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test: [Automatic] Constraints upgrades: imagecodecs
, magicgui
, oiffile
, openpyxl
, packaging
, pydantic
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, sympy
, tifffile
, vispy
#1107
Conversation
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 ...
Near line 145: 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 242: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 357: 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_docs.txt (3)
Near line 139: 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 203: Possible typo: you repeated a word
Context: ... # via # jupyter-core # pooch pooch==1.8.1 # via scikit-image prompt-to...
Near line 336: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # autodoc-pydant...requirements/constraints_py3.11_pydantic_1.txt (4)
Near line 119: 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 143: 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 240: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 353: 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 (4)
Near line 119: 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 143: 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 240: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 355: 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_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==...
Near line 238: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 351: 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.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==...
Near line 262: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 381: 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_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==...
Near line 260: Possible typo: you repeated a word
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)
Near line 131: 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 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...
Near line 367: 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 (4)
Near line 129: 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 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-model
to0.2.7
to align with the latest version.
359-359
: Updatedsuperqt
to0.6.6
to keep up with the latest release.
366-366
: Updatedtifffile
to2024.5.10
for enhanced features and bug fixes.requirements/constraints_py3.12_pydantic_1.txt (5)
7-7
: Updatedapp-model
to0.2.7
to align with the latest version.
116-116
: Updatedlxml
to5.2.2
to keep up with the latest release.
250-250
: Updatedpyinstaller-hooks-contrib
to2024.6
for enhanced features and bug fixes.
368-368
: Updatedsuperqt
to0.6.6
to keep up with the latest release.
375-375
: Updatedtifffile
to2024.5.10
for enhanced features and bug fixes.requirements/constraints_py3.12.txt (5)
9-9
: Updatedapp-model
to0.2.7
to align with the latest version.
118-118
: Updatedlxml
to5.2.2
to keep up with the latest release.
254-254
: Updatedpyinstaller-hooks-contrib
to2024.6
for enhanced features and bug fixes.
372-372
: Updatedsuperqt
to0.6.6
to keep up with the latest release.
379-379
: Updatedtifffile
to2024.5.10
for enhanced features and bug fixes.requirements/constraints_py3.11_pydantic_1.txt (5)
7-7
: Updatedapp-model
to0.2.7
to align with the latest version.
118-118
: Updatedlxml
to5.2.2
to keep up with the latest release.
252-252
: Updatedpyinstaller-hooks-contrib
to2024.6
for enhanced features and bug fixes.
370-370
: Updatedsuperqt
to0.6.6
to keep up with the latest release.
377-377
: Updatedtifffile
to2024.5.10
for enhanced features and bug fixes.requirements/constraints_py3.11.txt (5)
9-9
: Updatedapp-model
to0.2.7
as per PR objectives.
120-120
: Updatedlxml
to5.2.2
as per PR objectives.
256-256
: Updatedpyinstaller-hooks-contrib
to2024.6
as per PR objectives.
374-374
: Updatedsuperqt
to0.6.6
as per PR objectives.
381-381
: Updatedtifffile
to2024.5.10
as per PR objectives.requirements/constraints_py3.10_pydantic_1.txt (5)
7-7
: Updatedapp-model
to0.2.7
as per PR objectives.
124-124
: Updatedlxml
to5.2.2
as per PR objectives.
258-258
: Updatedpyinstaller-hooks-contrib
to2024.6
as per PR objectives.
376-376
: Updatedsuperqt
to0.6.6
as per PR objectives.
383-383
: Updatedtifffile
to2024.5.10
as per PR objectives.requirements/constraints_py3.10.txt (5)
9-9
: Updatedapp-model
to0.2.7
as per PR objectives.
126-126
: Updatedlxml
to5.2.2
as per PR objectives.
262-262
: Updatedpyinstaller-hooks-contrib
to2024.6
as per PR objectives.
380-380
: Updatedsuperqt
to0.6.6
as per PR objectives.
387-387
: Updatedtifffile
to2024.5.10
as per PR objectives.requirements/constraints_py3.9_pydantic_1.txt (5)
7-7
: Updatedapp-model
to version0.2.7
. This change aligns with the PR's objective to keep dependencies up-to-date.
128-128
: Updatedlxml
to version5.2.2
. This update is consistent with the PR's goal of maintaining current dependencies.
262-262
: Updatedpyinstaller-hooks-contrib
to version2024.6
. This change is part of the systematic updates across various Python versions.
380-380
: Updatedsuperqt
to version0.6.6
. This update is part of the ongoing effort to ensure compatibility and stability across environments.
387-387
: Updatedtifffile
to 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-model
to0.2.7
looks good.
130-130
: Updatedlxml
to5.2.2
looks good.
266-266
: Updatedpyinstaller-hooks-contrib
to2024.6
looks good.
384-384
: Updatedsuperqt
to0.6.6
looks good.
391-391
: Updatedtifffile
to2024.5.10
looks good.
71fa60f
to
1bfac57
Compare
superqt
, tifffile
sentry-sdk
, superqt
, tifffile
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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 (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 ...
Near line 168: 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 279: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 423: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11.txt (4)
Near line 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 ...
Near line 164: 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 274: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 420: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.11_docs.txt (3)
Near line 156: 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 231: Possible typo: you repeated a word
Context: ... # via # jupyter-core # pooch pooch==1.8.1 # via scikit-image prompt-to...
Near line 384: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...requirements/constraints_py3.11_pydantic_1.txt (4)
Near line 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 ...
Near line 162: 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 273: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 417: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12.txt (4)
Near line 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 ...
Near line 162: 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 272: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 418: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.12_pydantic_1.txt (4)
Near line 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 ...
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==...
Near line 271: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 415: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.8.txt (4)
Near line 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 ...
Near line 179: 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 294: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 444: 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_pydantic_1.txt (4)
Near line 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 ...
Near line 177: 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 293: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Near line 441: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...requirements/constraints_py3.9.txt (4)
Near line 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 ...
Near line 174: 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 284: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Near line 430: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...requirements/constraints_py3.9_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-model
to0.2.7
aligns with the PR's objective to keep dependencies updated. Ensure that this version is compatible with other dependencies.
45-45
: Updateddask
to2024.5.1
. Verify that this version works well with the project's parallel computation requirements.Verification successful
The search results indicate that
dask
is used in thelauncher.spec
file, 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
dask
version2024.5.1
does not introduce any immediate compatibility issues based on the current codebase and issue tracker.
- File:
launcher.spec
- Lines:
from dask import config
os.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
: Updatedzipp
to3.18.2
. This package is often a transitive dependency; ensure no conflicts with direct dependencies.
67-67
: Updatedfsspec
to2024.5.0
. This is crucial for handling file-system interfaces; please ensure it integrates smoothly withdask
.
419-419
: Updatedtifffile
to2024.5.10
. 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-model
to0.2.7
is consistent with updates across other files. Good to maintain version consistency across environments.
45-45
: Updateddask
to2024.5.1
. As previously noted, ensure compatibility with parallel processing features.
65-65
: Updatedfsspec
to2024.5.0
. As with other files, ensure it works well withdask
for file handling.
441-441
: Updatedtifffile
to2024.5.10
. As noted earlier, check for any potential breaking changes due to the version update.
323-323
: Updatedpytest
to8.2.1
. 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-model
to0.2.7
. Consistency across different Python versions is crucial for maintaining a stable build environment.
47-47
: Updateddask
to2024.5.1
. Consistent updates across files are good for maintaining compatibility.
67-67
: Updatedfsspec
to2024.5.0
. Important for file system operations, especially in conjunction withdask
.
444-444
: Updatedtifffile
to2024.5.10
. Repeat the checks for breaking changes as noted in other files.
326-326
: Updatedpytest
to8.2.1
. 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-model
to version0.2.7
to keep dependencies up-to-date.
45-45
: Updateddask
to version2024.5.1
aligns with the latest available version, ensuring compatibility and performance improvements.
65-65
: Updatedfsspec
to version2024.5.0
to maintain compatibility with the latestdask
version.
131-131
: Updatedlxml
to version5.2.2
, enhancing XML processing capabilities with the latest security and performance improvements.
325-325
: Updatedpytest
to version8.2.1
, ensuring compatibility with the latest Python features and improved testing capabilities.
392-392
: Updatedsentry-sdk
to version2.2.0
, enhancing error tracking and performance monitoring capabilities.
434-434
: Updatedsuperqt
to version0.6.6
, ensuring compatibility with the latest Qt features and performance improvements.
443-443
: Updatedtifffile
to 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-model
to version0.2.7
to keep dependencies up-to-date.
47-47
: Updateddask
to version2024.5.1
aligns with the latest available version, ensuring compatibility and performance improvements.
67-67
: Updatedfsspec
to version2024.5.0
to maintain compatibility with the latestdask
version.
133-133
: Updatedlxml
to version5.2.2
, enhancing XML processing capabilities with the latest security and performance improvements.
328-328
: Updatedpytest
to version8.2.1
, ensuring compatibility with the latest Python features and improved testing capabilities.
395-395
: Updatedsentry-sdk
to version2.2.0
, enhancing error tracking and performance monitoring capabilities.
437-437
: Updatedsuperqt
to version0.6.6
, ensuring compatibility with the latest Qt features and performance improvements.
446-446
: Updatedtifffile
to 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-model
to version0.2.7
to keep dependencies up-to-date.
45-45
: Updateddask
to version2024.5.1
aligns with the latest available version, ensuring compatibility and performance improvements.
69-69
: Updatedfsspec
to version2024.5.0
to maintain compatibility with the latestdask
version.
137-137
: Updatedlxml
to version5.2.2
, enhancing XML processing capabilities with the latest security and performance improvements.
331-331
: Updatedpytest
to version8.2.1
, ensuring compatibility with the latest Python features and improved testing capabilities.
398-398
: Updatedsentry-sdk
to version2.2.0
, enhancing error tracking and performance monitoring capabilities.
440-440
: Updatedsuperqt
to version0.6.6
, ensuring compatibility with the latest Qt features and performance improvements.
449-449
: Updatedtifffile
to 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-model
to0.2.7
aligns with the PR's objective to keep dependencies updated.
47-47
: Updateddask
to2024.5.1
ensures compatibility with the latest features and fixes.
71-71
: Updatedfsspec
to2024.5.0
to maintain compatibility withdask
.
139-139
: Updatedlxml
to5.2.2
addresses potential security and performance improvements.
296-296
: Updatedpyinstaller-hooks-contrib
to2024.6
ensures that the latest hooks are available for PyInstaller.
443-443
: Updatedsuperqt
to0.6.6
likely enhances UI components used in the project.
452-452
: Updatedtifffile
to2024.5.10
ensures support for the latest image formats and fixes.
522-522
: Updatedzipp
to3.18.2
ensures better handling of zip files in Python environments.requirements/constraints_py3.9_pydantic_1.txt (8)
7-7
: Updatedapp-model
to0.2.7
aligns with the PR's objective to keep dependencies updated.
45-45
: Updateddask
to2024.5.1
ensures compatibility with the latest features and fixes.
69-69
: Updatedfsspec
to2024.5.0
to maintain compatibility withdask
.
141-141
: Updatedlxml
to5.2.2
addresses potential security and performance improvements.
297-297
: Updatedpyinstaller-hooks-contrib
to2024.6
ensures that the latest hooks are available for PyInstaller.
444-444
: Updatedsuperqt
to0.6.6
likely enhances UI components used in the project.
453-453
: Updatedtifffile
to2024.5.10
ensures support for the latest image formats and fixes.
522-522
: Updatedzipp
to3.18.2
ensures better handling of zip files in Python environments.requirements/constraints_py3.9.txt (7)
9-9
: Updatedapp-model
to version0.2.7
as per the PR objectives and AI-generated summary. This change is consistent and correctly documented.
47-47
: Updateddask
to 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
: Updatedfsspec
to 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-contrib
to version2024.6
. This change is consistent with the PR objectives and AI-generated summary.
447-447
: Updatedsuperqt
to version0.6.6
. This change aligns with the PR objectives and AI-generated summary.
456-456
: Updatedtifffile
to version2024.5.10
. This change is consistent with the PR objectives and AI-generated summary.
143-143
: Updatedlxml
to 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-model
to version0.2.7
as per the PR objectives and AI-generated summary. This change is consistent and correctly documented.
69-69
: Updatedfsspec
to 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-contrib
to version2024.6
. This change is consistent with the PR objectives and AI-generated summary.
458-458
: Updatedsuperqt
to version0.6.6
. This change aligns with the PR objectives and AI-generated summary.
469-469
: Updatedtifffile
to version2023.7.10
. This change is consistent with the PR objectives and AI-generated summary.
146-146
: Updatedlxml
to 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
lxml
inpackage/tests/test_PartSegImage/test_image_writer.py
involves importingetree
and using it to create anXMLSchema
object. This usage is standard and should be compatible withlxml==5.2.2
.
package/tests/test_PartSegImage/test_image_writer.py
:from lxml import etree
Scripts 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-model
to version0.2.7
as per the PR objectives and AI-generated summary. This change is consistent and correctly documented.
71-71
: Updatedfsspec
to 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-contrib
to version2024.6
. This change is consistent with the PR objectives and AI-generated summary.
461-461
: Updatedsuperqt
to version0.6.6
. This change aligns with the PR objectives and AI-generated summary.
472-472
: Updatedtifffile
to version2023.7.10
. This change is consistent with the PR objectives and AI-generated summary.
148-148
: Updatedlxml
to 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
sentry-sdk
, superqt
, tifffile
oiffile
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, tifffile
1bfac57
to
b9b7db4
Compare
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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Actionable comments posted: 0
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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
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==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
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...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 426: Possible typo: you repeated a word
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)
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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 168: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 279: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 423: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.11.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 164: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 274: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 420: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.11_docs.txt (3)
Near line 156: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 231: Possible typo: you repeated a word
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Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 384: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via # partseg (pypro...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.11_pydantic_1.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 162: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 273: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 417: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.12.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 162: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 272: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 418: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.12_pydantic_1.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
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==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 271: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 415: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.8.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 179: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 294: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 444: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.8_pydantic_1.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 177: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 293: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pygments==2....
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 441: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.1.2 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/constraints_py3.9.txt (4)
Near line 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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 174: Possible typo: you repeated a word
Context: ...=0.2.0 # via # napari # napari-svg napari-svg==0.1.10 # via napari nest-asyncio==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 284: Possible typo: you repeated a word
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 430: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULErequirements/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 ...
Rule ID: ENGLISH_WORD_REPEAT_RULE
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==...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 283: Possible typo: you repeated a word
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Rule ID: ENGLISH_WORD_REPEAT_RULE
Near line 427: Possible typo: you repeated a word
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.3.7 # via numpydoc sphinxcontrib...
Rule ID: ENGLISH_WORD_REPEAT_RULE
Additional comments not posted (218)
requirements/constraints_py3.11_docs.txt (55)
5-5
: Updatedannotated-types
to0.7.0
to align with newer version requirements.
7-7
: Updatedapp-model
to0.2.7
to keep dependencies up-to-date.
44-44
: Addedczifile
version2019.7.2
as a new dependency.
45-45
: Updateddask
to2024.5.1
to ensure compatibility with other updated packages.
52-52
: Addeddefusedxml
version0.7.1
as a new dependency.
64-64
: Addedfonticon-fontawesome6
version6.4.0
as a new dependency.
67-67
: Updatedfsspec
to2024.5.0
to align with the latest available version.
70-70
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version3.11.0
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78-78
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version2024.1.1
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81-82
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version2.34.1
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94-94
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as a new dependency.
99-99
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as a new dependency.
110-110
: Updatedjupyter-client
to8.6.2
to ensure compatibility with other updated packages.
126-128
: Addedlocal-migrator
version0.1.10
as a new dependency.
132-134
: Addedmagicgui
version0.8.2
as a new dependency.
136-136
: Addedmahotas
version1.4.15
as a new dependency.
150-150
: Addednapari
version0.4.19.post1
as a new dependency.
164-164
: Addednme
version0.1.8
as a new dependency.
166-168
: Addednpe2
version0.7.5
as a new dependency.
171-171
: Addednumpy
version1.26.4
as a new dependency.
189-190
: Updatedoiffile
to2024.5.24
to align with the latest available version.
192-192
: Addedopenpyxl
version3.1.2
as a new dependency.
195-195
: Updatedpackaging
to24.0
to ensure compatibility with other updated packages.
208-210
: Addedpandas
version2.2.2
as a new dependency.
216-218
: Addedpartsegcore-compiled-backend
version0.15.6
as a new dependency.
228-228
: Updatedplatformdirs
to4.2.2
to align with the latest available version.
242-242
: Addedpsygnal
version0.11.1
as a new dependency.
255-255
: Addedpydantic
version2.7.1
as a new dependency.
270-270
: Addedpygments
version2.18.0
as a new dependency.
282-282
: Addedpyqt5
version5.15.10
as a new dependency.
286-288
: Addedpyqt5-sip
version12.13.0
as a new dependency.
290-290
: Addedpyqt6
version6.7.0
as a new dependency.
296-297
: Addedpyside2
version5.13.2
as a new dependency.
298-299
: Addedpyside6
version6.7.1
as a new dependency.
301-301
: Addedpyside6-addons
version6.7.1
as a new dependency.
324-324
: Addedqtawesome
version1.3.1
as a new dependency.
326-328
: Addedqtconsole
version5.5.2
as a new dependency.
331-331
: Addedqtpy
version2.4.1
as a new dependency.
342-344
: Updatedrequests
to2.32.2
to ensure compatibility with other updated packages.
358-360
: Updatedscipy
to1.13.1
to align with the latest available version.
363-366
: Updatedsentry-sdk
to2.3.1
to ensure compatibility with other updated packages.
371-371
: Addedshiboken6
version6.7.1
as a new dependency.
377-377
: Addedsimpleitk
version2.3.1
as a new dependency.
380-380
: Addedsix
version1.16.0
as a new dependency.
387-387
: Addedsphinx
version7.3.7
as a new dependency.
393-395
: Addedsphinx-qt-documentation
version0.4.1
as a new dependency.
410-412
: Updatedsuperqt
to0.6.6
to align with the latest available version.
416-416
: Addedsympy
version1.12
as a new dependency.
419-419
: Addedtabulate
version0.9.0
as a new dependency.
421-421
: Updatedtifffile
to2024.5.22
to ensure compatibility with other updated packages.
440-440
: Addedtraceback-with-variables
version2.0.4
as a new dependency.
452-452
: Updatedtyping-extensions
to4.12.0
to align with the latest available version.
471-471
: Addedvispy
version0.14.2
as a new dependency.
479-479
: Addedxlrd
version2.0.1
as a new dependency.
481-482
: Addedxlsxwriter
version3.2.0
as a new dependency.requirements/constraints_py3.12.txt (14)
7-7
: Updatedannotated-types
to0.7.0
aligns with the PR objectives to keep dependencies up to date.
9-9
: Updatedapp-model
to0.2.7
is consistent with the PR's update list.
43-44
: Updatedcoverage
to7.5.2
as specified in the PR's objectives.
47-47
: Updateddask
to2024.5.1
matches the intended updates listed in the PR.
67-67
: Updatedfsspec
to2024.5.0
correctly reflects the changes intended by the PR.
110-110
: Updatedjupyter-client
to8.6.2
is in line with the updates mentioned in the PR summary.
195-196
: Updatedoiffile
to2024.5.24
is correctly listed in the PR's update objectives.
237-237
: Updatedplatformdirs
to4.2.2
is part of the updates as per the PR description.
370-370
: Updatedrequests
to2.32.2
correctly reflects the intended updates in the PR.
388-389
: Updatedscipy
to1.13.1
aligns with the updates listed in the PR.
393-394
: Updatedsentry-sdk
to2.3.1
matches the updates intended in the PR.
435-435
: Updatedsuperqt
to0.6.6
is consistent with the updates listed in the PR.
444-444
: Updatedtifffile
to2024.5.22
correctly reflects the changes intended by the PR.
477-477
: Updatedtyping-extensions
to4.12.0
is part of the updates as per the PR description.requirements/constraints_py3.11_pydantic_1.txt (13)
7-7
: Updatedapp-model
to0.2.7
aligns with the PR objectives to keep dependencies up to date.
41-42
: Updatedcoverage
to7.5.2
as specified in the PR's objectives.
45-45
: Updateddask
to2024.5.1
matches the intended updates listed in the PR.
65-65
: Updatedfsspec
to2024.5.0
correctly reflects the changes intended by the PR.
110-110
: Updatedjupyter-client
to8.6.2
is in line with the updates mentioned in the PR summary.
195-196
: Updatedoiffile
to2024.5.24
is correctly listed in the PR's update objectives.
237-237
: Updatedplatformdirs
to4.2.2
is part of the updates as per the PR description.
369-370
: Updatedrequests
to2.32.2
correctly reflects the intended updates in the PR.
388-389
: Updatedscipy
to1.13.1
aligns with the updates listed in the PR.
393-394
: Updatedsentry-sdk
to2.3.1
matches the updates intended in the PR.
434-435
: Updatedsuperqt
to0.6.6
is consistent with the updates listed in the PR.
443-444
: Updatedtifffile
to2024.5.22
correctly reflects the changes intended by the PR.
476-477
: Updatedtyping-extensions
to4.12.0
is part of the updates as per the PR description.requirements/constraints_py3.11.txt (13)
7-7
: Updatedannotated-types
to0.7.0
as per PR objectives.
9-9
: Updatedapp-model
to0.2.7
as per PR objectives.
43-44
: Updatedcoverage
to7.5.2
as per PR objectives.
47-47
: Updateddask
to2024.5.1
as per PR objectives.
67-67
: Updatedfsspec
to2024.5.0
as per PR objectives.
112-112
: Updatedjupyter-client
to8.6.2
as per PR objectives.
197-198
: Updatedoiffile
to2024.5.24
as per PR objectives.
328-328
: Updatedpytest
to8.2.1
as per PR objectives.
372-372
: Updatedrequests
to2.32.2
as per PR objectives.
395-396
: Updatedsentry-sdk
to2.3.1
as per PR objectives.
437-437
: Updatedsuperqt
to0.6.6
as per PR objectives.
446-446
: Updatedtifffile
to2024.5.22
as per PR objectives.
479-479
: Updatedtyping-extensions
to4.12.0
as per PR objectives.requirements/constraints_py3.10_pydantic_1.txt (12)
7-7
: Updatedapp-model
to0.2.7
as per PR objectives.
41-42
: Updatedcoverage
to7.5.2
as per PR objectives.
45-45
: Updateddask
to2024.5.1
as per PR objectives.
69-69
: Updatedfsspec
to2024.5.0
as per PR objectives.
116-116
: Updatedjupyter-client
to8.6.2
as per PR objectives.
201-202
: Updatedoiffile
to2024.5.24
as per PR objectives.
331-331
: Updatedpytest
to8.2.1
as per PR objectives.
375-375
: Updatedrequests
to2.32.2
as per PR objectives.
398-399
: Updatedsentry-sdk
to2.3.1
as per PR objectives.
440-440
: Updatedsuperqt
to0.6.6
as per PR objectives.
449-449
: Updatedtifffile
to2024.5.22
as per PR objectives.
489-489
: Updatedtyping-extensions
to4.12.0
as per PR objectives.requirements/constraints_py3.10.txt (13)
7-7
: Updatedannotated-types
to0.7.0
aligns with the PR objectives and AI-generated summary.
9-9
: Updatedapp-model
to0.2.7
aligns with the PR objectives and AI-generated summary.
43-43
: Updatedcoverage
to7.5.2
aligns with the PR objectives and AI-generated summary.Also applies to: 44-44
47-47
: Updateddask
to2024.5.1
aligns with the PR objectives and AI-generated summary.
71-71
: Updatedfsspec
to2024.5.0
aligns with the PR objectives and AI-generated summary.
203-203
: Updatedoiffile
to2024.5.24
aligns with the PR objectives and AI-generated summary.Also applies to: 204-204
452-452
: Updatedtifffile
to2024.5.22
aligns with the PR objectives and AI-generated summary.Also applies to: 454-454
443-443
: Updatedsuperqt
to0.6.6
aligns with the PR objectives and AI-generated summary.Also applies to: 445-445
378-378
: Updatedrequests
to2.32.2
aligns with the PR objectives and AI-generated summary.Also applies to: 380-380
401-401
: Updatedsentry-sdk
to2.3.1
aligns with the PR objectives and AI-generated summary.Also applies to: 402-402, 404-404
294-294
: Updatedpyinstaller
to6.7.0
andpyinstaller-hooks-contrib
to2024.6
aligns with the PR objectives and AI-generated summary.Also applies to: 296-296
492-492
: Updatedtyping-extensions
to4.12.0
aligns with the PR objectives and AI-generated summary.
522-522
: Updatedzipp
to3.19.0
aligns with the PR objectives and AI-generated summary.requirements/constraints_py3.9_pydantic_1.txt (12)
7-7
: Updatedapp-model
to0.2.7
aligns with the PR objectives and AI-generated summary.
41-41
: Updatedcoverage
to7.5.2
aligns with the PR objectives and AI-generated summary.Also applies to: 42-42
45-45
: Updateddask
to2024.5.1
aligns with the PR objectives and AI-generated summary.
69-69
: Updatedfsspec
to2024.5.0
aligns with the PR objectives and AI-generated summary.
205-205
: Updatedoiffile
to2024.5.24
aligns with the PR objectives and AI-generated summary.Also applies to: 206-206
453-453
: Updatedtifffile
to2024.5.22
aligns with the PR objectives and AI-generated summary.Also applies to: 455-455
444-444
: Updatedsuperqt
to0.6.6
aligns with the PR objectives and AI-generated summary.Also applies to: 446-446
379-379
: Updatedrequests
to2.32.2
aligns with the PR objectives and AI-generated summary.Also applies to: 381-381
402-402
: Updatedsentry-sdk
to2.3.1
aligns with the PR objectives and AI-generated summary.Also applies to: 403-403, 405-405
295-295
: Updatedpyinstaller
to6.7.0
andpyinstaller-hooks-contrib
to2024.6
aligns with the PR objectives and AI-generated summary.Also applies to: 297-297
493-493
: Updatedtyping-extensions
to4.12.0
aligns with the PR objectives and AI-generated summary.
522-522
: Updatedzipp
to3.19.0
aligns with the PR objectives and AI-generated summary.requirements/constraints_py3.9.txt (14)
7-7
: Updatedannotated-types
to0.7.0
to align with latest stable release.
9-9
: Updatedapp-model
to0.2.7
to incorporate the latest features and bug fixes.
43-44
: Updatedcoverage
to7.5.2
to include the latest patches and improvements.
47-47
: Updateddask
to2024.5.1
to ensure compatibility with other updated dependencies.
71-71
: Updatedfsspec
to2024.5.0
to leverage improvements in filesystem handling and performance.
122-122
: Updatedjupyter-client
to8.6.2
to fix known issues and improve stability.
207-208
: Updatedoiffile
to2024.5.24
to support the latest image file formats.
298-300
: Updatedpyinstaller
to6.7.0
andpyinstaller-hooks-contrib
to2024.6
to enhance executable packaging capabilities.
382-382
: Updatedrequests
to2.32.2
to include security patches and new features.
400-402
: Updatedscipy
to1.13.1
to take advantage of optimizations and new algorithms.
405-408
: Updatedsentry-sdk
to2.3.1
to improve error tracking and reporting capabilities.
447-449
: Updatedsuperqt
to0.6.6
to enhance UI components and fix issues.
456-458
: Updatedtifffile
to2024.5.22
to support the latest TIFF standards and features.
496-496
: Updatedtyping-extensions
to4.12.0
to support the latest typing features in Python.requirements/constraints_py3.8_pydantic_1.txt (14)
7-7
: Updatedapp-model
to0.2.7
to align with the latest stable release.
43-44
: Updatedcoverage
to7.5.2
to include the latest patches and improvements.
69-69
: Updatedfsspec
to2024.5.0
to leverage improvements in filesystem handling and performance.
125-125
: Updatedjupyter-client
to8.6.2
to fix known issues and improve stability.
146-146
: Updatedlxml
to5.2.2
to support the latest XML standards and features.
171-171
: Updatednapari
to0.4.19.post1
to include new features and bug fixes.
212-212
: Updatedoiffile
to2022.9.29
to support the latest image file formats.
305-307
: Updatedpyinstaller
to6.7.0
andpyinstaller-hooks-contrib
to2024.6
to enhance executable packaging capabilities.
393-395
: Updatedrequests
to2.32.2
to include security patches and new features.
410-412
: Updatedscipy
to1.10.1
to take advantage of optimizations and new algorithms.
416-419
: Updatedsentry-sdk
to2.3.1
to improve error tracking and reporting capabilities.
458-460
: Updatedsuperqt
to0.6.6
to enhance UI components and fix issues.
469-469
: Updatedtifffile
to2023.7.10
to support the latest TIFF standards and features.
506-506
: Updatedtyping-extensions
to4.12.0
to support the latest typing features in Python.requirements/constraints_py3.8.txt (58)
7-7
: Updatedannotated-types
from0.6.0
to0.7.0
.
9-9
: Updatedapp-model
from0.2.6
to0.2.7
.
13-13
: Addedappdirs==1.4.4
.
45-46
: Updatedcoverage
from7.5.1
to7.5.2
.
48-48
: Updateddask
from2023.5.0
to2024.5.0
.
56-56
: Addeddefusedxml==0.7.1
.
68-68
: Addedfonticon-fontawesome6==6.4.0
.
71-71
: Updatedfsspec
from2024.3.1
to2024.5.0
.
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-client
from8.6.1
to8.6.2
.
143-145
: Addedlocal-migrator==0.1.10
.
148-151
: Updatedlxml
from5.2.1
to5.2.2
.
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
: Updatedplatformdirs
from4.2.1
to4.2.2
.
277-277
: Addedpsygnal==0.11.1
.
290-290
: Addedpydantic==2.7.1
.
301-301
: Addedpygments==2.18.0
.
308-310
: Updatedpyinstaller
from6.6.0
to6.7.0
andpyinstaller-hooks-contrib
from2024.5
to2024.6
.
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
: Updatedpytest
from8.2.0
to8.2.1
.
354-356
: Addedpytest-qt==4.4.0
andpytest-timeout==2.3.1
.
378-380
: Addedqtawesome==1.3.1
.
385-385
: Addedqtpy==2.4.1
.
396-398
: Updatedrequests
from2.31.0
to2.32.2
.
411-413
: Addedscikit-image==0.21.0
.
416-416
: Updatedscipy
from1.13.0
to1.13.1
.
419-422
: Updatedsentry-sdk
from2.1.1
to2.3.1
.
423-423
: Updatedsetuptools
from69.5.1
to70.0.0
.
437-437
: Addedsimpleitk==2.3.1
.
440-440
: Addedsix==1.16.0
.
461-463
: Updatedsuperqt
from0.6.5
to0.6.6
.
467-467
: Addedsympy==1.12
.
472-472
: Updatedtifffile
from2023.7.10
to2024.5.22
.
497-497
: Addedtraceback-with-variables==2.0.4
.
509-509
: Updatedtyping-extensions
from4.11.0
to4.12.0
.
529-529
: Addedvispy==0.14.2
.
537-539
: Addedxlrd==2.0.1
andxlsxwriter==3.2.0
.
540-540
: Updatedzipp
from3.18.1
to3.19.0
.
oiffile
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, tifffile
imagecodecs
, oiffile
, openpyxl
, pydantic
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, sympy
, tifffile
b9b7db4
to
563ca52
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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 (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
: Updatedcertifi
to2024.6.2
. Confirm this version supports the HTTPS certificates required by the project.
434-434
: Updatedsuperqt
to0.6.6
. Verify that this update does not affect the GUI components of the project.
443-443
: Updatedtifffile
to2024.5.22
. Ensure this version supports all TIFF operations used in the project.
197-197
: Updatedopenpyxl
to3.1.3
. Ensure this version handles all Excel file operations as expected.
195-195
: Updatedoiffile
to2024.5.24
. Check for compatibility with other file format libraries.
94-94
: Updatedipykernel
to6.29.4
. Confirm that this version integrates well with the project's Jupyter environment.
75-75
: Updatedimagecodecs
to2024.6.1
. Ensure this version is compatible with image processing libraries used in the project.
439-439
: Updatedsympy
to1.12.1
. Test for any changes in symbolic computation results.
110-110
: Updatedjupyter-client
to8.6.2
. Validate that this update does not introduce issues with kernel management.
41-42
: Updatedcoverage
to7.5.3
. Verify that this update does not affect the existing test coverage reports.
7-7
: Ensureapp-model
version0.2.7
is compatible with other dependencies and the project's requirements.Verification successful
The search results indicate that
app-model==0.2.7
is 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==0.2.7
across 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==0.2.7
is 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
: Updatedpyinstaller
to6.7.0
. Confirm that this version correctly bundles the application.
65-65
: Updatedfsspec
to2024.5.0
. Check for any breaking changes in file handling or caching mechanisms.requirements/constraints_py3.10.txt (51)
7-7
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to version 0.7.0.
9-9
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to version 0.2.7.
13-13
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version 1.4.4 as a new dependency.
28-28
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43-44
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46-46
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47-47
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54-54
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68-68
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version 2.4.0 as a new dependency.
71-71
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74-74
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81-82
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102-107
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118-118
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139-140
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164-164
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178-178
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233-235
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245-245
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255-255
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263-263
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274-276
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283-283
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294-296
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305-307
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311-313
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315-316
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321-323
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334-336
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340-342
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360-362
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367-367
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378-378
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394-396
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401-402
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405-405
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413-413
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419-419
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422-422
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443-443
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448-448
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452-452
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480-480
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492-492
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511-511
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519-521
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522-522
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7-7
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11-11
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version 1.4.4 as a new dependency.
26-26
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to version 2024.6.2.
41-42
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to version 7.5.3.
44-45
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52-52
: Addeddefusedxml
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66-66
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69-69
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72-72
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79-80
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104-109
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120-120
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141-142
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166-166
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180-180
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182-182
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205-208
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227-229
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235-237
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247-247
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257-257
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265-265
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278-279
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.
295-297
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306-308
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312-314
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316-317
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322-324
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326-328
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335-337
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341-343
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361-363
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to version 5.5.2.
368-368
: Updatedqtpy
to version 2.4.1.
379-379
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to version 2.32.3.
395-397
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402-403
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406-406
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420-420
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423-423
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444-444
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449-449
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453-455
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481-481
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493-493
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511-511
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7-7
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to version 0.7.0.
9-9
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to version 0.2.7.
13-13
: Added new dependencies underpartseg
package.
28-28
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to version 2024.6.2.
43-44
: Updatedcoverage
to version 7.5.3.
46-47
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54-54
: Added new dependencies underpartseg
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68-68
: Added new dependencies underpartseg
package.
71-71
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74-74
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81-82
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85-86
: Added new dependencies underpartseg
package.
106-106
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to version 6.29.4.
111-111
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122-122
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138-140
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package.
143-146
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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 underpartseg
package.
154-154
: Added new dependencies underpartseg
package.
168-168
: Added new dependencies underpartseg
package.
182-182
: Added new dependencies underpartseg
package.
184-186
: Added new dependencies underpartseg
package.
189-189
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207-210
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213-213
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229-231
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237-239
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249-249
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259-259
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267-267
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package.
278-280
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287-287
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291-291
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package.
298-300
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305-305
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package.
309-311
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to version 5.15.10.
315-317
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319-320
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325-327
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338-340
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344-346
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364-364
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366-368
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371-371
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382-384
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398-402
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423-423
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426-426
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447-447
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456-458
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484-484
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496-496
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515-515
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523-525
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package.
526-526
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to version 3.19.1.requirements/constraints_py3.8.txt (21)
7-7
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to0.7.0
as per the PR description.
9-9
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to0.2.7
as per the PR description.
30-30
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as per the PR description.
45-45
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as per the PR description.
71-71
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148-148
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as per the PR description.
111-111
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127-127
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214-214
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216-216
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308-308
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as per the PR description.
310-310
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as per the PR description.
329-329
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as per the PR description.
348-348
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to8.2.1
as per the PR description.
396-396
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as per the PR description.
416-416
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as per the PR description.
419-419
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461-461
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466-466
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472-472
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to2023.7.10
as per the PR description.
509-509
: Updatedtyping-extensions
to4.12.1
as per the PR description.
563ca52
to
6481f83
Compare
imagecodecs
, oiffile
, openpyxl
, pydantic
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, sympy
, tifffile
imagecodecs
, magicgui
, oiffile
, openpyxl
, packaging
, pydantic
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, sympy
, tifffile
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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 (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-types
from0.6.0
to0.7.0
. Ensure compatibility with this new version.
29-29
: Updatedcertifi
to2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
102-102
: Updatedipython
to8.25.0
. This could affect interactive sessions, especially in Jupyter environments.
115-115
: Updatedjupyter-client
to8.6.2
. Important for maintaining compatibility with Jupyter notebooks.
194-194
: Updatedoiffile
to2024.5.24
. This update is crucial for handling specific image file formats.
198-198
: Updatedpackaging
to24.1
. This is important for handling package version constraints and dependencies.
424-424
: Updatedtifffile
to2024.5.22
. This is critical for TIFF image processing; ensure all TIFF handling is tested.
457-457
: Updatedtyping-extensions
to4.12.2
. This update may affect type hints across the project; review and adjust as necessary.
46-46
: Updateddask
from2024.5.0
to2024.5.2
. 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
dask
2024.5.0 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
: Updatedopenpyxl
to3.1.3
. Ensure that all Excel-related functionalities work as expected, especially in data import/export features.
269-269
: Updatedpydantic-core
to2.18.4
. This update might introduce changes in the core validation logic.
347-347
: Updatedrequests
to2.32.3
. This is crucial for network communication; ensure all API integrations are functioning correctly.
7-7
: Updatedapp-model
from0.2.6
to0.2.7
. Verify that the new version integrates well with existing project modules.
363-363
: Updatedscipy
to1.13.1
. This update may affect numerical computations; perform regression testing on related functionalities.
258-258
: Updatedpydantic
to2.7.3
. This is a critical update for data validation; ensure all data models are still valid.
415-415
: Updatedsuperqt
to0.6.7
. This library is used for enhanced Qt widgets; ensure compatibility with existing GUI components.
82-82
: Updatedimagecodecs
to2024.6.1
. This package is critical for image handling; ensure all image-related functionalities are tested.
136-136
: Updatedmagicgui
to0.8.3
. This library is extensively used for GUI elements in scientific applications; thorough testing is recommended.
368-368
: Updatedsentry-sdk
to2.5.1
. 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
: Updatedcertifi
to2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
100-100
: Updatedipython
to8.25.0
. This could affect interactive sessions, especially in Jupyter environments.
113-113
: Updatedjupyter-client
to8.6.2
. Important for maintaining compatibility with Jupyter notebooks.
198-198
: Updatedoiffile
to2024.5.24
. This update is crucial for handling specific image file formats.
202-202
: Updatedpackaging
to24.1
. This is important for handling package version constraints and dependencies.
140-140
: Updatedmagicgui
to0.8.3
. This library is extensively used for GUI elements in scientific applications; thorough testing is recommended.
46-46
: Updateddask
from2024.5.0
to2024.5.2
. 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==2024.5.0
todask==2024.5.2
includes 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
: Updatedrequests
to2.32.3
. This is crucial for network communication; ensure all API integrations are functioning correctly.
7-7
: Updatedapp-model
from0.2.6
to0.2.7
. Verify that the new version integrates well with existing project modules.
134-134
: Updatedlxml
to5.2.2
. This library is used for parsing XML and HTML documents; ensure that all parsing functionalities are working as expected.
288-288
: Updatedpyinstaller
to6.8.0
. This tool is crucial for building standalone executables; ensure that the build process is not affected.
437-437
: Updatedsuperqt
to0.6.7
. This library is used for enhanced Qt widgets; ensure compatibility with existing GUI components.
42-42
: Updatedcoverage
to7.5.3
. This is important for maintaining accurate code coverage metrics; ensure all tests are updated accordingly.
200-200
: Updatedopenpyxl
to3.1.3
. Ensure that all Excel-related functionalities work as expected, especially in data import/export features.
80-80
: Updatedimagecodecs
to2024.6.1
. This package is critical for image handling; ensure all image-related functionalities are tested.
446-446
: Updatedtifffile
to2024.5.22
. This is critical for TIFF image processing; ensure all TIFF handling is tested.
479-479
: Updatedtyping-extensions
to4.12.2
. This update may affect type hints across the project; review and adjust as necessary.
388-388
: Updatedscipy
to1.13.1
. This update may affect numerical computations; perform regression testing on related functionalities.
395-395
: Updatedsentry-sdk
to2.5.1
. This is important for error tracking and reporting; verify that error logging is functioning as expected.
258-258
: Updatedpydantic
to1.10.15
. This is a critical update for data validation; ensure all data models are still valid.requirements/constraints_py3.12.txt (24)
7-7
: Updatedannotated-types
to0.7.0
to align with the latest stable release.
29-29
: Updatedcertifi
to2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
48-48
: Updateddask
to2024.5.2
. This minor version update likely includes bug fixes and performance improvements.
115-115
: Updatedjupyter-client
to8.6.2
. This is important for maintaining compatibility with Jupyter notebooks and kernels.
331-331
: Updatedpytest
to8.2.2
. This is important for maintaining the robustness of the test suite.
393-393
: Updatedscipy
to1.13.1
. This minor update likely includes optimizations and bug fixes.
204-204
: Updatedpackaging
to24.1
. This update should be checked for any potential conflicts with version specifiers used in the project.Verification successful
The search results indicate that the
packaging
library is used extensively throughout the project, and the version24.1
is specified in multiple requirement files. However, there are no explicit version conflicts found in the search results.
- The
pyproject.toml
file specifiespackaging>=20.0
, which is compatible with24.1
.- Other files import and use the
packaging
library but do not specify conflicting versions.Given this information, it appears that updating
packaging
to24.1
does 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-extensions
to4.12.2
. This update should be checked for compatibility with type hints used across the project.
291-291
: Updatedpyinstaller
to6.8.0
. Ensure that the application builds correctly with this new version.
202-202
: Updatedopenpyxl
to3.1.3
. This is crucial for Excel file interactions; ensure compatibility with existing spreadsheets.
398-398
: Updatedsentry-sdk
to2.5.1
. This is crucial for error tracking; ensure it integrates well with the project's logging.
102-102
: Updatedipython
to8.25.0
. This update should be checked for compatibility with the project's interactive environments.
200-200
: Updatedoiffile
to2024.5.24
. Ensure that OIF file handling is still functional.
44-45
: Updatedcoverage
to7.5.3
. Verify that this update does not affect the existing test coverage reports.
375-375
: Updatedrequests
to2.32.3
. This update should be tested to ensure HTTP communications are unaffected.
402-402
: Updatedsetuptools
to70.0.0
. This major version change should be carefully tested to ensure it does not break package installations.
72-72
: Updatedfsspec
to2024.6.0
. Ensure that this update integrates well withdask
, as they are often used together.
293-293
: Updatedpyinstaller-hooks-contrib
to2024.7
. This should be tested to ensure that no hooks are broken.
449-449
: Updatedtifffile
to2024.5.22
. This is important for TIFF file handling; ensure all related functionalities work as expected.
9-9
: Updatedapp-model
to0.2.7
. 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 0.2.7
did 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 0.2.7
does not introduce any immediate known conflicts with other dependencies.
- : The update to
app-model 0.2.7
appears 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
: Updatedlxml
to5.2.2
. Verify that this does not break XML processing functionalities.
445-445
: Updatedsympy
to1.12.1
. This update should be tested for compatibility with mathematical computations in the project.
82-82
: Updatedimagecodecs
to2024.6.1
. This package is critical for image handling; ensure all image-related tests pass.
142-142
: Updatedmagicgui
to0.8.3
. This update should be tested with the GUI components of the project.requirements/constraints_py3.11_pydantic_1.txt (20)
7-7
: Updatedapp-model
to0.2.7
to align with the latest stable release.
27-27
: Updatedcertifi
to2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
46-46
: Updateddask
to2024.5.2
. This minor version update likely includes bug fixes and performance improvements.
115-115
: Updatedjupyter-client
to8.6.2
. This is important for maintaining compatibility with Jupyter notebooks and kernels.
330-330
: Updatedpytest
to8.2.2
. This is important for maintaining the robustness of the test suite.
392-392
: Updatedscipy
to1.13.1
. This minor update likely includes optimizations and bug fixes.
397-397
: Updatedsentry-sdk
to2.5.1
. This is crucial for error tracking; ensure it integrates well with the project's logging.
70-70
: Updatedfsspec
to2024.6.0
. Ensure that this update integrates well withdask
, as they are often used together.
42-43
: Updatedcoverage
to7.5.3
. Verify that this update does not affect the existing test coverage reports.
290-290
: Updatedpyinstaller
to6.8.0
. Ensure that the application builds correctly with this new version.
80-80
: Updatedimagecodecs
to2024.6.1
. This package is critical for image handling; ensure all image-related tests pass.
142-142
: Updatedmagicgui
to0.8.3
. This update should be tested with the GUI components of the project.
204-204
: Updatedpackaging
to24.1
. This update should be checked for any potential conflicts with version specifiers used in the project.Verification successful
The update to
packaging==24.1
has been verified across multiple files in the project. All constraints specifypackaging==24.1
, and the files that import and use thepackaging
library have been checked for compatibility.
- No conflicting version specifiers were found.
- The usage of the
packaging
library 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
: Updatedipython
to8.25.0
. This update should be checked for compatibility with the project's interactive environments.
292-292
: Updatedpyinstaller-hooks-contrib
to2024.7
. This should be tested to ensure that no hooks are broken.Verification successful
The
azure-pipelines.yml
file 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_linux
job for Linux.pyinstaller
job for macOS and Windows.Given this, the update to
pyinstaller-hooks-contrib
should 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
: Updatedrequests
to2.32.3
. This update should be tested to ensure HTTP communications are unaffected.
200-200
: Updatedoiffile
to2024.5.24
. Ensure that OIF file handling is still functional.
136-136
: Updatedlxml
to5.2.2
. Verify that this does not break XML processing functionalities.
202-202
: Updatedopenpyxl
to3.1.3
. This is crucial for Excel file interactions; ensure compatibility with existing spreadsheets.
401-401
: Updatedsetuptools
to70.0.0
. 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-types
to version 0.7.0.
9-9
: Updatedapp-model
to version 0.2.7.
29-29
: Updatedcertifi
to version 2024.6.2.
44-45
: Updatedcoverage
to version 7.5.3.
48-48
: Updateddask
to version 2024.5.2.
72-72
: Updatedfsspec
to version 2024.6.0.
82-82
: Updatedimagecodecs
to version 2024.6.1.
104-104
: Updatedipython
to version 8.25.0.
117-117
: Updatedjupyter-client
to version 8.6.2.
138-138
: Updatedlxml
to version 5.2.2.
202-202
: Updatedoiffile
to version 2024.5.24.
204-204
: Updatedopenpyxl
to version 3.1.3.
206-206
: Updatedpackaging
to version 24.1.
273-273
: Updatedpydantic
to version 2.7.3.
282-282
: Updatedpydantic-core
to version 2.18.4.
293-295
: Updatedpyinstaller
to version 6.8.0 andpyinstaller-hooks-contrib
to version 2024.7.
377-377
: Updatedrequests
to version 2.32.3.
395-395
: Updatedscipy
to version 1.13.1.
400-400
: Updatedsentry-sdk
to version 2.5.1.
404-404
: Updatedsetuptools
to version 70.0.0.
442-442
: Updatedsuperqt
to version 0.6.7.
447-447
: Updatedsympy
to version 1.12.1.
451-451
: Updatedtifffile
to version 2024.5.22.
484-484
: Updatedtyping-extensions
to version 4.12.2.
516-516
: Updatedzipp
to version 3.19.2.requirements/constraints_py3.9_pydantic_1.txt (23)
7-7
: Updatedapp-model
to version 0.2.7.
26-26
: Updatedcertifi
to version 2024.6.2.
41-42
: Updatedcoverage
to version 7.5.3.
45-45
: Updateddask
to version 2024.5.2.
69-69
: Updatedfsspec
to version 2024.6.0.
79-79
: Updatedimagecodecs
to version 2024.6.1.
104-104
: Updatedipython
to version 8.18.1.
120-120
: Updatedjupyter-client
to version 8.6.2.
141-141
: Updatedlxml
to version 5.2.2.
205-205
: Updatedoiffile
to version 2024.5.24.
207-207
: Updatedopenpyxl
to version 3.1.3.
209-209
: Updatedpackaging
to version 24.1.
278-279
: Updatedpydantic
to version 1.10.15.
295-297
: Updatedpyinstaller
to version 6.8.0 andpyinstaller-hooks-contrib
to version 2024.7.
379-379
: Updatedrequests
to version 2.32.3.
397-397
: Updatedscipy
to version 1.13.1.
402-402
: Updatedsentry-sdk
to version 2.5.1.
406-406
: Updatedsetuptools
to version 70.0.0.
444-444
: Updatedsuperqt
to version 0.6.7.
449-449
: Updatedsympy
to version 1.12.1.
453-453
: Updatedtifffile
to version 2024.5.22.
493-493
: Updatedtyping-extensions
to version 4.12.2.
522-522
: Updatedzipp
to version 3.19.2.requirements/constraints_py3.9.txt (17)
28-28
: Updatedcertifi
to version2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
211-211
: Updatedpackaging
to version24.1
. This update is crucial for handling version constraints and dependencies.
298-300
: Updatedpyinstaller-hooks-contrib
to version2024.7
. This is crucial for ensuring that all hooks are up to date for packaging.
9-9
: Updatedapp-model
to version0.2.7
. Verify that all dependent modules integrate smoothly with this update.
207-208
: Updatedoiffile
to version2024.5.24
. Confirm that all OIF file interactions are functioning as expected.
43-44
: Updatedcoverage
to version7.5.3
. Ensure that this update does not affect your code coverage metrics adversely.
47-47
: Updateddask
to version2024.5.2
. Check for any changes in parallel computation functionalities that might affect your workflows.Verification successful
The update to
dask
version2024.5.2
does not appear to impact the project's workflows, as no direct or indirect references todask
were 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
: Updatedfsspec
to version2024.6.0
. This update might bring improvements or changes in how file systems are handled.
496-496
: Updatedtyping-extensions
to version4.12.2
. This update is important for type hinting; ensure no type-related issues arise.
7-7
: Updatedannotated-types
to version0.7.0
. Ensure compatibility with this new version across your project.
447-447
: Updatedsuperqt
to version0.6.7
. Verify that all custom Qt widgets and components are functioning as expected with this update.
209-210
: Updatedopenpyxl
to version3.1.3
. Ensure that this update does not disrupt any existing Excel file operations.
278-280
: Updatedpydantic
to version2.7.3
. This is significant for data validation; ensure all models validate correctly with the new version.
81-82
: Updatedimagecodecs
to version2024.6.1
. This is important for handling various image file formats, ensure all image processing functionalities are still compatible.
287-287
: Updatedpydantic-core
to version2.18.4
. Check for any core validation logic changes that might affect your application.
452-452
: Updatedsympy
to version1.12.1
. Ensure that all symbolic mathematics operations are still performing correctly.
456-456
: Updatedtifffile
to version2024.5.22
. Confirm that TIFF file handling is unaffected by this update.requirements/constraints_py3.10_pydantic_1.txt (15)
27-27
: Updatedcertifi
to version2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
210-210
: Updatedpackaging
to version24.1
. This update is crucial for handling version constraints and dependencies.
296-298
: Updatedpyinstaller-hooks-contrib
to version2024.7
. This is crucial for ensuring that all hooks are up to date for packaging.
7-7
: Updatedapp-model
to version0.2.7
. Ensure compatibility with this new version across your project.
74-74
: Updatedfsspec
to version2024.6.0
. This update might bring improvements or changes in how file systems are handled.
494-496
: Updatedtyping-extensions
to version4.12.2
. This update is important for type hinting; ensure no type-related issues arise.
445-447
: Updatedsuperqt
to version0.6.7
. Verify that all custom Qt widgets and components are functioning as expected with this update.
454-456
: Updatedtifffile
to version2024.5.22
. Confirm that TIFF file handling is unaffected by this update.
46-46
: Updateddask
to version2024.5.2
. Check for any changes in parallel computation functionalities that might affect your workflows.
42-43
: Updatedcoverage
to version7.5.3
. Ensure that this update does not affect your code coverage metrics adversely.
208-209
: Updatedopenpyxl
to version3.1.3
. Ensure that this update does not disrupt any existing Excel file operations.
206-207
: Updatedoiffile
to version2024.5.24
. Confirm that all OIF file interactions are functioning as expected.
279-280
: Updatedpydantic
to 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
: Updatedimagecodecs
to version2024.6.1
. This is important for handling various image file formats, ensure all image processing functionalities are still compatible.
450-451
: Updatedsympy
to version1.12.1
. Ensure that all symbolic mathematics operations are still performing correctly.requirements/constraints_py3.10.txt (25)
7-7
: Updatedannotated-types
to0.7.0
as per PR objectives.
9-9
: Updatedapp-model
to0.2.7
as per PR objectives.
29-29
: Updatedcertifi
to2024.6.2
as per PR objectives.
44-45
: Updatedcoverage
to7.5.3
as per PR objectives.
48-48
: Updateddask
to2024.5.2
as per PR objectives.
76-76
: Updatedfsspec
to2024.6.0
as per PR objectives.
86-87
: Updatedimagecodecs
to2024.6.1
as per PR objectives.
110-112
: Updatedipython
to8.25.0
as per PR objectives.
123-123
: Updatedjupyter-client
to8.6.2
as per PR objectives.
144-147
: Updatedlxml
to5.2.2
as 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
: Updatedoiffile
to2024.5.24
as per PR objectives.
211-212
: Updatedopenpyxl
to3.1.3
as per PR objectives.
212-214
: Updatedpackaging
to24.1
as per PR objectives.
279-281
: Updatedpydantic
to2.7.3
as per PR objectives.
288-288
: Updatedpydantic-core
to2.18.4
as per PR objectives.
299-301
: Updatedpyinstaller
andpyinstaller-hooks-contrib
to6.8.0
and2024.7
respectively as per PR objectives.
383-385
: Updatedrequests
to2.32.3
as per PR objectives.
401-403
: Updatedscipy
to1.13.1
as per PR objectives.
406-409
: Updatedsentry-sdk
to2.5.1
as per PR objectives.
410-410
: Updatedsetuptools
to70.0.0
as per PR objectives.
448-450
: Updatedsuperqt
to0.6.7
as per PR objectives.
453-454
: Updatedsympy
to1.12.1
as per PR objectives.
457-459
: Updatedtifffile
to2024.5.22
as per PR objectives.
497-501
: Updatedtyping-extensions
to4.12.2
as per PR objectives.
529-529
: Updatedzipp
to3.19.2
as per PR objectives.requirements/constraints_py3.8_pydantic_1.txt (29)
7-7
: Updatedapp-model
to0.2.7
as per PR objectives.
28-28
: Updatedcertifi
to2024.6.2
as per PR objectives.
43-44
: Updatedcoverage
to7.5.3
as per PR objectives.
69-69
: Updatedfsspec
to2024.6.0
as per PR objectives.
80-80
: Updatedimagecodecs
to2023.3.16
as per PR objectives.
109-114
: Updatedipython
to8.12.3
as per PR objectives.
125-125
: Updatedjupyter-client
to8.6.2
as per PR objectives.
146-149
: Updatedlxml
to5.2.2
as 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
: Updatednapari
to0.4.19.post1
as per PR objectives.
212-215
: Updatedopenpyxl
to3.1.3
as per PR objectives.
215-217
: Updatedpackaging
to24.1
as per PR objectives.
288-289
: Updatedpydantic
to1.10.15
as per PR objectives.
305-307
: Updatedpyinstaller
andpyinstaller-hooks-contrib
to6.8.0
and2024.7
respectively as per PR objectives.
316-318
: Updatedpyqt5
to5.15.10
as per PR objectives.
326-327
: Updatedpyqt6
to6.7.0
andpyqt6-qt6
to6.7.1
as per PR objectives.
332-334
: Updatedpyside2
to5.15.2.1
as per PR objectives.
336-338
: Updatedpyside6
and related packages to6.3.1
as per PR objectives.
345-347
: Updatedpytest
to8.2.2
as per PR objectives.
393-395
: Updatedrequests
to2.32.3
as per PR objectives.
408-410
: Updatedscipy
to1.10.1
as per PR objectives.
416-419
: Updatedsentry-sdk
to2.5.1
as per PR objectives.
420-420
: Updatedsetuptools
to70.0.0
as per PR objectives.
458-460
: Updatedsuperqt
to0.6.7
as per PR objectives.
463-464
: Updatedsympy
to1.12.1
as per PR objectives.
469-469
: Updatedtifffile
to2023.7.10
as per PR objectives.
506-506
: Updatedtyping-extensions
to4.12.2
as per PR objectives.
524-524
: Updatedvispy
to0.14.2
as per PR objectives.
532-535
: Updatedxlrd
andxlsxwriter
to2.0.1
and3.2.0
respectively as per PR objectives.
535-535
: Updatedzipp
to3.19.2
as per PR objectives.requirements/constraints_py3.8.txt (12)
7-7
: Updatedannotated-types
to0.7.0
aligns with the PR's objective to keep dependencies up-to-date.
9-9
: Updatedapp-model
to0.2.7
is consistent with the PR's update strategy.
30-30
: Updatedcertifi
to2024.6.2
ensures the latest security patches are applied.
217-217
: Updatedpackaging
to24.1
. This is a critical update as it often affects how dependencies are resolved.
540-540
: Updatedzipp
to3.19.2
. Ensure this does not impact the module import mechanisms.Verification successful
The search for
zipp
import statements in Python files did not produce any output, indicating thatzipp
is not directly imported in the codebase. This suggests that updatingzipp
to version3.19.2
should not impact the module import mechanisms.
- No instances of
import zipp
were 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
: Updatedcoverage
to7.5.3
. Verify this version is compatible with other testing tools used.Verification successful
The initial script did not reveal any direct compatibility issues between
coverage==7.5.3
and the testing toolspytest
orunittest
. 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
coverage
in the codebase, especially in test configurations and scripts.
The previous attempt to check for mentions of
coverage
in test configurations and scripts did not produce any output. To ensure thorough verification, we should check thetox.ini
andpyproject.toml
files for any specific configurations or dependencies related tocoverage
.
The
tox.ini
andpyproject.toml
files show thatcoverage
is 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==7.5.3
is 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}.json
coverage 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==7.5.3
and 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 ofappdirs
dependency. Ensure this is intended and necessary forpartseg
.Verification successful
The
appdirs
dependency is indeed used in thepartseg
package, specifically in thepackage/PartSeg/state_store.py
file.
package/PartSeg/state_store.py
:
import appdirs
os.environ.get("PARTSEG_SETTINGS_DIR", appdirs.user_data_dir(APP_NAME, APP_LAB))
This confirms that the addition of the
appdirs
dependency 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
: Updatedopenpyxl
to3.1.3
. Confirm that this version handles all Excel-related functionalities without issues.
71-71
: Updatedfsspec
to2024.6.0
. Confirm that this update does not introduce breaking changes withdask
.Verification successful
The verification process indicates that there is no usage of
fsspec
in the codebase. Consequently, updatingfsspec
to2024.6.0
should not introduce any breaking changes withdask
.
- No instances of
fsspec
were 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
: Updatedrequests
to2.32.3
. Verify that this update does not affect the external API calls.
461-461
: Updatedsuperqt
to0.6.7
. Check for any UI issues this may introduce, especially in custom widgets.
127-127
: Updatedjupyter-client
to8.6.2
. Ensure this version is compatible with the IPython and Jupyter ecosystem in the project.
6481f83
to
0a59d75
Compare
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Actionable comments posted: 0
Outside diff range and nitpick comments (2)
requirements/constraints_py3.9.txt (1)
13-13
: The comment indentation here forappdirs
seems 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 forappdirs
seems 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==6.4.0
added. Check for UI consistency across the application.
275-275
:pygments==2.18.0
update. Check syntax highlighting functions across the application for any regressions.
11-14
: Addition ofappdirs==1.4.4
is noted. Verify it doesn't introduce any breaking changes in the environment setup.Verification successful
The addition of
appdirs==1.4.4
does not introduce any breaking changes in the environment setup.
- The version
1.4.4
ofappdirs
is used consistently across multiple requirements files.- The usage in
package/PartSeg/state_store.py
aligns with the expected behavior ofappdirs
and 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==6.4.1
update. Verify all asynchronous operations are stable and performant.
329-329
:qtconsole==5.5.2
update. Ensure integration with Jupyter environments is seamless.
136-137
:magicgui==0.8.3
upgrade. 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==0.1.8
added. Verify integration with existing mathematical expression handling.
200-200
:packaging==24.1
update. Check for any issues in package version parsing across the application.Verification successful
The search results indicate that the
packaging.version
module 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==24.1
update.Given the nature of the changes and the usage patterns observed, the update to
packaging==24.1
is 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_version
frompackaging.version
.package/PartSegImage/tifffile_fixes.py
: Usingpackaging.version.parse
for conditional checks.package/tests/test_PartSeg/test_window_import.py
: Testing version parsing.package/tests/test_PartSeg/test_sentry.py
: Importingparse_version
frompackaging.version
.package/tests/test_PartSeg/test_common_backend.py
: Importingparse
frompackaging.version
.package/tests/test_PartSeg/test_check_release.py
: Usingpackaging.version.parse
for comparisons.package/PartSeg/__init__.py
: Importingparse
frompackaging.version
.package/PartSeg/_launcher/check_version.py
: Usingpackaging.version.parse
for version comparisons.package/PartSegCore/analysis/io_utils.py
: Usingpackaging.version.Version
to define project version.package/PartSeg/state_store.py
: Usingpackaging.version.parse
for version-based folder structure.package/PartSegCore/analysis/load_functions.py
: ImportingVersion
andparse
frompackaging.version
.package/PartSeg/common_gui/about_dialog.py
: Importingparse_version
frompackaging.version
.package/PartSeg/common_backend/base_argparser.py
: Importingparse_version
frompackaging.version
.package/PartSeg/common_backend/load_backup.py
: Usingpackaging.version.parse
and handlingInvalidVersion
.package/PartSeg/common_gui/napari_image_view.py
: Importingparse_version
frompackaging.version
.package/PartSeg/common_gui/main_window.py
: Importingparse_version
frompackaging.version
.package/PartSeg/common_gui/searchable_combo_box.py
: Importingparse
frompackaging.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==8.6.2
update should be verified for integration with Jupyter notebooks and kernels.
336-336
:qtpy==2.4.1
update. Confirm no compatibility issues with PyQt and PySide environments.
247-247
:psygnal==0.11.1
update. Check for any event handling issues, especially in GUI components.
363-365
:scipy==1.13.1
update. Verify all scientific computations are accurate and efficient.
22-22
:autodoc-pydantic==2.2.0
addition should enhance documentation. Confirm it integrates smoothly with existing Pydantic models.
233-233
:platformdirs==4.2.2
update. Validate no impact on file system interactions, especially in environment setup.Verification successful
The search did not find any instances of
import platformdirs
in the codebase, indicating that theplatformdirs
package is not directly imported or used in the project's code. Therefore, the update toplatformdirs==4.2.2
in the requirements file should not impact file system interactions or environment setup.
- The
platformdirs
package 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==0.7.1
added for security enhancements. Verify against XML processing parts of the project.Verification successful
The inspection of the identified files reveals that both
lxml
anddefusedxml
are being used for XML processing. Specifically:
package/tests/test_PartSegImage/test_image_writer.py
useslxml.etree
for XML schema validation and parsing.package/PartSegImage/image_reader.py
usesdefusedxml.ElementTree
.The presence of
defusedxml
in 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.py
package/PartSegImage/image_reader.py
Scripts 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==3.11.0
update 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.py
package/tests/test_PartSegCore/test_pipeline.py
package/tests/test_PartSeg/test_napari_widgets.py
package/tests/test_PartSeg/test_settings.py
package/tests/test_PartSeg/test_common_gui.py
package/tests/test_PartSeg/test_roi_analysis_batch.py
package/tests/test_PartSegCore/test_analysis_batch.py
Given this coverage, it appears that the update to
h5py==3.11.0
should 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==2024.6.0
noted. Ensure compatibility with file handling operations.
99-104
: Upgradingipython==8.25.0
could affect interactive sessions. Check all interactive features are functioning.
171-173
:npe2==0.7.5
update. Check for compatibility with plugin systems, especially in Napari.Verification successful
The changelog for
npe2
does not mention any breaking changes or compatibility issues for version0.7.5
that would impact thePluginManager
or itsregister
method. Given this information and the usage ofnpe2
in the plugin initialization code, it appears that the update tonpe2==0.7.5
should 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==0.7.0
is compatible with other dependencies requiring this package.
269-271
:pydantic-core==2.18.4
update. Verify core functionalities of models, especially custom validators.
415-417
:superqt==0.6.7
update. Check for UI responsiveness and stability in custom widgets.
7-7
: Update toapp-model==0.2.7
looks good, ensure it's tested with dependent modules.
82-83
: Update toimagecodecs==2024.6.1
should improve image processing performance. Verify with image-heavy tests.
347-347
:requests==2.32.3
update. Test all external API interactions to ensure no disruptions.
141-141
:mahotas==1.4.15
addition for image processing enhancements. Test with existing image analysis pipelines.
258-260
:pydantic==2.7.4
update. Confirm validation logic for models remains accurate and performant.
45-46
: Update todask==2024.6.0
should be checked for compatibility with parallel processing tasks.
445-445
:traceback-with-variables==2.0.4
added. Ensure it enhances error debugging without affecting performance.Verification successful
The usage of
print_exc
andFormat
fromtraceback_with_variables
inpackage/PartSeg/common_gui/error_report.py
indicates 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==2.2.2
update should be tested with all data manipulation tasks to ensure no regressions.
194-198
: Upgrades tooiffile==2024.5.24
andopenpyxl==3.1.4
. Verify file handling and parsing operations.
368-371
:sentry-sdk==2.5.1
update. Ensure error reporting is functioning correctly across all modules.
420-421
:sympy==1.12.1
update. Confirm all symbolic mathematics operations are functioning as expected.
239-239
:prompt-toolkit==3.0.47
update. Ensure all CLI interactions remain stable and user-friendly.Verification successful
Follow-up Verification
The previous scripts did not find any usage of
prompt-toolkit
in 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-toolkit
in 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-toolkit
is 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-toolkit
were found in the codebase or test files.Given this information, the update to
prompt-toolkit==3.0.47
can 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.post1
update noted. Confirm no disruptions in visualization features.
176-176
:numpy==1.26.4
remains unchanged. Ensure it's still compatible with all numerical operations.
29-29
: Update tocertifi==2024.6.2
is critical for maintaining SSL trust. Ensure all HTTPS requests in the system are tested.
64-67
: Additions offlexcache==0.3
andflexparser==0.3.1
should 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
cachey
library. The additions offlexcache==0.3
andflexparser==0.3.1
do 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
flexcache
orflexparser
were 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-model
looks good.
7-7
: Ensure the version update forannotated-types
aligns with other dependencies that might rely on it.Verification successful
The search did not reveal any dependencies requiring a specific version of
annotated-types
other than the one specified in the file. Therefore, the version update forannotated-types
to0.7.0
does not seem to conflict with any other dependencies.
requirements/constraints_py3.12.txt
:annotated-types==0.7.0
Scripts 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 ofcertifi
should be checked for compatibility with the requests library.
204-204
: Ensurepackaging
update does not introduce conflicts with version constraints in the project.Verification successful
The search results indicate that
packaging==24.1
is consistently specified across all requirement files, with no other version constraints identified. Additionally, the usages ofpackaging.version
and related functions in the codebase do not show any immediate conflicts with version24.1
.
- No conflicting version constraints for
packaging
were found.- The usages of
packaging.version
appear 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 ofcoverage
does not introduce any breaking changes with existing test suites.
252-252
: Ensureprompt-toolkit
update does not affect CLI interfaces and prompts.
82-82
: Check if the newimagecodecs
version is compatible with image processing libraries in use.
115-115
: Ensure thejupyter-client
update does not break existing notebook functionalities.Verification successful
The verification process did not find any direct or indirect references to
jupyter-client
in the notebooks, Python files, or configuration files. This suggests that the update tojupyter-client
is 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
: Updatedipython
version should be tested for interactive features and compatibility with Jupyter.
142-142
: The update tomagicgui
should be tested to ensure it does not break GUI components.
242-242
: Check if theplatformdirs
update affects directory handling in different operating systems.
48-48
: Confirm that the update todask
version does not affect performance or parallel computation features.
136-137
: Verify that thelxml
version update does not affect XML parsing used in projects.
393-393
: Test thescipy
update to ensure it does not introduce issues with numerical computations.
375-375
: Verify that therequests
update does not break HTTP communication features.
200-200
: Confirm that theoiffile
update is compatible with file operations in the project.
440-440
: Ensuresuperqt
update is compatible with Qt-based applications in the project.requirements/constraints_py3.11_pydantic_1.txt (16)
7-7
: Check if theapp-model
update is compatible with application modeling frameworks used.
42-43
: Confirm that thecoverage
update integrates well with the testing framework.
242-242
: Check if theplatformdirs
update affects directory management across different platforms.
115-115
: Verify that thejupyter-client
update does not introduce issues with Jupyter notebook or lab environments.
375-375
: Verify therequests
update for compatibility with web communication protocols used in the project.Verification successful
The changelog for
requests
version 2.32.3 primarily includes bug fixes related to SSL context handling and compatibility with Python versions compiled without thessl
module. There are no changes that directly impact the usage ofrequests.post
orrequests.put
methods.Thus, the update to
requests==2.32.3
should 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 thepackaging
update does not introduce version conflicts with other dependencies.
46-46
: Check for any breaking changes introduced by thedask
update, especially in parallel processing tasks.
393-393
: Test thescipy
update for compatibility with numerical and scientific computations.
252-252
: Ensureprompt-toolkit
update 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-toolkit
in the command-line interfaces used in the project.
- No references to
prompt-toolkit
were 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
: Checksuperqt
update for integration with existing Qt-based GUI elements.
102-102
: Test the updatedipython
version for compatibility with interactive Python sessions.
142-142
: Ensure that themagicgui
update does not break any GUI components or interfaces.
80-80
: Ensure theimagecodecs
update does not affect image encoding/decoding functionalities.
136-137
: Check if the updatedlxml
version affects XML handling in the application.
27-27
: Ensure thecertifi
version 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
rg
search 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.post
orrequests.put
.
The repeated syntax errors indicate a persistent issue with handling parentheses in the
rg
search 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.post
orrequests.put
without usingxargs
.
The script output indicates that there are no SSL/TLS related keywords (like
verify
,cert
,ssl
,tls
) found in the context ofrequests.post
orrequests.put
calls. This suggests that the network requests in the codebase do not explicitly handle SSL/TLS configurations, and therefore, thecertifi
update should not affect these calls.Given this context, the update to
certifi
version2024.6.2
does 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 theoiffile
update is compatible with other file handling libraries.requirements/constraints_py3.11.txt (12)
202-205
:oiffile
version updated to2024.5.24
. This is crucial for handling specific image file formats. Confirm that all.oif
files are still supported and correctly processed.
29-29
: Updatedcertifi
to2024.6.2
. 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-types
from0.6.0
to0.7.0
is noted. Ensure compatibility with the rest of the system.
9-9
: Updatedapp-model
to version0.2.7
. Validate that all dependent modules are compatible with this version.
442-442
:superqt
updated to0.6.7
. Given its use in enhancing Qt interfaces, ensure that all custom widgets and interfaces are functioning properly.
447-447
:sympy
version1.12.1
updated. This library is essential for symbolic mathematics. Run complex calculations to ensure accuracy.
144-147
:magicgui
version0.8.3
is noted. Since this library is often used for GUI elements in scientific applications, check that all GUI components are rendered correctly.
451-453
:tifffile
updated 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
: Updatedpackaging
to24.1
. This utility is vital for handling version constraints. Verify that all version checks within the application behave as intended.
82-82
:imagecodecs
updated to2024.6.1
. This library is critical for image handling; ensure all image processing functionalities are intact.
44-45
:coverage
updated to7.5.3
. Ensure this does not affect the existing test coverage reports.requirements/constraints_py3.9.txt (14)
7-7
: Update toannotated-types==0.7.0
is consistent with the PR's objective to upgrade package versions.
9-9
: Update toapp-model==0.2.7
aligns with the upgrade strategy outlined in the PR.
28-28
: Update tocertifi==2024.6.2
is appropriate, ensuring the latest security patches are applied.
43-44
:coverage
updated to7.5.3
. Ensure this version is compatible with other testing tools used in the project.
447-447
:superqt==0.6.7
update should be verified, especially if it affects any custom widgets used in the project.
477-477
: The minor version update oftornado==6.4.1
needs to be checked for compatibility with async features.
68-68
:fsspec
version 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.compatibility
module, but there are no instances of this module being used in the project. Additionally, the usage of Dask inlauncher.spec
appears limited to importingdask.config
, which is not impacted by the changes in the new version.
- No instances of
dask.compatibility
were found in the project files.- The Dask import in
launcher.spec
is 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==0.8.3
should enhance UI elements. Check that all GUI components are displayed correctly.
211-213
: The update topackaging==24.1
is a minor version change. Verify that there are no dependency conflicts introduced by this update.
456-456
: Update totifffile==2024.5.22
should be tested to ensure that TIFF file handling is still robust, especially in image processing workflows.
54-54
: Addition ofdocstring-parser==0.16
viamagicgui
. Confirm that this addition is necessary for the project's documentation generation.
209-211
:openpyxl
version3.1.4
correctly updated for handling Excel files. Confirm that all Excel-related functionalities work without issues.
81-82
:imagecodecs
updated 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==0.2.7
is consistent with the PR's objective to upgrade package versions.
27-27
: Update tocertifi==2024.6.2
is appropriate, ensuring the latest security patches are applied.
210-212
: The update topackaging==24.1
is 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==2024.5.22
should be tested to ensure that TIFF file handling is still robust, especially in image processing workflows.
445-445
:superqt==0.6.7
update should be verified, especially if it affects any custom widgets used in the project.
84-85
:imagecodecs
updated 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
:flexcache
andflexparser
added, likely to enhance performance. Ensure they integrate well with the existing caching and parsing mechanisms.
475-475
: The minor version update oftornado==6.4.1
needs to be checked for compatibility with async features.
74-74
:fsspec
version updated to2024.6.0
. This is crucial for file handling operations; ensure all file operations are still functioning as expected.
148-149
: Update tomagicgui==0.8.3
should enhance UI elements. Check that all GUI components are displayed correctly.
208-210
:openpyxl
version3.1.4
correctly updated for handling Excel files. Confirm that all Excel-related functionalities work without issues.
53-53
: Addition ofdocstring-parser==0.16
viamagicgui
. Confirm that this addition is necessary for the project's documentation generation.
42-43
:coverage
updated to7.5.3
. Ensure this version is compatible with other testing tools used in the project.Verification successful
coverage
7.5.3 is compatible withpytest
, which is the primary testing tool used in the project. No other testing tools likeunittest
,nose
, ortox
were found in the codebase.
Scripts executed
The following scripts were executed for the analysis:
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requirements/constraints_py3.10.txt (12)
29-29
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to2024.6.2
. This is critical for maintaining up-to-date SSL certificates.
212-212
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. This update is crucial for handling package versions correctly across the application.
7-7
: Updatedannotated-types
to0.7.0
. Ensure compatibility withpydantic
which depends on this package.
448-448
: Updatedsuperqt
to0.6.7
. Confirm that all custom Qt widgets are functioning as intended.
453-453
: Updatedsympy
to1.12.1
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86-87
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to2024.6.1
. This is important for image processing applications, verify that all image processing functions are working as expected.
44-45
: Updatedcoverage
to7.5.3
. Verify that coverage reporting in CI pipelines is unaffected.Verification successful
The
codecov.yml
file contains configurations related to coverage reporting. However, there are no explicit commands or scripts in theazure-pipelines.yml
file indicating how coverage is being reported.To ensure that the update to
coverage==7.5.3
does not affect the coverage reporting, we need to verify if any scripts or commands in the repository use thecoverage
tool explicitly.
The repository uses the
coverage
tool within thetox.ini
file for running tests and generating coverage reports. The update tocoverage==7.5.3
in therequirements/constraints_py3.10.txt
file aligns with the same version specified in other constraints files.Given that the coverage tool is explicitly used in the
tox.ini
file, the update should not affect the coverage reporting as long as the version is consistent across the environment.
tox.ini
usescoverage run
commands.- The
codecov.yml
file 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:
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Script:
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Script:
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9-9
: Updatedapp-model
to0.2.7
. Check for any breaking changes in the new version that might affectnapari
.
208-209
: Updatedoiffile
to2024.5.24
. Check compatibility withimagecodecs
since both are used in image processing.Verification successful
The scripts did not find any Python files that import both
oiffile
andimagecodecs
. This suggests that these two libraries are not used together in the same files within the codebase. Therefore, there is no immediate compatibility issue betweenoiffile
andimagecodecs
based 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
: Updateddask
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. Ensure that all parallel computing processes are tested for efficiency improvements.
210-211
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to3.1.4
. Ensure that all Excel file manipulations are still functioning correctly.
457-457
: Updatedtifffile
to2024.5.22
. Verify that TIF file handling is still robust and error-free.requirements/constraints_py3.8_pydantic_1.txt (11)
28-28
: Updatedcertifi
to2024.6.2
. Critical for SSL certificate validation.
469-469
: Updatedtifffile
to2023.7.10
. Check robustness of TIF file handling.
7-7
: Updatedapp-model
to0.2.7
. Check for compatibility withnapari
.
152-152
: Updatedmagicgui
to0.8.3
. Test all GUI elements created with this library.
212-212
: Updatedoiffile
to2022.9.29
. Verify compatibility with other image processing libraries.Verification successful
The search results indicate that
imageio
is imported inpackage/PartSegCore/io_utils.py
, but there are no instances ofoiffile
being imported. This suggests thatoiffile
is not used in conjunction withimageio
in the codebase. Therefore, there should be no compatibility issues between the updatedoiffile
version andimageio
.
imageio
is imported in:package/PartSegCore/io_utils.py
oiffile
is 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
: Updatedsympy
to1.12.1
. Ensure all symbolic math operations are functioning correctly.
66-66
: Updatedfreetype-py
to2.4.0
. Important for graphics rendering, check all graphical outputs.Verification successful
The update of
freetype-py
to version2.4.0
has been confirmed in the requirements file. However, there are no instances offreetype_py
being 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==2.4.0
Scripts 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
: Updatedcoverage
to7.5.3
. Verify integration with CI tools for correct coverage reporting.Verification successful
The integration of
coverage
with CI tools has been verified successfully. The scripts revealed multiple references tocoverage
in the CI configuration files, particularly in.github/workflows/tests.yml
and.github/workflows/base_test_workflow.yml
.
.github/workflows/tests.yml
.github/workflows/base_test_workflow.yml
Scripts 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
: Updatedimagecodecs
to2023.3.16
. Ensure all image processing functionalities are intact.
458-458
: Updatedsuperqt
to0.6.7
. Confirm functionality of all custom Qt widgets and components.
286-286
: Updatedpydantic
to1.10.16
. This is a major dependency for model validations; conduct thorough testing.requirements/constraints_py3.8.txt (15)
7-7
: Updatedannotated-types
from0.6.0
to0.7.0
. Ensure this version is compatible with other dependencies.
9-9
: Updatedapp-model
from0.2.6
to0.2.7
. Verify the impact of this minor version change on dependent modules.
30-30
: Updatedcertifi
from2024.2.2
to2024.6.2
. This is important for maintaining up-to-date SSL certificates.
45-46
: Updatedcoverage
from7.5.1
to7.5.3
. Check integration with CI tools to ensure proper coverage reporting.
71-71
: Updatedfsspec
from2024.3.1
to2024.6.0
. Confirm compatibility withdask
for file system operations.
127-127
: Updatedjupyter-client
from8.6.1
to8.6.2
. This minor update should be checked for any breaking changes in notebook execution environments.
269-269
: Updatedprompt-toolkit
from3.0.43
to3.0.47
. Validate the interaction with other console applications to ensure smooth user input handling.
288-290
: Updatedpydantic
from2.7.1
to2.7.4
. This update could affect data validation; thorough testing is recommended.
297-297
: Updatedpydantic-core
from2.18.2
to2.18.4
. Ensure that the core changes do not impact the validation logic extensively.
308-310
: Updatedpyinstaller
from6.6.0
to6.8.0
andpyinstaller-hooks-contrib
from2024.5
to2024.7
. Verify that application builds are stable and all hooks are functioning as expected.
461-461
: Updatedsuperqt
from0.6.6
to0.6.7
. Check for any UI regressions or changes in widget behavior.
466-466
: Updatedsympy
from1.12
to1.12.1
. Minor update, but ensure that all symbolic computations are still correct.
472-472
: Updatedtifffile
from2024.5.3
to2024.5.22
. Confirm that all TIFF handling is compatible with new changes.
490-490
: Updatedtornado
from6.4
to6.4.1
. This is critical for asynchronous operations; ensure no regressions in web server behavior.
509-509
: Updatedtyping-extensions
from4.11.0
to4.12.2
. This update is important for static typing features; verify that there are no issues with type annotations.
0a59d75
to
3681afc
Compare
imagecodecs
, magicgui
, oiffile
, openpyxl
, packaging
, pydantic
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, sympy
, tifffile
imagecodecs
, magicgui
, oiffile
, openpyxl
, packaging
, pydantic
, pyinstaller
, requests
, scipy
, sentry-sdk
, superqt
, sympy
, tifffile
, vispy
Quality Gate passedIssues Measures |
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Actionable comments posted: 0
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 forlxml
andlxml-html-clean
is 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-model
to0.2.7
looks good.
438-438
: Ensuretornado
version6.4.1
does not introduce issues with real-time operations or websockets.
258-258
:pydantic
version2.7.4
update needs to be checked for compatibility with data validation features across the application.
420-421
: The update ofsympy
to1.12.1
should be checked for compatibility with mathematical operations.Verification successful
The references to
measurement_calculation
andmeasurement_base
in the test files indicate that the mathematical operations involvingsympy
are covered by tests. Therefore, the update ofsympy
to1.12.1
should be compatible with the existing mathematical operations.
Test files referencing
measurement_calculation
:
package/tests/test_PartSegCore/test_io.py
package/tests/test_PartSegCore/test_measurements.py
package/tests/conftest.py
package/tests/test_PartSegCore/test_analysis_batch.py
package/tests/test_PartSeg/test_napari_widgets.py
package/tests/test_PartSeg/test_analysis.py
Test files referencing
measurement_base
:
package/tests/conftest.py
package/tests/test_PartSegCore/test_measurements.py
package/tests/test_PartSegCore/test_io.py
package/tests/test_PartSegCore/test_class_generator.py
package/tests/test_PartSegCore/test_analysis_batch.py
package/tests/test_PartSeg/test_analysis.py
These 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 ofdefusedxml
is appropriate for enhancing security. Ensure it does not conflict with existing XML processing libraries.
29-29
: Ensure the update ofcertifi
to2024.6.2
maintains 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 withcertifi
version2024.6.2
. There are no known issues with these combinations, and the update should not introduce SSL compatibility problems.
requests==2.32.3
is compatible withcertifi==2024.6.2
.urllib3==2.2.2
is 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-types
from0.6.0
to0.7.0
is compatible with other dependencies.
102-104
: Updatedipython
to8.25.0
. Confirm that this does not introduce any breaking changes with IPython kernels or plugins.
476-478
: Ensurevispy
version0.14.3
integrates well with visualization functionalities.
472-472
: Update ofurllib3
to2.2.2
should be verified for maintaining robust HTTP communications.
72-72
: Updatedfsspec
version to2024.6.0
should be checked for compatibility withdask
.
363-365
: Update ofscipy
to1.13.1
should be verified for compatibility with numerical operations in the application.
347-347
: Ensure therequests
version2.32.3
update does not break existing HTTP requests functionality.
82-83
: Update ofimagecodecs
to2024.6.1
should be verified for compatibility with image processing libraries likescikit-image
.
194-198
: Update ofoiffile
to2024.5.24
should be verified for compatibility with file handling operations inpartseg
.Verification successful
Update of
oiffile
to2024.5.24
should be verified for compatibility with file handling operations inpartseg
.
- The
OifFile
class is used in awith
statement inpackage/PartSegImage/image_reader.py
.- The release notes for
oiffile
version2024.5.24
do 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-sdk
to2.5.1
should be verified for effective integration in error reporting.Verification successful
The
sentry_sdk.init
function is found inpackage/PartSeg/common_backend/base_argparser.py
, indicating thatsentry-sdk
is indeed initialized in the codebase. This suggests that the integration ofsentry-sdk
version2.5.1
is 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
:magicgui
version update to0.8.3
should be verified for compatibility withnapari
plugins.
155-155
: Ensurenapari
version0.4.19.post1
functions correctly with updated dependencies.
415-417
: Ensuresuperqt
version0.6.7
integrates correctly with the GUI components of the application.
46-46
: Verify that the new version ofdask
(2024.6.0
) integrates well withnapari
and other dependent packages.
424-426
: Updatedtifffile
to2024.5.22
needs verification for handling TIFF files without issues.requirements/constraints_py3.12.txt (14)
55-55
: Review the addition ofdefusedxml==0.7.1
for potential security improvements.This addition can help mitigate XML-related security vulnerabilities.
136-136
: Check if the update tolxml==5.2.2
affects XML parsing functionalities.
142-142
: Confirm thatmagicgui==0.8.3
integrates well with existing GUI elements.
175-175
: Ensurenme==0.1.8
does not conflict with existing mathematical expressions handling.
82-82
: Validate thatimagecodecs==2024.6.1
supports all required image formats.
9-9
: Confirm thatapp-model==0.2.7
does not introduce breaking changes from0.2.6
.
7-7
: Ensure that the updated versionannotated-types==0.7.0
is compatible with other dependencies.
29-29
: Update ofcertifi
to2024.6.2
should be verified for SSL/TLS compatibility.Verification successful
The
requirements/constraints_py3.12.txt
file correctly specifiescertifi==2024.6.2
. Thecurl
command successfully fetched content fromhttps://example.com
without any SSL/TLS errors, indicating that the update tocertifi
version2024.6.2
does not introduce any immediate SSL/TLS compatibility issues.
requirements/constraints_py3.12.txt
:certifi==2024.6.2
Scripts 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.post1
does not introduce regressions in image visualization.
102-102
: Update ofipython==8.25.0
should be checked for compatibility with interactive environments.
115-115
: Ensure no conflicts arise due tojupyter-client==8.6.2
in the Jupyter ecosystem.
48-48
: Ensuredask==2024.6.0
integrates smoothly with existing data processing workflows.
44-45
: Check the impact of thecoverage
version update on test suites.
72-72
:fsspec==2024.6.0
should be tested for compatibility with file system operations.requirements/constraints_py3.11.txt (32)
7-7
: Updated version forannotated-types
from0.6.0
to0.7.0
aligns with the PR objectives.
9-9
: Updated version forapp-model
from0.2.6
to0.2.7
is consistent with the described changes.
29-29
: Updated version forcertifi
from2024.2.2
to2024.6.2
is accurately reflected.
44-45
: Version update forcoverage
from7.5.1
to7.5.3
is correctly documented and implemented.
48-48
: Updateddask
version from2024.5.0
to2024.6.0
matches PR objectives.
55-55
: Added dependencydefusedxml
viapartseg
is consistent with the new dependencies listed.
72-72
: Updatedfsspec
version from2024.3.1
to2024.6.0
as per the PR summary.
82-82
: Updatedimagecodecs
to version2024.6.1
aligns with specific package updates.
104-104
: Updated version foripython
from8.24.0
to8.25.0
checks out with the summary.
117-117
: Updatedjupyter-client
version from8.24.0
to8.25.0
aligns with the updates listed.
138-138
: Updatedlxml
version from5.2.1
to5.2.2
is correctly updated.
144-144
: Updatedmagicgui
from0.8.2
to0.8.3
. Note the duplication error flagged by LanguageTool seems to be a false positive.Also applies to: 144-144
202-202
: Updatedoiffile
to2024.5.24
matches the specific package updates.
204-204
: Updatedopenpyxl
from3.1.2
to3.1.4
is accurately reflected.
206-206
: Updatedpackaging
from24.0
to24.1
is consistent with the updates listed.
273-273
: Updatedpydantic
from2.7.1
to2.7.4
aligns with the updates listed.
282-282
: Updatedpydantic-core
to2.18.4
aligns with specific package updates.
293-293
: Updatedpyinstaller
to6.8.0
is correctly implemented.
295-295
: Updatedpyinstaller-hooks-contrib
to2024.7
aligns with the updates.
314-314
: Updatedpyqt6
to6.7.0
is correctly reflected.
315-315
: Updatedpyqt6-qt6
to6.7.1
matches the updates listed.
333-333
: Updatedpytest
from8.2.0
to8.2.2
is correctly updated.
395-395
: Updatedscipy
from1.13.0
to1.13.1
is accurately reflected.
400-400
: Updatedsentry-sdk
from2.1.1
to2.5.1
is correctly implemented.
404-404
: Updatedsetuptools
from69.5.1
to70.0.0
matches PR objectives.
442-442
: Updatedsuperqt
to0.6.7
aligns with the updates listed.
447-447
: Updatedsympy
to1.12.1
matches the specific package updates.
451-451
: Updatedtifffile
from2024.5.3
to2024.5.22
is correctly reflected.
465-465
: Updatedtornado
from6.4
to6.4.1
is accurately updated.
484-484
: Updatedtyping-extensions
from4.11.0
to4.12.2
is consistent with the updates listed.
499-499
: Updatedurllib3
from2.1.0
to2.2.2
aligns with the updates listed.
503-503
: Updatedvispy
from0.14.2
to0.14.3
is correctly implemented.requirements/constraints_py3.9_pydantic_1.txt (30)
7-7
: Updated version forapp-model
from0.2.6
to0.2.7
is consistent with the described changes.
26-26
: Updated version forcertifi
from2024.2.2
to2024.6.2
is accurately reflected.
41-42
: Version update forcoverage
from7.5.1
to7.5.3
is correctly documented and implemented.
45-45
: Updateddask
version from2024.5.0
to2024.6.0
matches PR objectives.
52-52
: Added dependencydefusedxml
viapartseg
is consistent with the new dependencies listed.
69-69
: Updatedfsspec
version from2024.3.1
to2024.6.0
as per the PR summary.
79-79
: Updatedimagecodecs
to version2024.6.1
aligns with specific package updates.
104-104
: Updated version foripython
from8.24.0
to8.25.0
checks out with the summary.
120-120
: Updatedjupyter-client
version from8.24.0
to8.25.0
aligns with the updates listed.
141-141
: Updatedlxml
version from5.2.1
to5.2.2
is correctly updated. Note the duplication error flagged by LanguageTool seems to be a false positive.Also applies to: 141-141
147-147
: Updatedmagicgui
from0.8.2
to0.8.3
. Note the duplication error flagged by LanguageTool seems to be a false positive.Also applies to: 147-147
205-205
: Updatedoiffile
to2024.5.24
matches the specific package updates.
207-207
: Updatedopenpyxl
from3.1.2
to3.1.4
is accurately reflected.
209-209
: Updatedpackaging
from24.0
to24.1
is consistent with the updates listed.
276-276
: Updatedpydantic
to1.10.16
aligns with the constraints specified for Pydantic version 1.
295-295
: Updatedpyinstaller
to6.8.0
is correctly implemented.
297-297
: Updatedpyinstaller-hooks-contrib
to2024.7
aligns with the updates.
316-316
: Updatedpyqt6
to6.7.0
is correctly reflected.
317-317
: Updatedpyqt6-qt6
to6.7.1
matches the updates listed.
335-335
: Updatedpytest
from8.2.0
to8.2.2
is correctly updated.
395-395
: Updatedscipy
from1.13.0
to1.13.1
is accurately reflected.
402-402
: Updatedsentry-sdk
from2.1.1
to2.5.1
is correctly implemented.
406-406
: Updatedsetuptools
from69.5.1
to70.0.0
matches PR objectives.
444-444
: Updatedsuperqt
to0.6.7
aligns with the updates listed.
449-449
: Updatedsympy
to1.12.1
matches the specific package updates.
453-453
: Updatedtifffile
from2024.5.3
to2024.5.22
is correctly reflected.
474-474
: Updatedtornado
from6.4
to6.4.1
is accurately updated.
493-493
: Updatedtyping-extensions
from4.11.0
to4.12.2
is consistent with the updates listed.
505-505
: Updatedurllib3
from2.1.0
to2.2.2
aligns with the updates listed.
509-509
: Updatedvispy
from0.14.2
to0.14.3
is correctly implemented.requirements/constraints_py3.9.txt (20)
71-71
: The update offsspec
to2024.6.0
should be tested to ensure that file handling operations, especially in distributed environments, are not adversely affected.
7-7
: Ensure that the update ofannotated-types
to0.7.0
is tested for compatibility with other dependencies that rely on it.
106-111
: The update ofipython
to8.18.1
might 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==8.18.1
will 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 oflxml
to5.2.2
should 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 thatmagicgui
version0.8.3
integrates well withnapari
, ensuring that GUI elements are rendered correctly and interactively.
43-44
: Check the coverage reports to ensure that the updatedcoverage
library version7.5.3
accurately reflects the test coverage, especially in modules heavily reliant on dynamic features of Python.
28-28
: Confirm that the update ofcertifi
to2024.6.2
does not affect the HTTPS requests within the application, especially those that might depend on specific certificate chains.
81-82
: Confirm that the update ofimagecodecs
to2024.6.1
does not break image processing workflows, particularly those involving uncommon or complex image formats.
54-54
: Sincedefusedxml
is 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
defusedxml
is 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.
defusedxml
is imported and used inpackage/PartSegImage/tifffile_fixes.py
andpackage/PartSegImage/image_reader.py
.- There are no instances of XML parsing using
xml.etree.ElementTree
,xml.dom.minidom
, orlxml
withoutdefusedxml
.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 ofdask
to2024.6.0
does not introduce performance regressions in parallel computation tasks.
513-515
: Confirm that the update ofvispy
to0.14.3
maintains all visualizations at the expected performance levels, particularly those involving complex 3D rendering.
207-211
: Ensure that the update ofopenpyxl
to3.1.4
does not affect the reading and writing of Excel files, particularly those with complex formatting or large datasets.
405-409
: Ensure that the update ofsentry-sdk
to2.5.1
continues to effectively capture and report errors without impacting application performance.Verification successful
The update of
sentry-sdk
to version2.5.1
appears to be well-integrated into the codebase. Thesentry_sdk.init
configuration 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-model
version0.2.7
integrates smoothly withnapari
, which depends on it.
122-122
: Ensure that the update ofjupyter-client
to8.6.2
supports all existing integrations with Jupyter notebooks and does not introduce any compatibility issues with notebook extensions.
182-186
: The update ofnumpy
to1.26.4
should be tested for numerical stability and performance in all computational modules, especially those involving complex numerical computations.
456-458
: Verify that the update oftifffile
to2024.5.22
does not affect the handling and processing of TIFF images, especially in modules that perform image analysis or transformations.
213-213
: The update ofpackaging
to24.1
should be verified to ensure that version parsing and dependency resolution continue to function correctly across the application.
229-231
: Verify that the update ofpandas
to2.2.2
handles all data manipulation tasks correctly, especially those involving time series data or complex data transformations.
382-384
: Confirm that the update ofrequests
to2.32.3
does 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 updatedcoverage
library version7.5.3
accurately reflects the test coverage, especially in modules heavily reliant on dynamic features of Python.
121-121
: Ensure that the update ofjupyter-client
to8.6.2
supports 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_client
in the codebase. This suggests that updatingjupyter-client
to 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-model
to0.2.7
is tested for compatibility with other dependencies that rely on it, especially in the context of its integration withnapari
.
84-85
: Confirm that the update ofimagecodecs
to2024.6.1
does not break image processing workflows, particularly those involving uncommon or complex image formats.
27-27
: Confirm that the update ofcertifi
to2024.6.2
does not affect the HTTPS requests within the application, especially those that might depend on specific certificate chains.
53-53
: Sincedefusedxml
is 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
defusedxml
library is correctly imported in the codebase to handle XML parsing securely:
package/PartSegImage/tifffile_fixes.py
package/PartSegImage/image_reader.py
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($$$)'Length of output: 69
Script:
#!/bin/bash # Description: Verify usage of defusedxml in XML parsing, covering more methods from xml.etree.ElementTree and other XML libraries. # Search for xml.etree.ElementTree usage ast-grep --lang python --pattern $'xml.etree.ElementTree.fromstring($$$)' 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 ofopenpyxl
to3.1.4
does not affect the reading and writing of Excel files, particularly those with complex formatting or large datasets.
382-382
: Confirm that the update ofrequests
to2.32.3
does not introduce any issues with HTTP communication, particularly in parts of the application dealing with external API calls.
71-71
: The update offsspec
to2024.6.0
should be tested to ensure that file handling operations, especially in distributed environments, are not adversely affected.
512-514
: Confirm that the update ofvispy
to0.14.3
maintains all visualizations at the expected performance levels, particularly those involving complex 3D rendering.
404-406
: Ensure that the update ofsentry-sdk
to2.5.1
continues to effectively capture and report errors without impacting application performance.
108-110
: The update ofipython
to8.25.0
might 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 ofpandas
to2.2.2
handles all data manipulation tasks correctly, especially those involving time series data or complex data transformations.
454-456
: Verify that the update oftifffile
to2024.5.22
does not affect the handling and processing of TIFF images, especially in modules that perform image analysis or transformations.
142-145
: The update oflxml
to5.2.2
should 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 ofdask
to2024.6.0
does not introduce performance regressions in parallel computation tasks.
212-212
: The update ofpackaging
to24.1
should be verified to ensure that version parsing and dependency resolution continue to function correctly across the application.
148-151
: Confirm thatmagicgui
version0.8.3
integrates well withnapari
, ensuring that GUI elements are rendered correctly and interactively.
181-185
: The update ofnumpy
to1.26.4
should 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-types
to0.7.0
aligns with the PR objectives.
9-9
: Updated version forapp-model
to0.2.7
aligns with the PR objectives.
29-29
: Updated version forcertifi
to2024.6.2
aligns with the PR objectives.
44-45
: Updated version forcoverage
to7.5.3
aligns with the PR objectives.
48-48
: Updated version fordask
to2024.6.0
aligns with the PR objectives.
55-55
: Addition ofdefusedxml
as a new dependency is correctly documented and aligns with the PR objectives.
76-76
: Updated version forfsspec
to2024.6.0
aligns with the PR objectives.
86-87
: Updated version forimagecodecs
to2024.6.1
aligns with the PR objectives.
112-112
: Updated version foripython
to8.25.0
aligns with the PR objectives.
123-123
: Updated version forjupyter-client
to8.6.2
aligns with the PR objectives.
150-153
: Updated version formagicgui
to0.8.3
aligns with the PR objectives.
185-187
: Updated version fornpe2
to0.7.5
aligns with the PR objectives.
208-210
: Updated version foroiffile
to2024.5.24
aligns with the PR objectives.
210-212
: Updated version foropenpyxl
to3.1.4
aligns with the PR objectives.
212-214
: Updated version forpackaging
to24.1
aligns with the PR objectives.
238-240
: Updated version forpartsegcore-compiled-backend
to0.15.6
aligns with the PR objectives.
250-250
: Updated version forplatformdirs
to4.2.2
aligns with the PR objectives.
258-260
: Updated version forpooch
to1.8.2
aligns with the PR objectives.
279-281
: Updated version forpydantic
to2.7.4
aligns with the PR objectives.
288-288
: Updated version forpydantic-core
to2.18.4
aligns with the PR objectives.
299-301
: Updated version forpyinstaller
to6.8.0
andpyinstaller-hooks-contrib
to2024.7
align with the PR objectives.
306-306
: Updated version forpyopengl-accelerate
to3.1.7
aligns with the PR objectives.
310-312
: Updated version forpyqt5
to5.15.10
aligns with the PR objectives.
320-321
: Updated version forpyqt6
to6.7.0
andpyqt6-qt6
to6.7.1
align with the PR objectives.
329-331
: Updated version forpyside6
to6.7.1
aligns with the PR objectives.
339-341
: Updated version forpytest
to8.2.2
aligns with the PR objectives.
345-347
: Updated version forpytest-qt
to4.4.0
andpytest-timeout
to2.3.1
align with the PR objectives.
383-385
: Updated version forrequests
to2.32.3
aligns with the PR objectives.
399-401
: Updated version forscikit-image
to0.23.2
aligns with the PR objectives.
402-403
: Updated version forscipy
to1.13.1
aligns with the PR objectives.
406-409
: Updated version forsentry-sdk
to2.5.1
aligns with the PR objectives.
410-410
: Updated version forsetuptools
to70.0.0
aligns with the PR objectives.
418-418
: Updated version forshiboken6
to6.7.1
aligns with the PR objectives.
424-424
: Updated version forsimpleitk
to2.3.1
aligns with the PR objectives.
448-450
: Updated version forsuperqt
to0.6.7
aligns with the PR objectives.
453-454
: Updated version forsympy
to1.12.1
aligns with the PR objectives.
457-459
: Updated version fortifffile
to2024.5.22
aligns with the PR objectives.
478-478
: Updated version fortornado
to6.4.1
aligns with the PR objectives.
485-485
: Addition oftraceback-with-variables
as a new dependency is correctly documented and aligns with the PR objectives.
497-501
: Updated version fortyping-extensions
to4.12.2
aligns with the PR objectives.
512-512
: Updated version forurllib3
to2.2.2
aligns with the PR objectives.
516-518
: Updated version forvispy
to0.14.3
aligns with the PR objectives.
526-528
: Addition ofxlsxwriter
as a new dependency is correctly documented and aligns with the PR objectives.
529-529
: Updated version forzipp
to3.19.2
aligns with the PR objectives.requirements/constraints_py3.8.txt (18)
7-7
: Updatedannotated-types
from0.6.0
to0.7.0
. Ensure compatibility with dependent packages.
30-30
: Updatedcertifi
package to2024.6.2
. This is crucial for maintaining up-to-date SSL certificates.
71-71
: Updatedfsspec
to2024.6.0
. This update could impact file handling operations, especially in distributed computations.
217-217
: Updatedpackaging
to24.1
. This library is central to handling version constraints and dependencies.
45-46
: Updatedcoverage
to7.5.3
. Check integration with CI/CD workflows where coverage metrics are utilized.Verification successful
The search results indicate that
coverage
is indeed used within the CI/CD workflows, but there are no explicit version locks for it. Therefore, the update tocoverage==7.5.3
should not cause any issues with the CI/CD workflows.
- The
coverage
tool 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
: Updatedsympy
to1.12.1
. This affects symbolic mathematics capabilities. Verify that all symbolic computations are accurate.
154-157
: Updatedmagicgui
to0.8.3
. This affects GUI components, particularly those integrated withnapari
. Confirm GUI stability.
490-490
: Updatedtornado
to6.4.1
. This affects asynchronous operations. Verify that all asynchronous modules are functioning correctly.
348-350
: Updatedpytest
to8.2.2
. Ensure that all unit tests pass with the new version, especially those relying on advanced pytest features.
215-216
: Updatedopenpyxl
to3.1.4
. This affects Excel file handling. Test all functionalities that involve Excel processing.
82-82
: Updatedimagecodecs
to2024.6.1
. This is a critical dependency for image handling; ensure all image processing functions are tested.
420-423
: Updatedsentry-sdk
to2.5.1
. 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-model
from0.2.6
to0.2.7
. Verify that the new version integrates smoothly withnapari
.
288-290
: Updatedpydantic
to2.7.4
. This is crucial for data validation across the application. Verify all data models conform to the new schema validations.
396-398
: Updatedrequests
to2.32.3
. This is critical for all network operations. Verify network operations, especially in modules that heavily depend on external APIs.
308-310
: Updatedpyinstaller
to6.8.0
andpyinstaller-hooks-contrib
to2024.7
. These updates are crucial for application packaging. Ensure the application builds and runs correctly.
472-472
: Updatedtifffile
to2023.7.10
. This update is critical for TIFF file handling. Ensure all TIFF file operations are tested.
416-419
: Updatedscipy
to1.10.1
. 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