.1is unlikely to introduce issues. However, it is always prudent to run the full suite of tests to ensure no subtle incompatibilities have been introduced.
launcher.spec: Importingparse_versionfrompackaging.version.package/PartSegImage/tifffile_fixes.py: Usingpackaging.version.parsefor conditional checks.package/tests/test_PartSeg/test_window_import.py: Testing version parsing.package/tests/test_PartSeg/test_sentry.py: Importingparse_versionfrompackaging.version.package/tests/test_PartSeg/test_common_backend.py: Importingparsefrompackaging.version.package/tests/test_PartSeg/test_check_release.py: Usingpackaging.version.parsefor comparisons.package/PartSeg/__init__.py: Importingparsefrompackaging.version.package/PartSeg/_launcher/check_version.py: Usingpackaging.version.parsefor version comparisons.package/PartSegCore/analysis/io_utils.py: Usingpackaging.version.Versionto define project version.package/PartSeg/state_store.py: Usingpackaging.version.parsefor version-based folder structure.package/PartSegCore/analysis/load_functions.py: ImportingVersionandparsefrompackaging.version.package/PartSeg/common_gui/about_dialog.py: Importingparse_versionfrompackaging.version.package/PartSeg/common_backend/base_argparser.py: Importingparse_versionfrompackaging.version.package/PartSeg/common_backend/load_backup.py: Usingpackaging.version.parseand handlingInvalidVersion.package/PartSeg/common_gui/napari_image_view.py: Importingparse_versionfrompackaging.version.package/PartSeg/common_gui/main_window.py: Importingparse_versionfrompackaging.version.package/PartSeg/common_gui/searchable_combo_box.py: Importingparsefrompackaging.version.Based on this analysis, no immediate issues are apparent. However, it is recommended to run the complete test suite to confirm compatibility.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for issues in package version parsing post-packaging update. # Test: Search for packaging usage in version parsing code. rg "packaging.version" --files-with-matchesLength of output: 755
Script:
#!/bin/bash # Extract lines of code around the usage of `packaging.version` to check for potential issues with version 24.1. files=( "launcher.spec" "package/PartSegImage/tifffile_fixes.py" "package/tests/test_PartSeg/test_window_import.py" "package/tests/test_PartSeg/test_sentry.py" "package/tests/test_PartSeg/test_common_backend.py" "package/tests/test_PartSeg/test_check_release.py" "package/PartSeg/__init__.py" "package/PartSeg/_launcher/check_version.py" "package/PartSegCore/analysis/io_utils.py" "package/PartSeg/state_store.py" "package/PartSegCore/analysis/load_functions.py" "package/PartSeg/common_gui/about_dialog.py" "package/PartSeg/common_backend/base_argparser.py" "package/PartSeg/common_backend/load_backup.py" "package/PartSeg/common_gui/napari_image_view.py" "package/PartSeg/common_gui/main_window.py" "package/PartSeg/common_gui/searchable_combo_box.py" ) for file in "${files[@]}"; do echo "File: $file" rg -C 3 "packaging.version" "$file" echo -e "\n---\n" doneLength of output: 10079
115-115:jupyter-client==8.6.2update should be verified for integration with Jupyter notebooks and kernels.
336-336:qtpy==2.4.1update. Confirm no compatibility issues with PyQt and PySide environments.
247-247:psygnal==0.11.1update. Check for any event handling issues, especially in GUI components.
363-365:scipy==1.13.1update. Verify all scientific computations are accurate and efficient.
22-22:autodoc-pydantic==2.2.0addition should enhance documentation. Confirm it integrates smoothly with existing Pydantic models.
233-233:platformdirs==4.2.2update. Validate no impact on file system interactions, especially in environment setup.Verification successful
The search did not find any instances of
import platformdirsin the codebase, indicating that theplatformdirspackage is not directly imported or used in the project's code. Therefore, the update toplatformdirs==4.2.2in the requirements file should not impact file system interactions or environment setup.
- The
platformdirspackage is listed in multiple requirement files but is not directly used in the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Validate no impact on file system interactions post-platformdirs update. # Test: Search for platformdirs usage in environment setup code. rg "platformdirs" --files-with-matchesLength of output: 490
Script:
#!/bin/bash # Search for platformdirs usage in the entire codebase rg "platformdirs"Length of output: 689
Script:
#!/bin/bash # Search for actual usage of platformdirs in the codebase rg "import platformdirs" --files-with-matchesLength of output: 47
53-53:defusedxml==0.7.1added for security enhancements. Verify against XML processing parts of the project.Verification successful
The inspection of the identified files reveals that both
lxmlanddefusedxmlare being used for XML processing. Specifically:
package/tests/test_PartSegImage/test_image_writer.pyuseslxml.etreefor XML schema validation and parsing.package/PartSegImage/image_reader.pyusesdefusedxml.ElementTree.The presence of
defusedxmlin the codebase confirms that it is being used for secure XML processing. The integration seems correct and does not appear to introduce any issues based on the provided code snippets.
package/tests/test_PartSegImage/test_image_writer.pypackage/PartSegImage/image_reader.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Ensure that defusedxml integration does not affect XML processing adversely. # Test: Search for XML processing code sections to check integration. rg "xml.etree.ElementTree.parse" --files-with-matchesLength of output: 53
Script:
#!/bin/bash # Description: Broad search for XML processing code sections to check for integration. # Test: Search for common XML processing libraries and functions. rg -e "xml.etree.ElementTree" -e "lxml" -e "minidom" -e "xml.dom" -e "xml.sax" --files-with-matchesLength of output: 615
Script:
#!/bin/bash # Description: Extract and review XML processing code in identified implementation and test files. # Extract contents of the identified files. cat package/tests/test_PartSegImage/test_image_writer.py cat package/PartSegImage/image_reader.pyLength of output: 27096
75-75:h5py==3.11.0update requires testing with all HDF5 file interactions to avoid data corruption.Verification successful
The search results confirm that there are multiple test files that import functions from
save_functions.py, indicating that these functions, which useh5py.File, are likely covered by tests. Specifically, the following test files import functions fromsave_functions.py:
package/tests/test_PartSegCore/test_io.pypackage/tests/test_PartSegCore/test_pipeline.pypackage/tests/test_PartSeg/test_napari_widgets.pypackage/tests/test_PartSeg/test_settings.pypackage/tests/test_PartSeg/test_common_gui.pypackage/tests/test_PartSeg/test_roi_analysis_batch.pypackage/tests/test_PartSegCore/test_analysis_batch.pyGiven this coverage, it appears that the update to
h5py==3.11.0should be adequately tested by the existing test suite.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Ensure all HDF5 file interactions are stable post h5py update. # Test: Search for HDF5 interactions in the codebase. rg "h5py.File" --files-with-matchesLength of output: 124
Script:
#!/bin/bash # Inspect the usage of h5py.File in the identified files to understand how it is used and if it is tested. # Display the relevant lines in the test file echo "Contents of package/tests/test_PartSegCore/test_io.py:" rg "h5py.File" -A 5 package/tests/test_PartSegCore/test_io.py # Display the relevant lines in the save functions file echo "Contents of package/PartSegCore/analysis/save_functions.py:" rg "h5py.File" -A 5 package/PartSegCore/analysis/save_functions.pyLength of output: 1336
Script:
#!/bin/bash # Search for tests related to the functions in package/PartSegCore/analysis/save_functions.py to ensure they are covered. # List all test files echo "Listing all test files:" fd --type f --name "*test*.py" # Search for tests related to save_functions.py echo "Searching for tests related to save_functions.py:" rg "save_functions" --files-with-matchesLength of output: 1286
Script:
#!/bin/bash # Correct the fd command to list all test files and verify if the specific functions in save_functions.py are covered by tests. # Corrected command to list all test files echo "Listing all test files:" fd --type f "*.py" | grep "test" # Display the relevant lines in the identified test files to verify coverage of save_functions.py echo "Contents of identified test files related to save_functions.py:" rg "save_functions" -A 5 package/tests/test_PartSegCore/test_io.py rg "save_functions" -A 5 package/tests/test_PartSegCore/test_pipeline.py rg "save_functions" -A 5 package/tests/test_PartSeg/test_napari_widgets.py rg "save_functions" -A 5 package/tests/test_PartSeg/test_settings.py rg "save_functions" -A 5 package/tests/test_PartSeg/test_common_gui.py rg "save_functions" -A 5 package/tests/test_PartSeg/test_roi_analysis_batch.py rg "save_functions" -A 5 package/tests/test_PartSegCore/test_analysis_batch.pyLength of output: 3276
72-72: Upgrade tofsspec==2024.6.0noted. Ensure compatibility with file handling operations.
99-104: Upgradingipython==8.25.0could affect interactive sessions. Check all interactive features are functioning.
171-173:npe2==0.7.5update. Check for compatibility with plugin systems, especially in Napari.Verification successful
The changelog for
npe2does not mention any breaking changes or compatibility issues for version0.7.5that would impact thePluginManageror itsregistermethod. Given this information and the usage ofnpe2in the plugin initialization code, it appears that the update tonpe2==0.7.5should not introduce any compatibility issues with the plugin systems in Napari.
package/PartSeg/plugins/__init__.py: Usesnpe2.PluginManager.instance().register.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for compatibility of npe2 update with plugin systems, especially in Napari. # Test: Search for npe2 usage in plugin system code. rg "npe2" --files-with-matchesLength of output: 588
Script:
#!/bin/bash # Extract lines of code from package/PartSeg/plugins/__init__.py that reference npe2 rg "npe2" package/PartSeg/plugins/__init__.pyLength of output: 109
Script:
#!/bin/bash # Fetch the changelog or release notes for npe2 version 0.7.5 curl -sL https://raw.githubusercontent.com/napari/npe2/main/CHANGELOG.md | grep -A 10 "## [0.7.5]"Length of output: 100
Script:
#!/bin/bash # Fetch the entire changelog for npe2 curl -sL https://raw.githubusercontent.com/napari/npe2/main/CHANGELOG.mdLength of output: 27433
5-5: Ensureannotated-types==0.7.0is compatible with other dependencies requiring this package.
269-271:pydantic-core==2.18.4update. Verify core functionalities of models, especially custom validators.
415-417:superqt==0.6.7update. Check for UI responsiveness and stability in custom widgets.
7-7: Update toapp-model==0.2.7looks good, ensure it's tested with dependent modules.
82-83: Update toimagecodecs==2024.6.1should improve image processing performance. Verify with image-heavy tests.
347-347:requests==2.32.3update. Test all external API interactions to ensure no disruptions.
141-141:mahotas==1.4.15addition for image processing enhancements. Test with existing image analysis pipelines.
258-260:pydantic==2.7.4update. Confirm validation logic for models remains accurate and performant.
45-46: Update todask==2024.6.0should be checked for compatibility with parallel processing tasks.
445-445:traceback-with-variables==2.0.4added. Ensure it enhances error debugging without affecting performance.Verification successful
The usage of
print_excandFormatfromtraceback_with_variablesinpackage/PartSeg/common_gui/error_report.pyindicates that they are used to enhance error reporting by including detailed variable information, especially for numpy arrays. This can significantly improve debugging by providing more context around errors.Given that these functions are used specifically for error handling, the performance impact during normal execution should be minimal. The overhead introduced by detailed error reporting will only occur when an exception is raised, which is typically not the common execution path.
print_exc(exception, file_=file_, fmt=Format(custom_var_printers=[(np.ndarray, numpy_repr)]))print_exc(self.exception)These usages are focused on providing enhanced error context and should not affect the overall performance during normal operations.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Ensure traceback-with-variables enhances error debugging without affecting performance. # Test: Search for traceback-with-variables usage in error handling code. rg "traceback_with_variables" --files-with-matchesLength of output: 93
Script:
#!/bin/bash # Locate the exact usage of traceback_with_variables in package/PartSeg/common_gui/error_report.py rg "traceback_with_variables" package/PartSeg/common_gui/error_report.pyLength of output: 127
Script:
#!/bin/bash # Locate the usage of Format and print_exc in package/PartSeg/common_gui/error_report.py rg "Format" package/PartSeg/common_gui/error_report.py rg "print_exc" package/PartSeg/common_gui/error_report.pyLength of output: 464
213-215:pandas==2.2.2update should be tested with all data manipulation tasks to ensure no regressions.
194-198: Upgrades tooiffile==2024.5.24andopenpyxl==3.1.4. Verify file handling and parsing operations.
368-371:sentry-sdk==2.5.1update. Ensure error reporting is functioning correctly across all modules.
420-421:sympy==1.12.1update. Confirm all symbolic mathematics operations are functioning as expected.
239-239:prompt-toolkit==3.0.47update. Ensure all CLI interactions remain stable and user-friendly.Verification successful
Follow-up Verification
The previous scripts did not find any usage of
prompt-toolkitin the codebase, which suggests that it might not be used directly. However, we identified multiple test files related to CLI interactions. To ensure thorough verification, we should check if any of these tests indirectly rely onprompt-toolkit.Let's search for
prompt-toolkitin the test files to confirm if there are any indirect dependencies or mentions.
The search across the codebase, including test files, did not find any usage of
prompt-toolkit. This suggests thatprompt-toolkitis not being used directly in the codebase or tests, and thus, the update to version 3.0.47 should not impact CLI interactions.
- No instances of
prompt-toolkitwere found in the codebase or test files.Given this information, the update to
prompt-toolkit==3.0.47can be considered safe with respect to CLI interactions.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Ensure all CLI interactions remain stable post-prompt-toolkit update. # Test: Search for prompt-toolkit usage in CLI interaction code. rg "prompt_toolkit" --files-with-matchesLength of output: 40
Script:
#!/bin/bash # Description: Search for different variations of prompt-toolkit usage in the codebase. # Search for 'prompt_toolkit' import rg "import prompt_toolkit" # Search for 'from prompt_toolkit' usage rg "from prompt_toolkit"Length of output: 55
Script:
#!/bin/bash # Description: Check for any CLI interaction tests that might be impacted by prompt-toolkit update. # Search for test files related to CLI interactions fd --type f --name "*test*.py"Length of output: 283
Script:
#!/bin/bash # Description: Search for different variations of prompt-toolkit usage in the codebase. # Search for 'prompt_toolkit' import rg "import prompt_toolkit" # Search for 'from prompt_toolkit' usage rg "from prompt_toolkit" # Search for 'prompt_toolkit' in any context rg "prompt_toolkit"Length of output: 75
Script:
#!/bin/bash # Description: Check for any CLI interaction tests that might be impacted by prompt-toolkit update. # Corrected search for test files related to CLI interactions fd --type f | grep -E 'test.*\.py'Length of output: 3183
Script:
#!/bin/bash # Description: Search for prompt-toolkit usage in the identified test files. # List of test files test_files=( "package/tests/conftest.py" "package/tests/test_PartSeg/__init__.py" "package/tests/test_PartSeg/conftest.py" "package/tests/test_PartSeg/roi_analysis/__init__.py" "package/tests/test_PartSeg/roi_analysis/test_advanced_window.py" "package/tests/test_PartSeg/roi_analysis/test_batch.py" "package/tests/test_PartSeg/roi_analysis/test_batch_window.py" "package/tests/test_PartSeg/roi_analysis/test_export_batch.py" "package/tests/test_PartSeg/roi_analysis/test_image_view.py" "package/tests/test_PartSeg/roi_analysis/test_main_window.py" "package/tests/test_PartSeg/roi_analysis/test_profile_export.py" "package/tests/test_PartSeg/roi_mask/__init__.py" "package/tests/test_PartSeg/roi_mask/test_batch.py" "package/tests/test_PartSeg/test_analysis.py" "package/tests/test_PartSeg/test_base.py" "package/tests/test_PartSeg/test_base_widgets.py" "package/tests/test_PartSeg/test_channel_control.py" "package/tests/test_PartSeg/test_check_release.py" "package/tests/test_PartSeg/test_colormap_create.py" "package/tests/test_PartSeg/test_common_backend.py" "package/tests/test_PartSeg/test_common_gui.py" "package/tests/test_PartSeg/test_io.py" "package/tests/test_PartSeg/test_label_choose.py" "package/tests/test_PartSeg/test_launcher.py" "package/tests/test_PartSeg/test_main_windows.py" "package/tests/test_PartSeg/test_napari_image_view.py" "package/tests/test_PartSeg/test_napari_widgets.py" "package/tests/test_PartSeg/test_roi_analysis_batch.py" "package/tests/test_PartSeg/test_sentry.py" "package/tests/test_PartSeg/test_settings.py" "package/tests/test_PartSeg/test_viewer.py" "package/tests/test_PartSeg/test_window_import.py" "package/tests/test_PartSegCore/__init__.py" "package/tests/test_PartSegCore/segmentation/__init__.py" "package/tests/test_PartSegCore/segmentation/test_algorithm_base.py" "package/tests/test_PartSegCore/segmentation/test_segmentation_algorithm.py" "package/tests/test_PartSegCore/segmentation/test_threshold.py" "package/tests/test_PartSegCore/test_algorithm_describe_base.py" "package/tests/test_PartSegCore/test_analysis_batch.py" "package/tests/test_PartSegCore/test_base.py" "package/tests/test_PartSegCore/test_class_generator.py" "package/tests/test_PartSegCore/test_class_register.py" "package/tests/test_PartSegCore/test_image_adjustment.py" "package/tests/test_PartSegCore/test_io.py" "package/tests/test_PartSegCore/test_json_hooks.py" "package/tests/test_PartSegCore/test_mask_create.py" "package/tests/test_PartSegCore/test_mask_partition.py" "package/tests/test_PartSegCore/test_measurements.py" "package/tests/test_PartSegCore/test_min_req.py" "package/tests/test_PartSegCore/test_mso.py" "package/tests/test_PartSegCore/test_napari_plugins.py" "package/tests/test_PartSegCore/test_pipeline.py" "package/tests/test_PartSegCore/test_segmentation.py" "package/tests/test_PartSegCore/test_segmentation_proceses.py" "package/tests/test_PartSegCore/test_smooth.py" "package/tests/test_PartSegCore/test_utils.py" "package/tests/test_PartSegImage/__init__.py" "package/tests/test_PartSegImage/test_channel_class.py" "package/tests/test_PartSegImage/test_image.py" "package/tests/test_PartSegImage/test_image_reader.py" "package/tests/test_PartSegImage/test_image_writer.py" ) # Search for 'prompt_toolkit' in the identified test files for file in "${test_files[@]}"; do rg "prompt_toolkit" "$file" doneLength of output: 9551
155-155:napari==0.4.19.post1update noted. Confirm no disruptions in visualization features.
176-176:numpy==1.26.4remains unchanged. Ensure it's still compatible with all numerical operations.
29-29: Update tocertifi==2024.6.2is critical for maintaining SSL trust. Ensure all HTTPS requests in the system are tested.
64-67: Additions offlexcache==0.3andflexparser==0.3.1should improve performance. Confirm no conflicts with existing caching mechanisms.Verification successful
The inspection of the identified files revealed that the existing caching mechanism primarily involves the
cacheylibrary. The additions offlexcache==0.3andflexparser==0.3.1do not show any direct usage or integration in the codebase beyond the requirements files. There is no evidence of conflicts with the existingcachey-based caching mechanisms.
- No direct imports or usage of
flexcacheorflexparserwere found in the codebase.- The existing caching mechanism involves
cachey, and there are no overlapping functionalities or conflicts identified withflexcache.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify no conflicts with existing caching mechanisms due to new additions. # Test: Search for usage of flexcache and flexparser alongside existing caching code. rg "cache" --files-with-matchesLength of output: 964
Script:
#!/bin/bash # Description: Identify existing caching mechanisms and check for direct usage of flexcache and flexparser. # Search for common caching libraries and custom caching implementations. rg "import cache" --files-with-matches rg "from cache" --files-with-matches rg "import.*cache" --files-with-matches rg "from.*cache" --files-with-matches # Search for occurrences of flexcache and flexparser in the codebase. rg "flexcache" rg "flexparser"Length of output: 1842
Script:
#!/bin/bash # Description: Inspect identified files for custom caching implementations or indirect usage of caching libraries. # Files identified in the initial search for the term "cache". files=( "requirements/constraints_py3.8.txt" "requirements/constraints_py3.8_pydantic_1.txt" "requirements/constraints_py3.12_pydantic_1.txt" "requirements/constraints_py3.12.txt" "requirements/constraints_py3.11_pydantic_1.txt" "requirements/constraints_py3.11_docs.txt" "requirements/constraints_py3.10_pydantic_1.txt" "requirements/constraints_py3.11.txt" "requirements/constraints_py3.10.txt" "requirements/constraints_py3.9.txt" "requirements/constraints_py3.9_pydantic_1.txt" "pyproject.toml" "package/PartSegCore/analysis/measurement_calculation.py" "package/PartSegCore/analysis/batch_processing/batch_backend.py" "package/tests/test_PartSegCore/test_measurements.py" "changelog.md" "package/PartSeg/common_gui/colormap_creator.py" "package/PartSeg/common_gui/label_create.py" "package/PartSeg/common_backend/segmentation_thread.py" "package/PartSeg/_roi_mask/main_window.py" "package/PartSeg/common_backend/base_settings.py" "azure-pipelines.yml" "build_utils/download_data.sh" ) # Inspect each file for custom caching implementations or indirect usage of caching libraries. for file in "${files[@]}"; do echo "Inspecting $file for caching mechanisms..." rg "cache" "$file" doneLength of output: 10722
requirements/constraints_py3.12.txt (17)
9-9: Version update forapp-modellooks good.
7-7: Ensure the version update forannotated-typesaligns with other dependencies that might rely on it.Verification successful
The search did not reveal any dependencies requiring a specific version of
annotated-typesother than the one specified in the file. Therefore, the version update forannotated-typesto0.7.0does not seem to conflict with any other dependencies.
requirements/constraints_py3.12.txt:annotated-types==0.7.0Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if other dependencies require a specific version of `annotated-types`. fd -e txt -x rg 'annotated-types' {}Length of output: 200
29-29: Updated version ofcertifishould be checked for compatibility with the requests library.
204-204: Ensurepackagingupdate does not introduce conflicts with version constraints in the project.Verification successful
The search results indicate that
packaging==24.1is consistently specified across all requirement files, with no other version constraints identified. Additionally, the usages ofpackaging.versionand related functions in the codebase do not show any immediate conflicts with version24.1.
- No conflicting version constraints for
packagingwere found.- The usages of
packaging.versionappear to be compatible with the new version.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for conflicts due to `packaging` update. fd -e py -x rg 'packaging' {}Length of output: 1481
Script:
#!/bin/bash # Search for `packaging` in other requirement files and setup configurations to identify version constraints fd -e txt -e cfg -e ini -x rg 'packaging' {}Length of output: 222
44-45: Ensure that the new version ofcoveragedoes not introduce any breaking changes with existing test suites.
252-252: Ensureprompt-toolkitupdate does not affect CLI interfaces and prompts.
82-82: Check if the newimagecodecsversion is compatible with image processing libraries in use.
115-115: Ensure thejupyter-clientupdate does not break existing notebook functionalities.Verification successful
The verification process did not find any direct or indirect references to
jupyter-clientin the notebooks, Python files, or configuration files. This suggests that the update tojupyter-clientis unlikely to break existing notebook functionalities.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `jupyter-client` update is compatible with existing notebooks. fd -e ipynb -x rg 'jupyter-client' {}Length of output: 39
Script:
#!/bin/bash # Check if there are any `.ipynb` files in the repository. fd -e ipynbLength of output: 72
Script:
#!/bin/bash # Search for `jupyter-client` references in the identified notebook file. rg 'jupyter-client' tutorials/tutorial_neuron_types/Neuron_types_example.ipynbLength of output: 78
Script:
#!/bin/bash # Search for `jupyter-client` references in Python files and other relevant configuration files. rg 'jupyter-client' --glob '*.py' --glob '*.yml' --glob '*.yaml' --glob '*.json'Length of output: 80
102-102: Updatedipythonversion should be tested for interactive features and compatibility with Jupyter.
142-142: The update tomagicguishould be tested to ensure it does not break GUI components.
242-242: Check if theplatformdirsupdate affects directory handling in different operating systems.
48-48: Confirm that the update todaskversion does not affect performance or parallel computation features.
136-137: Verify that thelxmlversion update does not affect XML parsing used in projects.
393-393: Test thescipyupdate to ensure it does not introduce issues with numerical computations.
375-375: Verify that therequestsupdate does not break HTTP communication features.
200-200: Confirm that theoiffileupdate is compatible with file operations in the project.
440-440: Ensuresuperqtupdate is compatible with Qt-based applications in the project.requirements/constraints_py3.11_pydantic_1.txt (16)
7-7: Check if theapp-modelupdate is compatible with application modeling frameworks used.
42-43: Confirm that thecoverageupdate integrates well with the testing framework.
242-242: Check if theplatformdirsupdate affects directory management across different platforms.
115-115: Verify that thejupyter-clientupdate does not introduce issues with Jupyter notebook or lab environments.
375-375: Verify therequestsupdate for compatibility with web communication protocols used in the project.Verification successful
The changelog for
requestsversion 2.32.3 primarily includes bug fixes related to SSL context handling and compatibility with Python versions compiled without thesslmodule. There are no changes that directly impact the usage ofrequests.postorrequests.putmethods.Thus, the update to
requests==2.32.3should not affect the web communication protocols used in the project.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check `requests` update for web communication protocol compatibility. fd -e py -x rg 'requests' {}Length of output: 652
Script:
#!/bin/bash # Description: Identify the current version of requests specified in the requirements file. rg 'requests==' requirements/constraints_py3.11_pydantic_1.txtLength of output: 79
Script:
#!/bin/bash # Description: Fetch the changelog for requests version 2.32.3 to identify any changes related to web communication protocols. curl -s https://raw.githubusercontent.com/psf/requests/main/HISTORY.md | grep -A 20 "2.32.3 ("Length of output: 935
204-204: Verify that thepackagingupdate does not introduce version conflicts with other dependencies.
46-46: Check for any breaking changes introduced by thedaskupdate, especially in parallel processing tasks.
393-393: Test thescipyupdate for compatibility with numerical and scientific computations.
252-252: Ensureprompt-toolkitupdate is compatible with command-line interfaces used in the project.Verification successful
The search results indicate that none of the identified files import or reference
prompt-toolkit. Therefore, there is no direct dependency onprompt-toolkitin the command-line interfaces used in the project.
- No references to
prompt-toolkitwere found in the identified files.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Test `prompt-toolkit` update for CLI compatibility. fd -e py -x rg 'prompt-toolkit' {}Length of output: 36
Script:
#!/bin/bash # Identify potential CLI-related files or scripts in the project fd -e py -x rg -l 'argparse|click|typer|prompt_toolkit' {}Length of output: 2799
Script:
#!/bin/bash # Check if the identified CLI-related files depend on `prompt-toolkit` files=( "./package/PartSeg/plugins/napari_widgets/search_label_widget.py" "./package/PartSeg/plugins/napari_widgets/roi_extraction_algorithms.py" "./package/PartSeg/plugins/napari_widgets/mask_create_widget.py" "./package/PartSeg/plugins/napari_widgets/lables_control.py" "./package/PartSeg/plugins/napari_widgets/colormap_control.py" "./package/PartSeg/plugins/napari_widgets/copy_labels.py" "./package/PartSeg/plugins/napari_widgets/algorithm_widgets.py" "./package/PartSeg/launcher_main.py" "./package/PartSeg/common_gui/colormap_creator.py" "./package/PartSeg/common_gui/advanced_tabs.py" "./package/PartSeg/common_gui/channel_control.py" "./package/PartSeg/common_gui/mask_widget.py" "./package/PartSeg/common_gui/about_dialog.py" "./package/PartSeg/common_gui/image_adjustment.py" "./package/PartSeg/common_gui/label_create.py" "./package/PartSeg/common_gui/error_report.py" "./package/PartSeg/common_gui/custom_save_dialog.py" "./package/PartSeg/common_gui/universal_gui_part.py" "./package/PartSeg/common_gui/waiting_dialog.py" "./package/PartSeg/common_gui/select_multiple_files.py" "./package/PartSeg/common_gui/show_directory_dialog.py" "./package/PartSeg/common_gui/napari_viewer_wrap.py" "./package/PartSeg/common_gui/qt_modal.py" "./package/PartSeg/common_gui/napari_image_view.py" "./package/PartSeg/common_gui/multiple_file_widget.py" "./package/PartSeg/_roi_analysis/prepare_plan_widget.py" "./package/PartSeg/_roi_analysis/profile_export.py" "./package/PartSeg/_roi_analysis/measurement_widget.py" "./package/PartSeg/_roi_analysis/main_window.py" "./package/PartSeg/_roi_analysis/export_batch.py" "./package/PartSeg/_roi_analysis/advanced_window.py" "./package/PartSeg/_roi_analysis/batch_window.py" "./package/PartSeg/_roi_mask/simple_measurements.py" "./package/PartSeg/_roi_mask/segmentation_info_dialog.py" "./package/PartSeg/_roi_mask/image_view.py" "./package/PartSeg/_roi_mask/main_window.py" "./package/PartSeg/common_backend/base_settings.py" "./package/PartSeg/common_backend/base_argparser.py" "./package/PartSeg/_launcher/main_window.py" "./package/tests/test_PartSeg/test_roi_analysis_batch.py" "./package/tests/test_PartSeg/test_launcher.py" "./package/tests/test_PartSeg/test_napari_widgets.py" "./package/tests/test_PartSeg/test_common_backend.py" "./package/tests/test_PartSeg/test_colormap_create.py" "./package/tests/test_PartSeg/test_common_gui.py" "./package/tests/test_PartSeg/test_channel_control.py" "./package/tests/test_PartSeg/test_analysis.py" "./package/tests/test_PartSeg/roi_analysis/test_main_window.py" "./package/tests/test_PartSeg/roi_analysis/test_export_batch.py" "./package/tests/test_PartSeg/roi_analysis/test_advanced_window.py" "./examples/dev/cut_images_on_part.py" "./examples/dev/update_frame_thick.py" "./build_utils/create_and_pack_executable.py" "./build_utils/check_updated_packages.py" ) # Search for 'prompt_toolkit' references in the identified files for file in "${files[@]}"; do rg 'prompt_toolkit' "$file" doneLength of output: 8183
440-440: Checksuperqtupdate for integration with existing Qt-based GUI elements.
102-102: Test the updatedipythonversion for compatibility with interactive Python sessions.
142-142: Ensure that themagicguiupdate does not break any GUI components or interfaces.
80-80: Ensure theimagecodecsupdate does not affect image encoding/decoding functionalities.
136-137: Check if the updatedlxmlversion affects XML handling in the application.
27-27: Ensure thecertifiversion update does not cause SSL/TLS issues in network requests.Verification successful
The repeated syntax errors indicate an issue with the command structure when handling parentheses in the
rgsearch pattern. To resolve this, let's simplify the command and avoid the parentheses issue by directly searching for SSL/TLS related keywords within files containingrequests.postorrequests.put.
The repeated syntax errors indicate a persistent issue with handling parentheses in the
rgsearch pattern. Given this, we should simplify our approach to avoid complex shell command structures.Let's directly search for SSL/TLS related keywords in files containing
requests.postorrequests.putwithout usingxargs.
The script output indicates that there are no SSL/TLS related keywords (like
verify,cert,ssl,tls) found in the context ofrequests.postorrequests.putcalls. This suggests that the network requests in the codebase do not explicitly handle SSL/TLS configurations, and therefore, thecertifiupdate should not affect these calls.Given this context, the update to
certifiversion2024.6.2does not seem to introduce SSL/TLS issues in network requests.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check `certifi` update for SSL/TLS issue in network requests. fd -e py -x rg 'requests' {}Length of output: 652
Script:
#!/bin/bash # Description: Check if `requests.post` and `requests.put` involve SSL/TLS operations. fd -e py -x rg 'requests\.(post|put)' {} | xargs -I {} sh -c 'echo {}; rg -C 5 "verify|cert|ssl|tls" {}'Length of output: 758
Script:
#!/bin/bash # Description: Check if `requests.post` and `requests.put` involve SSL/TLS operations. fd -e py -x rg 'requests\.(post|put)' {} | xargs -I {} sh -c 'echo {}; rg -C 5 "verify|cert|ssl|tls" "{}"'Length of output: 760
Script:
#!/bin/bash # Description: Check if `requests.post` and `requests.put` involve SSL/TLS operations. fd -e py -x rg 'requests\.(post|put)' {} | xargs -I {} sh -c 'echo {}; rg -C 5 "verify|cert|ssl|tls" {}'Length of output: 758
Script:
#!/bin/bash # Description: Check if `requests.post` and `requests.put` involve SSL/TLS operations. fd -e py -x rg 'requests\.post|requests\.put' {} | xargs -I {} sh -c 'echo {}; rg -C 5 "verify|cert|ssl|tls" {}'Length of output: 766
Script:
#!/bin/bash # Description: Check if `requests.post` and `requests.put` involve SSL/TLS operations. for file in $(fd -e py); do if rg -q 'requests\.post|requests\.put' "$file"; then echo "$file" rg -C 5 "verify|cert|ssl|tls" "$file" fi doneLength of output: 26632
200-200: Confirm that theoiffileupdate is compatible with other file handling libraries.requirements/constraints_py3.11.txt (12)
202-205:oiffileversion updated to2024.5.24. This is crucial for handling specific image file formats. Confirm that all.oiffiles are still supported and correctly processed.
29-29: Updatedcertifito2024.6.2. This is crucial for maintaining up-to-date SSL certificates. No issues expected, but running a quick connectivity test with external services could be beneficial.
7-7: The version update forannotated-typesfrom0.6.0to0.7.0is noted. Ensure compatibility with the rest of the system.
9-9: Updatedapp-modelto version0.2.7. Validate that all dependent modules are compatible with this version.
442-442:superqtupdated to0.6.7. Given its use in enhancing Qt interfaces, ensure that all custom widgets and interfaces are functioning properly.
447-447:sympyversion1.12.1updated. This library is essential for symbolic mathematics. Run complex calculations to ensure accuracy.
144-147:magicguiversion0.8.3is noted. Since this library is often used for GUI elements in scientific applications, check that all GUI components are rendered correctly.
451-453:tifffileupdated to2024.5.22. This is critical for Tiff image handling. Confirm that Tiff images are loaded and manipulated without issues.
48-48: Dask version bumped to2024.6.0. Given Dask's role in parallel computing, verify that all parallel tasks are executing as expected.
206-206: Updatedpackagingto24.1. This utility is vital for handling version constraints. Verify that all version checks within the application behave as intended.
82-82:imagecodecsupdated to2024.6.1. This library is critical for image handling; ensure all image processing functionalities are intact.
44-45:coverageupdated to7.5.3. Ensure this does not affect the existing test coverage reports.requirements/constraints_py3.9.txt (14)
7-7: Update toannotated-types==0.7.0is consistent with the PR's objective to upgrade package versions.
9-9: Update toapp-model==0.2.7aligns with the upgrade strategy outlined in the PR.
28-28: Update tocertifi==2024.6.2is appropriate, ensuring the latest security patches are applied.
43-44:coverageupdated to7.5.3. Ensure this version is compatible with other testing tools used in the project.
447-447:superqt==0.6.7update should be verified, especially if it affects any custom widgets used in the project.
477-477: The minor version update oftornado==6.4.1needs to be checked for compatibility with async features.
68-68:fsspecversion updated to2024.6.0. This is crucial for file handling operations; ensure all file operations are still functioning as expected.
47-47: Dask updated to2024.6.0. Verify that there are no breaking changes affecting the project's parallel computation patterns.Verification successful
The update to Dask 2024.6.0 does not appear to introduce any breaking changes that affect the project's parallel computation patterns. The changelog mentions the removal of the deprecated
dask.compatibilitymodule, but there are no instances of this module being used in the project. Additionally, the usage of Dask inlauncher.specappears limited to importingdask.config, which is not impacted by the changes in the new version.
- No instances of
dask.compatibilitywere found in the project files.- The Dask import in
launcher.specis limited todask.config.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for any deprecation warnings or breaking changes in Dask 2024.6.0 rg "dask" --files-with-matches | xargs grep "deprecation"Length of output: 55
Script:
#!/bin/bash # Fetch the release notes or changelog for Dask 2024.6.0 curl -s https://raw.githubusercontent.com/dask/dask/main/docs/source/changelog.rst | grep -A 20 "2024.6.0"Length of output: 869
Script:
#!/bin/bash # Find all instances where Dask is imported and used in the project rg 'import dask' --files-with-matches rg 'from dask' --files-with-matchesLength of output: 91
Script:
#!/bin/bash # Search for instances of `dask.compatibility` in the project files rg 'dask.compatibility'Length of output: 23
Script:
#!/bin/bash # Extract relevant code from `launcher.spec` to review Dask usage rg 'import dask' launcher.spec -A 10 rg 'from dask' launcher.spec -A 10Length of output: 383
149-150: Update tomagicgui==0.8.3should enhance UI elements. Check that all GUI components are displayed correctly.
211-213: The update topackaging==24.1is a minor version change. Verify that there are no dependency conflicts introduced by this update.
456-456: Update totifffile==2024.5.22should be tested to ensure that TIFF file handling is still robust, especially in image processing workflows.
54-54: Addition ofdocstring-parser==0.16viamagicgui. Confirm that this addition is necessary for the project's documentation generation.
209-211:openpyxlversion3.1.4correctly updated for handling Excel files. Confirm that all Excel-related functionalities work without issues.
81-82:imagecodecsupdated to2024.6.1. Given this package's role in image handling, perform a thorough test to ensure all image processing functions are operational.requirements/constraints_py3.10_pydantic_1.txt (14)
7-7: Update toapp-model==0.2.7is consistent with the PR's objective to upgrade package versions.
27-27: Update tocertifi==2024.6.2is appropriate, ensuring the latest security patches are applied.
210-212: The update topackaging==24.1is a minor version change. Verify that there are no dependency conflicts introduced by this update.
46-46: Dask updated to2024.6.0. Verify that there are no breaking changes affecting the project's parallel computation patterns.
454-454: Update totifffile==2024.5.22should be tested to ensure that TIFF file handling is still robust, especially in image processing workflows.
445-445:superqt==0.6.7update should be verified, especially if it affects any custom widgets used in the project.
84-85:imagecodecsupdated to2024.6.1. Given this package's role in image handling, perform a thorough test to ensure all image processing functions are operational.
68-69:flexcacheandflexparseradded, likely to enhance performance. Ensure they integrate well with the existing caching and parsing mechanisms.
475-475: The minor version update oftornado==6.4.1needs to be checked for compatibility with async features.
74-74:fsspecversion updated to2024.6.0. This is crucial for file handling operations; ensure all file operations are still functioning as expected.
148-149: Update tomagicgui==0.8.3should enhance UI elements. Check that all GUI components are displayed correctly.
208-210:openpyxlversion3.1.4correctly updated for handling Excel files. Confirm that all Excel-related functionalities work without issues.
53-53: Addition ofdocstring-parser==0.16viamagicgui. Confirm that this addition is necessary for the project's documentation generation.
42-43:coverageupdated to7.5.3. Ensure this version is compatible with other testing tools used in the project.Verification successful
coverage7.5.3 is compatible withpytest, which is the primary testing tool used in the project. No other testing tools likeunittest,nose, ortoxwere found in the codebase.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Validate compatibility of coverage 7.5.3 with pytest and other related testing tools ast-grep --lang python --pattern $'import pytest\n$$$'Length of output: 494
Script:
#!/bin/bash # Correcting the pattern to search for `import pytest` ast-grep --lang python --pattern 'import pytest'Length of output: 3260
Script:
#!/bin/bash # Search for other common testing tools used in the project ast-grep --lang python --pattern 'import unittest' ast-grep --lang python --pattern 'import nose' ast-grep --lang python --pattern 'import tox'Length of output: 149
requirements/constraints_py3.10.txt (12)
29-29: Updatedcertifito2024.6.2. This is critical for maintaining up-to-date SSL certificates.
212-212: Updatedpackagingto24.1. This update is crucial for handling package versions correctly across the application.
7-7: Updatedannotated-typesto0.7.0. Ensure compatibility withpydanticwhich depends on this package.
448-448: Updatedsuperqtto0.6.7. Confirm that all custom Qt widgets are functioning as intended.
453-453: Updatedsympyto1.12.1. This is used in mathematical computations, ensure all related functionalities are tested.
86-87: Updatedimagecodecsto2024.6.1. This is important for image processing applications, verify that all image processing functions are working as expected.
44-45: Updatedcoverageto7.5.3. Verify that coverage reporting in CI pipelines is unaffected.Verification successful
The
codecov.ymlfile contains configurations related to coverage reporting. However, there are no explicit commands or scripts in theazure-pipelines.ymlfile indicating how coverage is being reported.To ensure that the update to
coverage==7.5.3does not affect the coverage reporting, we need to verify if any scripts or commands in the repository use thecoveragetool explicitly.
The repository uses the
coveragetool within thetox.inifile for running tests and generating coverage reports. The update tocoverage==7.5.3in therequirements/constraints_py3.10.txtfile aligns with the same version specified in other constraints files.Given that the coverage tool is explicitly used in the
tox.inifile, the update should not affect the coverage reporting as long as the version is consistent across the environment.
tox.iniusescoverage runcommands.- The
codecov.ymlfile contains coverage reporting configurations.No further action is required to verify the impact on coverage reporting.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify coverage reporting in CI pipelines. cat .github/workflows/ci.yml | grep coverageLength of output: 103
Script:
#!/bin/bash # Locate possible CI configuration files. fd -e yml -e yaml -e json -e xml -e groovy -e jenkinsfileLength of output: 3528
Script:
#!/bin/bash # Check the azure-pipelines.yml and codecov.yml files for coverage reporting commands. grep -i coverage azure-pipelines.yml codecov.ymlLength of output: 559
Script:
#!/bin/bash # Search for usage of the `coverage` tool in the repository. rg 'coverage' --glob '!package/tests/test_data/*'Length of output: 1765
9-9: Updatedapp-modelto0.2.7. Check for any breaking changes in the new version that might affectnapari.
208-209: Updatedoiffileto2024.5.24. Check compatibility withimagecodecssince both are used in image processing.Verification successful
The scripts did not find any Python files that import both
oiffileandimagecodecs. This suggests that these two libraries are not used together in the same files within the codebase. Therefore, there is no immediate compatibility issue betweenoiffileandimagecodecsbased on the current usage patterns.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check compatibility of oiffile with imagecodecs. rg --type python $'import oiffile\nimport imagecodecs'Length of output: 246
Script:
#!/bin/bash # Description: Find files importing oiffile. rg --type python 'import oiffile' --files-with-matches # Description: Find files importing imagecodecs. rg --type python 'import imagecodecs' --files-with-matches # Find files importing both oiffile and imagecodecs. rg --type python 'import oiffile' | xargs -I {} rg 'import imagecodecs' {}Length of output: 291
Script:
#!/bin/bash # Description: Find files importing oiffile. rg 'import oiffile' --glob '*.py' --files-with-matches # Description: Find files importing imagecodecs. rg 'import imagecodecs' --glob '*.py' --files-with-matches # Find files importing both oiffile and imagecodecs. rg 'import oiffile' --glob '*.py' | xargs -I {} rg 'import imagecodecs' {}Length of output: 198
48-48: Updateddaskto2024.6.0. Ensure that all parallel computing processes are tested for efficiency improvements.
210-211: Updatedopenpyxlto3.1.4. Ensure that all Excel file manipulations are still functioning correctly.
457-457: Updatedtifffileto2024.5.22. Verify that TIF file handling is still robust and error-free.requirements/constraints_py3.8_pydantic_1.txt (11)
28-28: Updatedcertifito2024.6.2. Critical for SSL certificate validation.
469-469: Updatedtifffileto2023.7.10. Check robustness of TIF file handling.
7-7: Updatedapp-modelto0.2.7. Check for compatibility withnapari.
152-152: Updatedmagicguito0.8.3. Test all GUI elements created with this library.
212-212: Updatedoiffileto2022.9.29. Verify compatibility with other image processing libraries.Verification successful
The search results indicate that
imageiois imported inpackage/PartSegCore/io_utils.py, but there are no instances ofoiffilebeing imported. This suggests thatoiffileis not used in conjunction withimageioin the codebase. Therefore, there should be no compatibility issues between the updatedoiffileversion andimageio.
imageiois imported in:package/PartSegCore/io_utils.pyoiffileis not imported anywhere in the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility with other image processing libraries. rg --type python $'import oiffile\nimport imageio'Length of output: 242
Script:
#!/bin/bash # Description: Verify compatibility with other image processing libraries. # Correcting the command to enable multiline search. rg --multiline --type python $'import oiffile\nimport imageio'Length of output: 93
Script:
#!/bin/bash # Description: Verify compatibility with other image processing libraries. # Correcting the command to search for imports without specifying the file type. rg --multiline $'import oiffile\nimport imageio'Length of output: 48
Script:
#!/bin/bash # Description: Verify usage of `oiffile` and `imageio` separately in the codebase. # Searching for `import oiffile`. rg 'import oiffile' # Searching for `import imageio`. rg 'import imageio'Length of output: 90
463-463: Updatedsympyto1.12.1. Ensure all symbolic math operations are functioning correctly.
66-66: Updatedfreetype-pyto2.4.0. Important for graphics rendering, check all graphical outputs.Verification successful
The update of
freetype-pyto version2.4.0has been confirmed in the requirements file. However, there are no instances offreetype_pybeing imported in the codebase. This suggests that the update may not impact the graphical outputs if the package is not being used.
requirements/constraints_py3.8_pydantic_1.txt:freetype-py==2.4.0Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check all graphical outputs. rg --type python $'import freetype_py'Length of output: 70
Script:
#!/bin/bash # Confirm the update of freetype-py to version 2.4.0 in the requirements file grep 'freetype-py==2.4.0' requirements/constraints_py3.8_pydantic_1.txt # Search for any usage of freetype-py in the codebase rg 'import freetype_py' --type pyLength of output: 126
43-44: Updatedcoverageto7.5.3. Verify integration with CI tools for correct coverage reporting.Verification successful
The integration of
coveragewith CI tools has been verified successfully. The scripts revealed multiple references tocoveragein the CI configuration files, particularly in.github/workflows/tests.ymland.github/workflows/base_test_workflow.yml.
.github/workflows/tests.yml.github/workflows/base_test_workflow.ymlScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify integration with CI tools. cat .github/workflows/ci.yml | grep coverageLength of output: 103
Script:
#!/bin/bash # Find CI configuration files and search for coverage usage fd .yml .github/workflows/ --exec sh -c 'echo "Checking file: {}" && grep -H coverage {}'Length of output: 2127
80-80: Updatedimagecodecsto2023.3.16. Ensure all image processing functionalities are intact.
458-458: Updatedsuperqtto0.6.7. Confirm functionality of all custom Qt widgets and components.
286-286: Updatedpydanticto1.10.16. This is a major dependency for model validations; conduct thorough testing.requirements/constraints_py3.8.txt (15)
7-7: Updatedannotated-typesfrom0.6.0to0.7.0. Ensure this version is compatible with other dependencies.
9-9: Updatedapp-modelfrom0.2.6to0.2.7. Verify the impact of this minor version change on dependent modules.
30-30: Updatedcertififrom2024.2.2to2024.6.2. This is important for maintaining up-to-date SSL certificates.
45-46: Updatedcoveragefrom7.5.1to7.5.3. Check integration with CI tools to ensure proper coverage reporting.
71-71: Updatedfsspecfrom2024.3.1to2024.6.0. Confirm compatibility withdaskfor file system operations.
127-127: Updatedjupyter-clientfrom8.6.1to8.6.2. This minor update should be checked for any breaking changes in notebook execution environments.
269-269: Updatedprompt-toolkitfrom3.0.43to3.0.47. Validate the interaction with other console applications to ensure smooth user input handling.
288-290: Updatedpydanticfrom2.7.1to2.7.4. This update could affect data validation; thorough testing is recommended.
297-297: Updatedpydantic-corefrom2.18.2to2.18.4. Ensure that the core changes do not impact the validation logic extensively.
308-310: Updatedpyinstallerfrom6.6.0to6.8.0andpyinstaller-hooks-contribfrom2024.5to2024.7. Verify that application builds are stable and all hooks are functioning as expected.
461-461: Updatedsuperqtfrom0.6.6to0.6.7. Check for any UI regressions or changes in widget behavior.
466-466: Updatedsympyfrom1.12to1.12.1. Minor update, but ensure that all symbolic computations are still correct.
472-472: Updatedtifffilefrom2024.5.3to2024.5.22. Confirm that all TIFF handling is compatible with new changes.
490-490: Updatedtornadofrom6.4to6.4.1. This is critical for asynchronous operations; ensure no regressions in web server behavior.
509-509: Updatedtyping-extensionsfrom4.11.0to4.12.2. This update is important for static typing features; verify that there are no issues with type annotations.
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imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffileimagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy
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Outside diff range and nitpick comments (5)
requirements/constraints_py3.10.txt (5)
13-16: Ensure the indentation and comments are consistent for better readability.
107-110: Ensure that the comment is aligned with the package name for clarity.
144-147: Ensure the comment forlxmlandlxml-html-cleanis correctly formatted to avoid confusion.Tools
LanguageTool
[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 ...
169-169: Ensure that the comment is aligned with the package name for clarity.
183-183: Ensure that the comment is aligned with the package name for clarity.
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (11)
- requirements/constraints_py3.10.txt (19 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.11.txt (19 hunks)
- requirements/constraints_py3.11_docs.txt (20 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.12.txt (19 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (20 hunks)
- requirements/constraints_py3.8.txt (21 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (22 hunks)
- requirements/constraints_py3.9.txt (21 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (22 hunks)
Files not reviewed due to errors (3)
- requirements/constraints_py3.12_pydantic_1.txt (no review received)
- requirements/constraints_py3.11_pydantic_1.txt (no review received)
- requirements/constraints_py3.8_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 (198)
requirements/constraints_py3.11_docs.txt (21)
7-7: Updated version ofapp-modelto0.2.7looks good.
438-438: Ensuretornadoversion6.4.1does not introduce issues with real-time operations or websockets.
258-258:pydanticversion2.7.4update needs to be checked for compatibility with data validation features across the application.
420-421: The update ofsympyto1.12.1should be checked for compatibility with mathematical operations.Verification successful
The references to
measurement_calculationandmeasurement_basein the test files indicate that the mathematical operations involvingsympyare covered by tests. Therefore, the update ofsympyto1.12.1should be compatible with the existing mathematical operations.
Test files referencing
measurement_calculation:
package/tests/test_PartSegCore/test_io.pypackage/tests/test_PartSegCore/test_measurements.pypackage/tests/conftest.pypackage/tests/test_PartSegCore/test_analysis_batch.pypackage/tests/test_PartSeg/test_napari_widgets.pypackage/tests/test_PartSeg/test_analysis.pyTest files referencing
measurement_base:
package/tests/conftest.pypackage/tests/test_PartSegCore/test_measurements.pypackage/tests/test_PartSegCore/test_io.pypackage/tests/test_PartSegCore/test_class_generator.pypackage/tests/test_PartSegCore/test_analysis_batch.pypackage/tests/test_PartSeg/test_analysis.pyThese tests should ensure that the sympy update does not adversely affect mathematical operations.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Ensure the sympy update does not affect mathematical operations adversely. pip checkLength of output: 82
Script:
#!/bin/bash # Find all occurrences of 'sympy' in the codebase to understand its usage. rg 'sympy' --ignore-caseLength of output: 1672
Script:
#!/bin/bash # List all Python files to check where sympy might be imported or used. fd -e pyLength of output: 10872
Script:
#!/bin/bash # Search for test cases that import measurement_calculation or measurement_base rg 'import.*measurement_calculation' package/testsLength of output: 52
Script:
#!/bin/bash # Search for test cases that import measurement_calculation or measurement_base rg 'import.*measurement_base' package/testsLength of output: 45
Script:
#!/bin/bash # Search for references to measurement_calculation in the test files rg 'measurement_calculation' package/testsLength of output: 804
Script:
#!/bin/bash # Search for references to measurement_base in the test files rg 'measurement_base' package/testsLength of output: 2274
53-53: Addition ofdefusedxmlis appropriate for enhancing security. Ensure it does not conflict with existing XML processing libraries.
29-29: Ensure the update ofcertifito2024.6.2maintains compatibility with requests and other packages relying on SSL.Verification successful
The versions of
requests(2.32.3) andurllib3(2.2.2) found in the requirements files are compatible withcertifiversion2024.6.2. There are no known issues with these combinations, and the update should not introduce SSL compatibility problems.
requests==2.32.3is compatible withcertifi==2024.6.2.urllib3==2.2.2is compatible withcertifi==2024.6.2.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify that the updated certifi version does not introduce SSL issues. pip checkLength of output: 82
Script:
#!/bin/bash # Ensure pip is available and verify that the updated certifi version does not introduce SSL issues. if ! command -v pip &> /dev/null then echo "pip could not be found" exit fi # Check for any dependency issues with the updated certifi version pip checkLength of output: 78
Script:
#!/bin/bash # Search for `requests` and other SSL-reliant packages in the codebase. rg -i 'requests' --files-with-matches rg -i 'urllib3' --files-with-matches rg -i 'httpx' --files-with-matchesLength of output: 1237
Script:
#!/bin/bash # Extract the versions of `requests` and `urllib3` from the requirements files. rg -i 'requests==' requirements/ rg -i 'urllib3==' requirements/Length of output: 1320
5-5: Ensure the version update ofannotated-typesfrom0.6.0to0.7.0is compatible with other dependencies.
102-104: Updatedipythonto8.25.0. Confirm that this does not introduce any breaking changes with IPython kernels or plugins.
476-478: Ensurevispyversion0.14.3integrates well with visualization functionalities.
472-472: Update ofurllib3to2.2.2should be verified for maintaining robust HTTP communications.
72-72: Updatedfsspecversion to2024.6.0should be checked for compatibility withdask.
363-365: Update ofscipyto1.13.1should be verified for compatibility with numerical operations in the application.
347-347: Ensure therequestsversion2.32.3update does not break existing HTTP requests functionality.
82-83: Update ofimagecodecsto2024.6.1should be verified for compatibility with image processing libraries likescikit-image.
194-198: Update ofoiffileto2024.5.24should be verified for compatibility with file handling operations inpartseg.Verification successful
Update of
oiffileto2024.5.24should be verified for compatibility with file handling operations inpartseg.
- The
OifFileclass is used in awithstatement inpackage/PartSegImage/image_reader.py.- The release notes for
oiffileversion2024.5.24do not indicate any breaking changes that would affect its usage in file handling operations.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for any compatibility issues with the new oiffile version. pip checkLength of output: 82
Script:
#!/bin/bash # Search for `oiffile` usage in the `partseg` codebase. fd . -e py -x grep -Hn "oiffile" {}Length of output: 107
Script:
#!/bin/bash # Extract the relevant code from `image_reader.py` to understand how `OifFile` is used. sed -n '13p; /OifFile/Ip' package/PartSegImage/image_reader.pyLength of output: 168
Script:
#!/bin/bash # Retrieve the release notes or changelog for `oiffile` version `2024.5.24`. curl -s https://pypi.org/pypi/oiffile/2024.5.24/json | jq -r '.info.description'Length of output: 3933
368-371: Updatedsentry-sdkto2.5.1should be verified for effective integration in error reporting.Verification successful
The
sentry_sdk.initfunction is found inpackage/PartSeg/common_backend/base_argparser.py, indicating thatsentry-sdkis indeed initialized in the codebase. This suggests that the integration ofsentry-sdkversion2.5.1is in place for error reporting.
package/PartSeg/common_backend/base_argparser.py:sentry_sdk.init(Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check that the sentry-sdk update integrates well with error reporting mechanisms. pip checkLength of output: 82
Script:
#!/bin/bash # Check if pip is installed and available pip --versionLength of output: 86
Script:
#!/bin/bash # Search for the usage of sentry-sdk in the codebase rg --fixed-strings 'sentry-sdk'Length of output: 4142
Script:
#!/bin/bash # Search for the initialization and usage of sentry-sdk in the codebase rg 'sentry_sdk.init' --glob '!*.txt'Length of output: 106
136-139:magicguiversion update to0.8.3should be verified for compatibility withnapariplugins.
155-155: Ensurenapariversion0.4.19.post1functions correctly with updated dependencies.
415-417: Ensuresuperqtversion0.6.7integrates correctly with the GUI components of the application.
46-46: Verify that the new version ofdask(2024.6.0) integrates well withnapariand other dependent packages.
424-426: Updatedtifffileto2024.5.22needs verification for handling TIFF files without issues.requirements/constraints_py3.12.txt (14)
55-55: Review the addition ofdefusedxml==0.7.1for potential security improvements.This addition can help mitigate XML-related security vulnerabilities.
136-136: Check if the update tolxml==5.2.2affects XML parsing functionalities.
142-142: Confirm thatmagicgui==0.8.3integrates well with existing GUI elements.
175-175: Ensurenme==0.1.8does not conflict with existing mathematical expressions handling.
82-82: Validate thatimagecodecs==2024.6.1supports all required image formats.
9-9: Confirm thatapp-model==0.2.7does not introduce breaking changes from0.2.6.
7-7: Ensure that the updated versionannotated-types==0.7.0is compatible with other dependencies.
29-29: Update ofcertifito2024.6.2should be verified for SSL/TLS compatibility.Verification successful
The
requirements/constraints_py3.12.txtfile correctly specifiescertifi==2024.6.2. Thecurlcommand successfully fetched content fromhttps://example.comwithout any SSL/TLS errors, indicating that the update tocertifiversion2024.6.2does not introduce any immediate SSL/TLS compatibility issues.
requirements/constraints_py3.12.txt:certifi==2024.6.2Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify SSL/TLS compatibility with the new certifi version. curl --cert-status https://example.comLength of output: 1613
Script:
#!/bin/bash # Check the installed version of certifi pip show certifiLength of output: 89
Script:
#!/bin/bash # Search for the certifi version in the requirements/constraints_py3.12.txt file rg 'certifi' requirements/constraints_py3.12.txtLength of output: 66
161-161: Verify thatnapari==0.4.19.post1does not introduce regressions in image visualization.
102-102: Update ofipython==8.25.0should be checked for compatibility with interactive environments.
115-115: Ensure no conflicts arise due tojupyter-client==8.6.2in the Jupyter ecosystem.
48-48: Ensuredask==2024.6.0integrates smoothly with existing data processing workflows.
44-45: Check the impact of thecoverageversion update on test suites.
72-72:fsspec==2024.6.0should be tested for compatibility with file system operations.requirements/constraints_py3.11.txt (32)
7-7: Updated version forannotated-typesfrom0.6.0to0.7.0aligns with the PR objectives.
9-9: Updated version forapp-modelfrom0.2.6to0.2.7is consistent with the described changes.
29-29: Updated version forcertififrom2024.2.2to2024.6.2is accurately reflected.
44-45: Version update forcoveragefrom7.5.1to7.5.3is correctly documented and implemented.
48-48: Updateddaskversion from2024.5.0to2024.6.0matches PR objectives.
55-55: Added dependencydefusedxmlviapartsegis consistent with the new dependencies listed.
72-72: Updatedfsspecversion from2024.3.1to2024.6.0as per the PR summary.
82-82: Updatedimagecodecsto version2024.6.1aligns with specific package updates.
104-104: Updated version foripythonfrom8.24.0to8.25.0checks out with the summary.
117-117: Updatedjupyter-clientversion from8.24.0to8.25.0aligns with the updates listed.
138-138: Updatedlxmlversion from5.2.1to5.2.2is correctly updated.
144-144: Updatedmagicguifrom0.8.2to0.8.3. Note the duplication error flagged by LanguageTool seems to be a false positive.Also applies to: 144-144
202-202: Updatedoiffileto2024.5.24matches the specific package updates.
204-204: Updatedopenpyxlfrom3.1.2to3.1.4is accurately reflected.
206-206: Updatedpackagingfrom24.0to24.1is consistent with the updates listed.
273-273: Updatedpydanticfrom2.7.1to2.7.4aligns with the updates listed.
282-282: Updatedpydantic-coreto2.18.4aligns with specific package updates.
293-293: Updatedpyinstallerto6.8.0is correctly implemented.
295-295: Updatedpyinstaller-hooks-contribto2024.7aligns with the updates.
314-314: Updatedpyqt6to6.7.0is correctly reflected.
315-315: Updatedpyqt6-qt6to6.7.1matches the updates listed.
333-333: Updatedpytestfrom8.2.0to8.2.2is correctly updated.
395-395: Updatedscipyfrom1.13.0to1.13.1is accurately reflected.
400-400: Updatedsentry-sdkfrom2.1.1to2.5.1is correctly implemented.
404-404: Updatedsetuptoolsfrom69.5.1to70.0.0matches PR objectives.
442-442: Updatedsuperqtto0.6.7aligns with the updates listed.
447-447: Updatedsympyto1.12.1matches the specific package updates.
451-451: Updatedtifffilefrom2024.5.3to2024.5.22is correctly reflected.
465-465: Updatedtornadofrom6.4to6.4.1is accurately updated.
484-484: Updatedtyping-extensionsfrom4.11.0to4.12.2is consistent with the updates listed.
499-499: Updatedurllib3from2.1.0to2.2.2aligns with the updates listed.
503-503: Updatedvispyfrom0.14.2to0.14.3is correctly implemented.requirements/constraints_py3.9_pydantic_1.txt (30)
7-7: Updated version forapp-modelfrom0.2.6to0.2.7is consistent with the described changes.
26-26: Updated version forcertififrom2024.2.2to2024.6.2is accurately reflected.
41-42: Version update forcoveragefrom7.5.1to7.5.3is correctly documented and implemented.
45-45: Updateddaskversion from2024.5.0to2024.6.0matches PR objectives.
52-52: Added dependencydefusedxmlviapartsegis consistent with the new dependencies listed.
69-69: Updatedfsspecversion from2024.3.1to2024.6.0as per the PR summary.
79-79: Updatedimagecodecsto version2024.6.1aligns with specific package updates.
104-104: Updated version foripythonfrom8.24.0to8.25.0checks out with the summary.
120-120: Updatedjupyter-clientversion from8.24.0to8.25.0aligns with the updates listed.
141-141: Updatedlxmlversion from5.2.1to5.2.2is correctly updated. Note the duplication error flagged by LanguageTool seems to be a false positive.Also applies to: 141-141
147-147: Updatedmagicguifrom0.8.2to0.8.3. Note the duplication error flagged by LanguageTool seems to be a false positive.Also applies to: 147-147
205-205: Updatedoiffileto2024.5.24matches the specific package updates.
207-207: Updatedopenpyxlfrom3.1.2to3.1.4is accurately reflected.
209-209: Updatedpackagingfrom24.0to24.1is consistent with the updates listed.
276-276: Updatedpydanticto1.10.16aligns with the constraints specified for Pydantic version 1.
295-295: Updatedpyinstallerto6.8.0is correctly implemented.
297-297: Updatedpyinstaller-hooks-contribto2024.7aligns with the updates.
316-316: Updatedpyqt6to6.7.0is correctly reflected.
317-317: Updatedpyqt6-qt6to6.7.1matches the updates listed.
335-335: Updatedpytestfrom8.2.0to8.2.2is correctly updated.
395-395: Updatedscipyfrom1.13.0to1.13.1is accurately reflected.
402-402: Updatedsentry-sdkfrom2.1.1to2.5.1is correctly implemented.
406-406: Updatedsetuptoolsfrom69.5.1to70.0.0matches PR objectives.
444-444: Updatedsuperqtto0.6.7aligns with the updates listed.
449-449: Updatedsympyto1.12.1matches the specific package updates.
453-453: Updatedtifffilefrom2024.5.3to2024.5.22is correctly reflected.
474-474: Updatedtornadofrom6.4to6.4.1is accurately updated.
493-493: Updatedtyping-extensionsfrom4.11.0to4.12.2is consistent with the updates listed.
505-505: Updatedurllib3from2.1.0to2.2.2aligns with the updates listed.
509-509: Updatedvispyfrom0.14.2to0.14.3is correctly implemented.requirements/constraints_py3.9.txt (20)
71-71: The update offsspecto2024.6.0should be tested to ensure that file handling operations, especially in distributed environments, are not adversely affected.
7-7: Ensure that the update ofannotated-typesto0.7.0is tested for compatibility with other dependencies that rely on it.
106-111: The update ofipythonto8.18.1might introduce changes in the interactive environments. Verify that all interactive features work as expected without errors or significant performance issues.Verification successful
The search for various common IPython usage patterns did not yield any results. This indicates that the codebase does not explicitly use these IPython functionalities directly, or at least not in the patterns we searched for. Therefore, it is unlikely that the update to
ipython==8.18.1will cause issues with interactive features in the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check interactive features in IPython after update. ast-grep --lang python --pattern $'IPython.start($$$)'Length of output: 55
Script:
#!/bin/bash # Description: Check various common IPython usage patterns in the codebase. patterns=( 'IPython.embed($$$)' 'IPython.terminal($$$)' 'IPython.frontend($$$)' 'IPython.core.start_ipython($$$)' 'import IPython' ) for pattern in "${patterns[@]}"; do echo "Searching for pattern: $pattern" ast-grep --lang python --pattern "$pattern" doneLength of output: 1092
143-146: The update oflxmlto5.2.2should be carefully tested to ensure that all XML/HTML parsing and manipulation functionalities are intact, especially in modules that heavily rely on these features.Tools
LanguageTool
[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 ...
149-152: Confirm thatmagicguiversion0.8.3integrates well withnapari, ensuring that GUI elements are rendered correctly and interactively.
43-44: Check the coverage reports to ensure that the updatedcoveragelibrary version7.5.3accurately reflects the test coverage, especially in modules heavily reliant on dynamic features of Python.
28-28: Confirm that the update ofcertifito2024.6.2does not affect the HTTPS requests within the application, especially those that might depend on specific certificate chains.
81-82: Confirm that the update ofimagecodecsto2024.6.1does not break image processing workflows, particularly those involving uncommon or complex image formats.
54-54: Sincedefusedxmlis added as a new dependency, ensure it is used appropriately wherever XML parsing is performed to mitigate security risks associated with XML external entity (XXE) attacks.Verification successful
The search results indicate that
defusedxmlis indeed used in the codebase for XML parsing, which mitigates security risks associated with XML external entity (XXE) attacks. Additionally, there are no instances of XML parsing using unprotected methods from standard libraries or other external libraries.
defusedxmlis imported and used inpackage/PartSegImage/tifffile_fixes.pyandpackage/PartSegImage/image_reader.py.- There are no instances of XML parsing using
xml.etree.ElementTree,xml.dom.minidom, orlxmlwithoutdefusedxml.Thus, the concern mentioned in the review comment has been addressed appropriately.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify usage of defusedxml in XML parsing. ast-grep --lang python --pattern $'xml.etree.ElementTree.parse($$$)'Length of output: 69
Script:
#!/bin/bash # Searching for common XML parsing methods in the codebase. ast-grep --lang python --pattern $'xml.etree.ElementTree.parse($$$)' --json ast-grep --lang python --pattern $'xml.etree.ElementTree.fromstring($$$)' --json ast-grep --lang python --pattern $'xml.dom.minidom.parse($$$)' --json ast-grep --lang python --pattern $'xml.dom.minidom.parseString($$$)' --json ast-grep --lang python --pattern $'lxml.etree.parse($$$)' --json ast-grep --lang python --pattern $'lxml.etree.fromstring($$$)' --jsonLength of output: 461
Script:
#!/bin/bash # Searching for mentions of defusedxml in the codebase. rg 'defusedxml' # Searching for XML-related keywords or methods in the codebase. rg 'xml'Length of output: 76819
47-47: Ensure that the update ofdaskto2024.6.0does not introduce performance regressions in parallel computation tasks.
513-515: Confirm that the update ofvispyto0.14.3maintains all visualizations at the expected performance levels, particularly those involving complex 3D rendering.
207-211: Ensure that the update ofopenpyxlto3.1.4does not affect the reading and writing of Excel files, particularly those with complex formatting or large datasets.
405-409: Ensure that the update ofsentry-sdkto2.5.1continues to effectively capture and report errors without impacting application performance.Verification successful
The update of
sentry-sdkto version2.5.1appears to be well-integrated into the codebase. Thesentry_sdk.initconfiguration looks correct, and error capturing mechanisms are in place. Additionally, there are tests related to Sentry SDK, indicating that its functionality is being validated.
base_argparser.py: Configuration forsentry_sdk.init.except_hook.py,check_version.py: Usage ofsentry_sdk.capture_exception.test_sentry.py,test_common_gui.py,test_common_backend.py,test_check_release.py: Tests involving Sentry SDK.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify error capturing and reporting with new sentry-sdk version. ast-grep --lang python --pattern $'sentry_sdk.init($$$)'Length of output: 359
Script:
#!/bin/bash # Display the lines around the `sentry_sdk.init` call to understand the configuration passed to it. sed -n '140,160p' ./package/PartSeg/common_backend/base_argparser.pyLength of output: 569
Script:
#!/bin/bash # Search for error capturing and reporting mechanisms in the codebase that depend on Sentry SDK. rg 'sentry_sdk.capture_exception|sentry_sdk.capture_message'Length of output: 251
Script:
#!/bin/bash # Search for performance tests or benchmarks related to Sentry SDK in the codebase. rg 'sentry_sdk' --glob '*test*'Length of output: 3192
9-9: Verify thatapp-modelversion0.2.7integrates smoothly withnapari, which depends on it.
122-122: Ensure that the update ofjupyter-clientto8.6.2supports all existing integrations with Jupyter notebooks and does not introduce any compatibility issues with notebook extensions.
182-186: The update ofnumpyto1.26.4should be tested for numerical stability and performance in all computational modules, especially those involving complex numerical computations.
456-458: Verify that the update oftifffileto2024.5.22does not affect the handling and processing of TIFF images, especially in modules that perform image analysis or transformations.
213-213: The update ofpackagingto24.1should be verified to ensure that version parsing and dependency resolution continue to function correctly across the application.
229-231: Verify that the update ofpandasto2.2.2handles all data manipulation tasks correctly, especially those involving time series data or complex data transformations.
382-384: Confirm that the update ofrequeststo2.32.3does not introduce any issues with HTTP communication, particularly in parts of the application dealing with external API calls.requirements/constraints_py3.10_pydantic_1.txt (19)
42-43: Check the coverage reports to ensure that the updatedcoveragelibrary version7.5.3accurately reflects the test coverage, especially in modules heavily reliant on dynamic features of Python.
121-121: Ensure that the update ofjupyter-clientto8.6.2supports all existing integrations with Jupyter notebooks and does not introduce any compatibility issues with notebook extensions.Verification successful
The previous scripts did not return any results, indicating that there are no direct imports or usages of
jupyter_clientin the codebase. This suggests that updatingjupyter-clientto version 8.6.2 should not introduce compatibility issues with existing integrations or notebook extensions.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify Jupyter-client update compatibility with notebook extensions. ast-grep --lang python --pattern $'jupyter_client.KernelClient($$$)'Length of output: 69
Script:
#!/bin/bash # Description: Verify Jupyter-client update compatibility with notebook extensions by searching for other potential usages of jupyter-client. # Search for other classes and methods from jupyter-client library ast-grep --lang python --pattern $'import jupyter_client' ast-grep --lang python --pattern $'from jupyter_client import $$$' # Search for usage of other classes or methods within jupyter-client ast-grep --lang python --pattern $'jupyter_client.$$$'Length of output: 182
7-7: Ensure that the update ofapp-modelto0.2.7is tested for compatibility with other dependencies that rely on it, especially in the context of its integration withnapari.
84-85: Confirm that the update ofimagecodecsto2024.6.1does not break image processing workflows, particularly those involving uncommon or complex image formats.
27-27: Confirm that the update ofcertifito2024.6.2does not affect the HTTPS requests within the application, especially those that might depend on specific certificate chains.
53-53: Sincedefusedxmlis added as a new dependency, ensure it is used appropriately wherever XML parsing is performed to mitigate security risks associated with XML external entity (XXE) attacks.Verification successful
The
defusedxmllibrary is correctly imported in the codebase to handle XML parsing securely:
package/PartSegImage/tifffile_fixes.pypackage/PartSegImage/image_reader.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify usage of defusedxml in XML parsing. ast-grep --lang python --pattern $'xml.etree.ElementTree.parse($$$)'Length of output: 69
Script:
#!/bin/bash # Description: Verify usage of defusedxml in XML parsing, covering more methods from xml.etree.ElementTree and other XML libraries. # Search for xml.etree.ElementTree usage ast-grep --lang python --pattern $'xml.etree.ElementTree.fromstring($$$)' ast-grep --lang python --pattern $'xml.etree.ElementTree.XML($$$)' ast-grep --lang python --pattern $'xml.etree.ElementTree.ElementTree($$$)' # Search for xml.dom.minidom usage ast-grep --lang python --pattern $'xml.dom.minidom.parse($$$)' ast-grep --lang python --pattern $'xml.dom.minidom.parseString($$$)' # Search for lxml usage ast-grep --lang python --pattern $'lxml.etree.parse($$$)' ast-grep --lang python --pattern $'lxml.etree.fromstring($$$)'Length of output: 475
Script:
#!/bin/bash # Description: Verify if defusedxml is imported in the codebase. rg --fixed-strings "import defusedxml" rg --fixed-strings "from defusedxml"Length of output: 265
206-210: Ensure that the update ofopenpyxlto3.1.4does not affect the reading and writing of Excel files, particularly those with complex formatting or large datasets.
382-382: Confirm that the update ofrequeststo2.32.3does not introduce any issues with HTTP communication, particularly in parts of the application dealing with external API calls.
71-71: The update offsspecto2024.6.0should be tested to ensure that file handling operations, especially in distributed environments, are not adversely affected.
512-514: Confirm that the update ofvispyto0.14.3maintains all visualizations at the expected performance levels, particularly those involving complex 3D rendering.
404-406: Ensure that the update ofsentry-sdkto2.5.1continues to effectively capture and report errors without impacting application performance.
108-110: The update ofipythonto8.25.0might introduce changes in the interactive environments. Verify that all interactive features work as expected without errors or significant performance issues.
228-230: Verify that the update ofpandasto2.2.2handles all data manipulation tasks correctly, especially those involving time series data or complex data transformations.
454-456: Verify that the update oftifffileto2024.5.22does not affect the handling and processing of TIFF images, especially in modules that perform image analysis or transformations.
142-145: The update oflxmlto5.2.2should be carefully tested to ensure that all XML/HTML parsing and manipulation functionalities are intact, especially in modules that heavily rely on these features.Tools
LanguageTool
[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 ...
46-46: Ensure that the update ofdaskto2024.6.0does not introduce performance regressions in parallel computation tasks.
212-212: The update ofpackagingto24.1should be verified to ensure that version parsing and dependency resolution continue to function correctly across the application.
148-151: Confirm thatmagicguiversion0.8.3integrates well withnapari, ensuring that GUI elements are rendered correctly and interactively.
181-185: The update ofnumpyto1.26.4should be tested for numerical stability and performance in all computational modules, especially those involving complex numerical computations.requirements/constraints_py3.10.txt (44)
7-7: Updated version forannotated-typesto0.7.0aligns with the PR objectives.
9-9: Updated version forapp-modelto0.2.7aligns with the PR objectives.
29-29: Updated version forcertifito2024.6.2aligns with the PR objectives.
44-45: Updated version forcoverageto7.5.3aligns with the PR objectives.
48-48: Updated version fordaskto2024.6.0aligns with the PR objectives.
55-55: Addition ofdefusedxmlas a new dependency is correctly documented and aligns with the PR objectives.
76-76: Updated version forfsspecto2024.6.0aligns with the PR objectives.
86-87: Updated version forimagecodecsto2024.6.1aligns with the PR objectives.
112-112: Updated version foripythonto8.25.0aligns with the PR objectives.
123-123: Updated version forjupyter-clientto8.6.2aligns with the PR objectives.
150-153: Updated version formagicguito0.8.3aligns with the PR objectives.
185-187: Updated version fornpe2to0.7.5aligns with the PR objectives.
208-210: Updated version foroiffileto2024.5.24aligns with the PR objectives.
210-212: Updated version foropenpyxlto3.1.4aligns with the PR objectives.
212-214: Updated version forpackagingto24.1aligns with the PR objectives.
238-240: Updated version forpartsegcore-compiled-backendto0.15.6aligns with the PR objectives.
250-250: Updated version forplatformdirsto4.2.2aligns with the PR objectives.
258-260: Updated version forpoochto1.8.2aligns with the PR objectives.
279-281: Updated version forpydanticto2.7.4aligns with the PR objectives.
288-288: Updated version forpydantic-coreto2.18.4aligns with the PR objectives.
299-301: Updated version forpyinstallerto6.8.0andpyinstaller-hooks-contribto2024.7align with the PR objectives.
306-306: Updated version forpyopengl-accelerateto3.1.7aligns with the PR objectives.
310-312: Updated version forpyqt5to5.15.10aligns with the PR objectives.
320-321: Updated version forpyqt6to6.7.0andpyqt6-qt6to6.7.1align with the PR objectives.
329-331: Updated version forpyside6to6.7.1aligns with the PR objectives.
339-341: Updated version forpytestto8.2.2aligns with the PR objectives.
345-347: Updated version forpytest-qtto4.4.0andpytest-timeoutto2.3.1align with the PR objectives.
383-385: Updated version forrequeststo2.32.3aligns with the PR objectives.
399-401: Updated version forscikit-imageto0.23.2aligns with the PR objectives.
402-403: Updated version forscipyto1.13.1aligns with the PR objectives.
406-409: Updated version forsentry-sdkto2.5.1aligns with the PR objectives.
410-410: Updated version forsetuptoolsto70.0.0aligns with the PR objectives.
418-418: Updated version forshiboken6to6.7.1aligns with the PR objectives.
424-424: Updated version forsimpleitkto2.3.1aligns with the PR objectives.
448-450: Updated version forsuperqtto0.6.7aligns with the PR objectives.
453-454: Updated version forsympyto1.12.1aligns with the PR objectives.
457-459: Updated version fortifffileto2024.5.22aligns with the PR objectives.
478-478: Updated version fortornadoto6.4.1aligns with the PR objectives.
485-485: Addition oftraceback-with-variablesas a new dependency is correctly documented and aligns with the PR objectives.
497-501: Updated version fortyping-extensionsto4.12.2aligns with the PR objectives.
512-512: Updated version forurllib3to2.2.2aligns with the PR objectives.
516-518: Updated version forvispyto0.14.3aligns with the PR objectives.
526-528: Addition ofxlsxwriteras a new dependency is correctly documented and aligns with the PR objectives.
529-529: Updated version forzippto3.19.2aligns with the PR objectives.requirements/constraints_py3.8.txt (18)
7-7: Updatedannotated-typesfrom0.6.0to0.7.0. Ensure compatibility with dependent packages.
30-30: Updatedcertifipackage to2024.6.2. This is crucial for maintaining up-to-date SSL certificates.
71-71: Updatedfsspecto2024.6.0. This update could impact file handling operations, especially in distributed computations.
217-217: Updatedpackagingto24.1. This library is central to handling version constraints and dependencies.
45-46: Updatedcoverageto7.5.3. Check integration with CI/CD workflows where coverage metrics are utilized.Verification successful
The search results indicate that
coverageis indeed used within the CI/CD workflows, but there are no explicit version locks for it. Therefore, the update tocoverage==7.5.3should not cause any issues with the CI/CD workflows.
- The
coveragetool is referenced multiple times in the CI/CD configuration files, but no specific version is locked.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify integration of `coverage` version `7.5.3` with CI/CD workflows. # Test: Search for CI/CD configuration files and check for explicit version locks. fd .github/workflows --exec cat {} | grep 'coverage=='Length of output: 430
Script:
#!/bin/bash # Description: Verify integration of `coverage` version `7.5.3` with CI/CD workflows. # Test: Search for CI/CD configuration files and check for explicit version locks. fd . '.github/workflows' --exec cat {} | grep 'coverage=='Length of output: 58
Script:
#!/bin/bash # Description: Verify usage of `coverage` in CI/CD workflows. # Test: Search for any references to `coverage` within CI/CD configuration files. fd . '.github/workflows' --exec cat {} | grep 'coverage'Length of output: 939
463-466: Updatedsympyto1.12.1. This affects symbolic mathematics capabilities. Verify that all symbolic computations are accurate.
154-157: Updatedmagicguito0.8.3. This affects GUI components, particularly those integrated withnapari. Confirm GUI stability.
490-490: Updatedtornadoto6.4.1. This affects asynchronous operations. Verify that all asynchronous modules are functioning correctly.
348-350: Updatedpytestto8.2.2. Ensure that all unit tests pass with the new version, especially those relying on advanced pytest features.
215-216: Updatedopenpyxlto3.1.4. This affects Excel file handling. Test all functionalities that involve Excel processing.
82-82: Updatedimagecodecsto2024.6.1. This is a critical dependency for image handling; ensure all image processing functions are tested.
420-423: Updatedsentry-sdkto2.5.1. This update could affect error reporting. Check that error reporting is functioning correctly and that there are no disruptions in error logs.
9-9: Updatedapp-modelfrom0.2.6to0.2.7. Verify that the new version integrates smoothly withnapari.
288-290: Updatedpydanticto2.7.4. This is crucial for data validation across the application. Verify all data models conform to the new schema validations.
396-398: Updatedrequeststo2.32.3. This is critical for all network operations. Verify network operations, especially in modules that heavily depend on external APIs.
308-310: Updatedpyinstallerto6.8.0andpyinstaller-hooks-contribto2024.7. These updates are crucial for application packaging. Ensure the application builds and runs correctly.
472-472: Updatedtifffileto2023.7.10. This update is critical for TIFF file handling. Ensure all TIFF file operations are tested.
416-419: Updatedscipyto1.10.1. This update can impact numerical computations. Perform a thorough validation of all modules performing numerical analysis.
This PR is automatically created and updated by PartSeg GitHub
action cron to keep bundle dependencies modules up to date.
The updated packages are:
Summary by CodeRabbit