-
Notifications
You must be signed in to change notification settings - Fork 11
test: [Automatic] Constraints upgrades: imagecodecs
, ipython
, pydantic
, sentry-sdk
, superqt
, tifffile
#1255
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Conversation
Reviewer's Guide by SourceryThis pull request updates constraint files for various Python versions and configurations, upgrading packages like No diagrams generated as the changes look simple and do not need a visual representation. File-Level Changes
Tips and commandsInteracting with Sourcery
Customizing Your ExperienceAccess your dashboard to:
Getting Help
|
WalkthroughThis pull request updates the version numbers of several dependencies across multiple requirements files for different Python versions. The updates cover files for standard, pydantic, and documentation configurations. Most files receive updates for packages such as Changes
Possibly related PRs
Poem
Tip ⚡💬 Agentic Chat (Pro Plan, General Availability)
🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Hey @Czaki - I've reviewed your changes and they look great!
Here's what I looked at during the review
- 🟢 General issues: all looks good
- 🟢 Security: all looks good
- 🟢 Testing: all looks good
- 🟢 Complexity: all looks good
- 🟢 Documentation: all looks good
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
c37f640
to
5767104
Compare
sentry-sdk
, superqt
imagecodecs
, pydantic
, sentry-sdk
, superqt
, tifffile
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Actionable comments posted: 0
🧹 Nitpick comments (8)
requirements/constraints_py3.9.txt (2)
43-527
: Dependency Version Bumps are Consistent
The updated versions for key packages such as “coverage”, “fsspec”, “iniconfig”, “platformdirs”, “pyinstaller-hooks-contrib”, “imagecodecs”, “sentry-sdk”, “setuptools”, “superqt”, “typing-extensions”, “tzdata”, and the addition of “typing-inspection==0.4.0” are in line with the coordinated maintenance update.🧰 Tools
🪛 LanguageTool
[duplication] ~150-~150: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.1 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~287-~287: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~423-~423: Possible typo: you repeated a word.
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==7.4.7 # via numpydoc sphinxcontrib...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
504-504
: Duplicate 'typing-inspection' Entry Detected
Static analysis indicates that the dependency “typing-inspection==0.4.0” appears twice (e.g. “typing-inspection typing-inspection==0.4.0”) near the end of the file. Please review and remove any redundant occurrence to avoid confusion.🧰 Tools
🪛 LanguageTool
[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11.txt (2)
43-349
: Upgraded Dependency Versions are Correct
The file updates several packages (for example, “dask” to 2025.3.0, “imagecodecs” to 2025.3.30, “iniconfig” to 2.1.0, “pydantic” to 2.11.1, “pydantic-core” to 2.33.0, etc.) in a manner consistent with other constraints files. These changes support compatibility across Python 3.11 environments.🧰 Tools
🪛 LanguageTool
[duplication] ~142-~142: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.1 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~279-~279: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...(ENGLISH_WORD_REPEAT_RULE)
490-490
: Possible Duplicate Text for 'typing-inspection'
A duplicate mention of “typing-inspection==0.4.0” appears to be present in the tail of the file. Please double-check if one instance should be removed.🧰 Tools
🪛 LanguageTool
[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12_docs.txt (1)
440-442
: Recheck Duplicate 'typing-inspection' Entry
Static analysis flagged a duplicate entry for “typing-inspection==0.4.0.” Please inspect these lines (around ~441) in the autogenerated file and remove any unintentional repetition.🧰 Tools
🪛 LanguageTool
[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.10.txt (1)
490-492
: Duplicate 'typing-inspection' Warning
A repeated occurrence of “typing-inspection==0.4.0” has been observed. Please verify whether the duplicate text is needed or if one instance should be removed.requirements/constraints_py3.12.txt (2)
43-508
: Comprehensive Version Bumps Across Dependencies
The file shows updates for many dependencies—including the important ones like “pydantic”, “pydantic-core”, “pyinstaller-hooks-contrib”, “pyside6” (now upgraded to 6.8.3), “tifffile”, and more—which are now in line with the latest available releases. Overall, the changes are consistent across the different constraint files.🧰 Tools
🪛 LanguageTool
[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.1 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~277-~277: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~414-~414: Possible typo: you repeated a word.
Context: ...teutil snowballstemmer==2.2.0 # via sphinx sphinx==8.2.3 # via numpydoc sphinxcontrib...(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
486-488
: Address Duplicate Text for 'typing-inspection'
Static analysis hints at a potential duplicate line for “typing-inspection==0.4.0” (i.e. the word “typing-inspection” appears twice consecutively before the version spec). Please review and remove the redundant text if it is not intentional.🧰 Tools
🪛 LanguageTool
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (9)
requirements/constraints_py3.10.txt
(15 hunks)requirements/constraints_py3.10_pydantic_1.txt
(13 hunks)requirements/constraints_py3.11.txt
(15 hunks)requirements/constraints_py3.11_pydantic_1.txt
(13 hunks)requirements/constraints_py3.12.txt
(16 hunks)requirements/constraints_py3.12_docs.txt
(13 hunks)requirements/constraints_py3.12_pydantic_1.txt
(14 hunks)requirements/constraints_py3.9.txt
(13 hunks)requirements/constraints_py3.9_pydantic_1.txt
(11 hunks)
🚧 Files skipped from review as they are similar to previous changes (4)
- requirements/constraints_py3.11_pydantic_1.txt
- requirements/constraints_py3.9_pydantic_1.txt
- requirements/constraints_py3.10_pydantic_1.txt
- requirements/constraints_py3.12_pydantic_1.txt
🧰 Additional context used
🪛 LanguageTool
requirements/constraints_py3.10.txt
[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11.txt
[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12.txt
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12_docs.txt
[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.9.txt
[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
⏰ Context from checks skipped due to timeout of 300000ms (27)
- GitHub Check: 4DNucleome.PartSeg (Tests_other test windows)
- GitHub Check: 4DNucleome.PartSeg (Tests_other test macos)
- GitHub Check: 4DNucleome.PartSeg (Tests_linux test_linux)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller windows)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos_arm)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos)
- GitHub Check: 4DNucleome.PartSeg (Builds sdist)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller_linux)
- GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
- GitHub Check: Base py3.11 / windows-latest py 3.11 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
- GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
- GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
- GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
- GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
- GitHub Check: Base py3.11 / macos-13 py 3.11 latest PyQt5
- GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
- GitHub Check: Test PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
- GitHub Check: Test PartSeg conda
- GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
- GitHub Check: 4DNucleome.PartSeg (formatting_check check_formating)
- GitHub Check: 4DNucleome.PartSeg (Documentation_check help)
- GitHub Check: 4DNucleome.PartSeg (GetTestData linux)
- GitHub Check: 4DNucleome.PartSeg (Documentation_check Notebook_check)
- GitHub Check: Codacy Static Code Analysis
🔇 Additional comments (2)
requirements/constraints_py3.12_docs.txt (1)
45-72
: Documentation Constraints: Versions Updated Properly
All version bumps (including updates for “dask”, “fsspec”, “imagecodecs”, “platformdirs”, etc.) are updated to their latest releases. This helps ensure the docs build uses the current dependencies.requirements/constraints_py3.10.txt (1)
43-104
: Dependency Updates on Python 3.10 Constraints are Consistent
The version changes (e.g. “coverage” to 7.8.0, “dask” to 2025.3.0, “iniconfig” to 2.1.0, etc.) appear well coordinated with the other Python version constraints.
5767104
to
91123be
Compare
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Actionable comments posted: 0
🧹 Nitpick comments (2)
requirements/constraints_py3.12_docs.txt (1)
440-443
: Remove Duplicate Typing-Inspection EntryStatic analysis indicates that the dependency "typing-inspection==0.4.0" may be declared twice in this file. Please verify this occurrence and remove any duplicate to avoid redundancy.
🧰 Tools
🪛 LanguageTool
[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12.txt (1)
480-488
: Eliminate Duplicate Typing-Inspection DeclarationStatic analysis highlights a potential duplicate occurrence of "typing-inspection==0.4.0". To maintain clarity and avoid redundancy in the constraints file, please confirm this entry and remove any duplicate if present.
🧰 Tools
🪛 LanguageTool
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (9)
requirements/constraints_py3.10.txt
(16 hunks)requirements/constraints_py3.10_pydantic_1.txt
(14 hunks)requirements/constraints_py3.11.txt
(16 hunks)requirements/constraints_py3.11_pydantic_1.txt
(14 hunks)requirements/constraints_py3.12.txt
(17 hunks)requirements/constraints_py3.12_docs.txt
(13 hunks)requirements/constraints_py3.12_pydantic_1.txt
(15 hunks)requirements/constraints_py3.9.txt
(14 hunks)requirements/constraints_py3.9_pydantic_1.txt
(12 hunks)
🚧 Files skipped from review as they are similar to previous changes (4)
- requirements/constraints_py3.9_pydantic_1.txt
- requirements/constraints_py3.11_pydantic_1.txt
- requirements/constraints_py3.10_pydantic_1.txt
- requirements/constraints_py3.12_pydantic_1.txt
🧰 Additional context used
🪛 LanguageTool
requirements/constraints_py3.10.txt
[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11.txt
[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12.txt
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12_docs.txt
[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.9.txt
[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
⏰ Context from checks skipped due to timeout of 300000ms (27)
- GitHub Check: 4DNucleome.PartSeg (Tests_other test windows)
- GitHub Check: 4DNucleome.PartSeg (Tests_other test macos)
- GitHub Check: 4DNucleome.PartSeg (Tests_linux test_linux)
- GitHub Check: 4DNucleome.PartSeg (Builds sdist)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller windows)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos_arm)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller_linux)
- GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
- GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
- GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
- GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
- GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
- GitHub Check: Base py3.11 / macos-13 py 3.11 latest PyQt5
- GitHub Check: Base py3.11 / windows-latest py 3.11 latest PyQt5
- GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
- GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
- GitHub Check: Test PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
- GitHub Check: Test PartSeg conda
- GitHub Check: 4DNucleome.PartSeg (Documentation_check Notebook_check)
- GitHub Check: 4DNucleome.PartSeg (Documentation_check help)
- GitHub Check: 4DNucleome.PartSeg (GetTestData linux)
- GitHub Check: 4DNucleome.PartSeg (formatting_check check_formating)
- GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
- GitHub Check: Codacy Static Code Analysis
🔇 Additional comments (5)
requirements/constraints_py3.12_docs.txt (1)
40-50
: Dependency Version Increments ConsistencyAll updated dependency versions—such as
• dask==2025.3.0,
• fsspec==2025.3.2,
• imagecodecs==2025.3.30,
• pydantic==2.11.2,
• pydantic-core==2.33.1,
• python-dotenv==1.1.0,
• pytz==2025.2,
• pyzmq==26.4.0,
• rich==14.0.0,
• rpds-py==0.24.0,
• sentry-sdk==2.25.1,
• superqt==0.7.3, and
• tifffile==2025.3.30
—have been upgraded in line with our dependency-maintenance objectives. Please double-check that these new versions are fully compatible with the rest of the project.requirements/constraints_py3.9.txt (1)
42-50
: Version Bump Review for Python 3.9 ConstraintsThe file now shows consistent dependency version updates—for example, coverage has been bumped to 7.8.0, fsspec to 2025.3.2, iniconfig to 2.1.0, and lxml to 5.3.2. These adjustments match the coordinated upgrade plan. Please ensure compatibility with other parts of the project.
requirements/constraints_py3.11.txt (1)
41-50
: Dependencies Updates Consistency in Python 3.11The updated versions for dependencies—including dask, fsspec, imagecodecs, pydantic, and others—are accurate and in line with our overall upgrade strategy. Confirm that these increments meet the compatibility requirements for the 3.11 environment.
requirements/constraints_py3.10.txt (1)
1-10
: Coherent Dependency Updates for Python 3.10This file reflects the coordinated version bumps (coverage, dask, fsspec, imagecodecs, iniconfig, etc.) seen across our constraint files. All changes appear coherent with the PR objectives.
requirements/constraints_py3.12.txt (1)
40-50
: Comprehensive Version Upgrade Check for Python 3.12The dependency updates in this file are consistent with our overall strategy. Notably, the upgrades for packages such as pyside6 (from 6.8.2.1 to 6.9.0) and shiboken6 (from 6.8.2.1 to 6.9.0) have been applied alongside the other coordinated version increments. Please verify that these new versions integrate smoothly with your project.
imagecodecs
, pydantic
, sentry-sdk
, superqt
, tifffile
imagecodecs
, ipython
, pydantic
, sentry-sdk
, superqt
, tifffile
91123be
to
cfdda70
Compare
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Actionable comments posted: 0
🧹 Nitpick comments (11)
requirements/constraints_py3.9_pydantic_1.txt (1)
147-147
: Duplication Warning in Comment Block
Static analysis flagged a possible duplicate wording for thelxml-html-clean
dependency (around line 147). Since this file is auto-generated, if this redundancy is expected from the tool, you may ignore it; otherwise, consider cleaning up the duplicated text for clarity.requirements/constraints_py3.12_docs.txt (1)
441-441
: Duplication in Typing-Inspection Entry
A static analysis warning indicates a potential duplicate of “typing-inspection” on or around line 441. If this duplication is an artifact of the auto-generation process, it may be safe to ignore; otherwise, consider removing the redundant text to improve readability.🧰 Tools
🪛 LanguageTool
[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12_pydantic_1.txt (1)
138-138
: Duplicate Wording in Lxml-html-clean Entry
Static analysis notes a possible duplicate word in the comment associated with thelxml-html-clean
dependency around line 138. Review this duplication and remove the extra wording if it isn’t intentional.🧰 Tools
🪛 LanguageTool
[duplication] ~138-~138: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.9.txt (2)
150-150
: Duplication Alert: lxml-html-clean Entry
A static analysis warning shows a possible duplicate in thelxml-html-clean
entry at line 150. Confirm whether this duplication is necessary due to auto-generation or if it should be manually cleaned up.🧰 Tools
🪛 LanguageTool
[duplication] ~150-~150: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
504-504
: Duplication Alert in Typing-Inspection Entry
The entry fortyping-inspection
appears to be duplicated at line 504. Please verify if this is intended by the auto-generation process or if it should be corrected.🧰 Tools
🪛 LanguageTool
[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11.txt (1)
490-490
: Duplication in Typing-Inspection Entry
A static analysis warning indicates a repeated wording in thetyping-inspection
entry on line 490. Please review and adjust if this repetition is not intentional.🧰 Tools
🪛 LanguageTool
[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.10_pydantic_1.txt (1)
141-145
: [Static Analysis] Possible Duplicate Comment for lxml-html-clean
A static analysis warning indicates a duplicate or redundant reference near thelxml-html-clean==0.4.2
declaration. This appears in the commented lines preceding the dependency. Please review whether the repeated phrase is an artifact of auto-generation and if it can be cleaned up for clarity.🧰 Tools
🪛 LanguageTool
[duplication] ~144-~144: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11_pydantic_1.txt (1)
137-141
: [Static Analysis] Possible Duplicate Comment in lxml-html-clean Section
Similar to the previous constraints file, there is a possible duplicate mention in the lxml/html-clean comments. As this file is auto-generated, consider verifying if the duplication can be suppressed or cleaned up to improve readability.🧰 Tools
🪛 LanguageTool
[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.10.txt (2)
146-146
: [Static Analysis] Duplicate Comment in lxml-html-clean Section
Static analysis flagged a possible duplicate in the commentary precedinglxml-html-clean==0.4.2
. Please review to see if this repetition can be tidied up even if it is auto-generated.🧰 Tools
🪛 LanguageTool
[duplication] ~146-~146: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...(ENGLISH_WORD_REPEAT_RULE)
500-500
: [Static Analysis] Duplicate Expression in Typing-Inspection Section
There is a warning about a duplicated phrase near the typing-inspection declaration. It may be a false positive due to auto-generation; please verify and adjust if necessary for clarity.🧰 Tools
🪛 LanguageTool
[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12.txt (1)
486-486
: [Static Analysis] Possible Duplicate Expression in Typing-Inspection Section
A static analysis warning flags a duplicate phrase near the typing-inspection block. Although auto-generated content can be noisy, please review whether this repetition should be addressed to improve clarity.🧰 Tools
🪛 LanguageTool
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (9)
requirements/constraints_py3.10.txt
(16 hunks)requirements/constraints_py3.10_pydantic_1.txt
(14 hunks)requirements/constraints_py3.11.txt
(16 hunks)requirements/constraints_py3.11_pydantic_1.txt
(14 hunks)requirements/constraints_py3.12.txt
(16 hunks)requirements/constraints_py3.12_docs.txt
(14 hunks)requirements/constraints_py3.12_pydantic_1.txt
(14 hunks)requirements/constraints_py3.9.txt
(14 hunks)requirements/constraints_py3.9_pydantic_1.txt
(12 hunks)
🧰 Additional context used
🪛 LanguageTool
requirements/constraints_py3.10.txt
[duplication] ~146-~146: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.10_pydantic_1.txt
[duplication] ~144-~144: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11.txt
[duplication] ~142-~142: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~490-~490: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.11_pydantic_1.txt
[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12.txt
[duplication] ~140-~140: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~486-~486: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12_docs.txt
[duplication] ~441-~441: Possible typo: you repeated a word.
Context: ...g # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12_pydantic_1.txt
[duplication] ~138-~138: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.9.txt
[duplication] ~150-~150: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~504-~504: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....
(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.9_pydantic_1.txt
[duplication] ~148-~148: Possible typo: you repeated a word.
Context: ... # partseg (pyproject.toml) # lxml-html-clean lxml-html-clean==0.4.2 # via lxml magicgui==0.10.0 ...
(ENGLISH_WORD_REPEAT_RULE)
⏰ Context from checks skipped due to timeout of 300000ms (26)
- GitHub Check: 4DNucleome.PartSeg (Tests_other test windows)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller_linux)
- GitHub Check: 4DNucleome.PartSeg (Builds sdist)
- GitHub Check: 4DNucleome.PartSeg (Tests_linux test_linux)
- GitHub Check: 4DNucleome.PartSeg (Tests_other test macos)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller windows)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos_arm)
- GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos)
- GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
- GitHub Check: Base py3.11 / windows-latest py 3.11 latest PyQt5
- GitHu 8000 b Check: Base py3.11 / macos-13 py 3.11 latest PyQt5
- GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
- GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
- GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
- GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
- GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
- GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
- GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
- GitHub Check: Test PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
- GitHub Check: Test PartSeg conda
- GitHub Check: 4DNucleome.PartSeg (Documentation_check help)
- GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
- GitHub Check: 4DNucleome.PartSeg (formatting_check check_formating)
- GitHub Check: 4DNucleome.PartSeg (GetTestData linux)
- GitHub Check: 4DNucleome.PartSeg (Documentation_check Notebook_check)
🔇 Additional comments (37)
requirements/constraints_py3.9_pydantic_1.txt (1)
41-47
: Dependency Version Updates and Consistency Check
All dependency versions (e.g.,coverage==7.8.0
,debugpy==1.8.14
,fsspec==2025.3.2
,iniconfig==2.1.0
) have been updated in accordance with the latest releases. Please verify that these updates do not introduce conflicts with other parts of the dependency graph.Also applies to: 73-92
requirements/constraints_py3.12_docs.txt (1)
45-50
: Dependency Updates and New Additions Verification
The dependency versions have been updated (for example,dask==2025.3.0
,debugpy==1.8.14
,fsspec==2025.3.2
, andimagecodecs==2025.3.30
). Also, note the update ofpython-dotenv
to1.1.0
. These changes look consistent with similar updates in other constraint files. Please double-check that these versions are compatible with your docs build process.Also applies to: 70-82
requirements/constraints_py3.12_pydantic_1.txt (1)
41-47
: Pydantic Constraint File Update Verification
The file correctly updates key dependencies for the Pydantic 1 constraints (e.g.,pydantic==2.11.3
andpydantic-core==2.33.1
). Please ensure these constraints are compatible with downstream use as defined inrequirements/pydantic_1.txt
.Also applies to: 65-75
requirements/constraints_py3.9.txt (1)
41-50
: Python 3.9 Dependency Constraint Updates
The file now reflects up-to-date dependency versions (for instance,coverage==7.8.0
,iniconfig==2.1.0
, andpillow==11.2.1
). These updates appear consistent with similar constraint files. Please just verify that the updated versions work harmoniously within your environment.Also applies to: 73-80, 106-112
requirements/constraints_py3.11.txt (1)
41-50
: Python 3.11 Dependency Constraint Updates
The dependency versions (e.g.,coverage==7.8.0
,dask==2025.3.0
,debugpy==1.8.14
,fsspec==2025.3.2
, and others) have been updated consistently. This supports maintained compatibility across different Python versions. A quick integration test is recommended to ensure no unexpected conflicts arise.Also applies to: 73-80, 95-102
requirements/constraints_py3.10_pydantic_1.txt (6)
41-41
: [Dependency Update] Coverage Version Change
The file updatescoverage
from 7.7.0 to 7.8.0. Please verify that this new version is compatible with our existing tooling and that no unexpected breaking changes are introduced.
45-45
: [Dependency Update] Dask Version Change
dask
has been updated to 2025.3.0. Confirm that any functionality relying on Dask’s APIs remains stable after this update.
47-47
: [Dependency Update] Debugpy Update
The update todebugpy==1.8.14
appears to be routine. Please check that debugging integrations (e.g. with ipykernel) are not adversely affected.
73-73
: [Dependency Update] fsspec Version Update
The new versionfsspec==2025.3.2
is now in use. It’s important to ensure that file system operations in Dask or related data workflows continue to operate correctly.
83-83
: [Dependency Update] imagecodecs Updated
imagecodecs
has been updated to 2025.3.30. Please verify this version provides the required performance and compatibility, especially if image processing bugs were previously reported.
100-100
: [Dependency Update] iniconfig Version Change
The upgrade toiniconfig==2.1.0
seems standard. Confirm that configuration parsing in our tests (and any other tooling using this package) remains correct.requirements/constraints_py3.11_pydantic_1.txt (7)
41-41
: [Dependency Update] Coverage Version Update
The update tocoverage==7.8.0
looks correct. Please double-check compatibility with our test suites and reporting integrations.
45-45
: [Dependency Update] Dask Version Change
dask
is now set to 2025.3.0. Ensure that any parallel or delayed computations relying on Dask are thoroughly tested with this newer release.
47-47
: [Dependency Update] Debugpy Updated
debugpy
has been updated to 1.8.14. Please confirm that remote debugging and breakpoint functionality continue to operate as expected.
70-70
: [Dependency Update] fsspec Version Update
The upgrade tofsspec==2025.3.2
is reflected here too. Verify that file system abstraction layers behave properly with this change.
79-79
: [Dependency Update] imagecodecs Update
imagecodecs
is now updated to 2025.3.30. Please check for any regressions in image I/O functions if they are actively used in our workflows.
94-94
: [Dependency Update] iniconfig Version Change
The new versioniniconfig==2.1.0
is now in place. Verify that our testing and configuration scripts using this library continue to parse configuration files accurately.
101-101
: [Dependency Update] ipython Version Update
ipython
has been updated to 9.1.0. Please review that the interactive shell and any IPython-dependent features (e.g. notebooks and qtconsole) are not disrupted by this change.requirements/constraints_py3.10.txt (10)
43-43
: [Dependency Update] Coverage Version Change
The change tocoverage==7.8.0
is noted. Make sure that the newer version does not alter our coverage thresholds or reporting outputs unexpectedly.
47-47
: [Dependency Update] Dask Update
dask
is updated to 2025.3.0. Confirm that scheduling and task graph optimizations with this release meet our performance expectations.
49-49
: [Dependency Update] Debugpy Version Change
The file now listsdebugpy==1.8.14
. Please review that this update does not break our debugging integrations in development and CI environments.
75-75
: [Dependency Update] fsspec Version Update
The update tofsspec==2025.3.2
should be verified against any custom file-handling logic, especially in our Dask workflows.
85-85
: [Dependency Update] imagecodecs Version Change
imagecodecs
has been updated to 2025.3.30. Please ensure that any image I/O operations in the project function correctly with this change.
102-102
: [Dependency Update] iniconfig Version Change
The update toiniconfig==2.1.0
is applied here. A quick validation for configuration parsing processes might be beneficial.
109-109
: [Dependency Update] ipython Updated
ipython
is now updated to version 8.35.0. Please verify that interactive sessions and any Jupyter integrations operate as expected.
240-240
: [Dependency Update] Pillow Update
The upgrade topillow==11.2.1
is included. Ensure that any image processing pipelines or thumbnail generators continue to work without regression.
247-247
: [Dependency Update] Platformdirs Version Change
platformdirs
is updated to 4.3.7. Verify that any filesystem or platform-specific configurations continue to be resolved correctly.
498-502
: [New Dependency Addition] Typing-Inspection and Related Updates
A new dependencytyping-inspection==0.4.0
has been added along with updates totzdata
andurllib3
. Please confirm that these additions are required for compatibility with the updated Pydantic and that no conflicts arise in environments using dependency pinning.🧰 Tools
🪛 LanguageTool
[duplication] ~500-~500: Possible typo: you repeated a word.
Context: ...h # superqt # typer # typing-inspection typing-inspection==0.4.0 # via pydantic tzdata==2025....(ENGLISH_WORD_REPEAT_RULE)
requirements/constraints_py3.12.txt (9)
43-43
: [Dependency Update] Coverage Update
coverage==7.8.0
is now specified. As with other constraint files, confirm that our coverage collection and reporting remain consistent with this change.
47-47
: [Dependency Update] Dask Version Change
The file updatesdask
to 2025.3.0. Please ensure that task scheduling and distributed computing features work as expected with this new version.
49-49
: [Dependency Update] Debugpy Version Update
Withdebugpy==1.8.14
now included, it is advisable to confirm that all debugging and live inspection features remain operational.
71-71
: [Dependency Update] fsspec Update
The new versionfsspec==2025.3.2
appears here as well. Please test that any file system abstractions used (for example in Dask or other I/O operations) remain fully functional.
81-81
: [Dependency Update] imagecodecs Upgrade
Updated toimagecodecs==2025.3.30
—ensure any image handling routines are validated with the new release.
94-94
: [Dependency Update] iniconfig Version Change
The upgrade toiniconfig==2.1.0
has been applied. A brief verification that our configuration parsers continue to behave normally is recommended.
101-101
: [Dependency Update] ipython Update
ipython==9.1.0
is specified now. Please ensure that any interactive features (e.g. notebooks or qtconsole) are tested against this version.
271-280
: [Dependency Update Group] Pydantic and Related Packages
The updates forpydantic==2.11.3
,pydantic-compat==0.1.2
, andpydantic-core==2.33.1
have been applied. These are critical for type validation and data parsing. It is essential to run a full test suite to ensure that changes in these libraries do not break our data models or API contracts.🧰 Tools
🪛 LanguageTool
[duplication] ~277-~277: Possible typo: you repeated a word.
Context: ...del # napari # npe2 # pydantic-compat pydantic-compat==0.1.2 # via app-model pydantic-cor...(ENGLISH_WORD_REPEAT_RULE)
308-316
: [Dependency Update] PyQt6 and Pyside6 Updates
The updates topyqt6==6.9.0
,pyqt6-qt6==6.9.0
and the Pyside6 packages (includingpyside6==6.9.0
,pyside6-addons==6.9.0
, andpyside6-essentials==6.9.0
) are now present. Verify that these UI framework updates do not introduce regression in our QT-based interfaces.
|
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