test: napari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile
#1183
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WalkthroughThe recent updates include incrementing the version specifications of multiple Python package dependencies across various requirement files. Key upgrades involve Changes
Sequence Diagram(s)sequenceDiagram
participant A as User
participant B as Application
participant C as Dependency Manager
A->>B: Request to run application
B->>C: Check dependencies
C->>C: Update to latest versions
C-->>B: Dependencies updated
B-->>A: Application runs with updated dependencies
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Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
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Files selected for processing (11)
- requirements/constraints_py3.10.txt (6 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (6 hunks)
- requirements/constraints_py3.11.txt (6 hunks)
- requirements/constraints_py3.11_docs.txt (6 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (6 hunks)
- requirements/constraints_py3.12.txt (6 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (6 hunks)
- requirements/constraints_py3.8.txt (5 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (5 hunks)
- requirements/constraints_py3.9.txt (4 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (4 hunks)
Files skipped from review due to trivial changes (8)
- requirements/constraints_py3.10.txt
- requirements/constraints_py3.11.txt
- requirements/constraints_py3.12.txt
- requirements/constraints_py3.12_pydantic_1.txt
- requirements/constraints_py3.8.txt
- requirements/constraints_py3.8_pydantic_1.txt
- requirements/constraints_py3.9.txt
- requirements/constraints_py3.9_pydantic_1.txt
Additional comments not posted (18)
requirements/constraints_py3.11_docs.txt (6)
46-46: Minor update fordask.The update from
2024.8.0to2024.8.1is a minor version change, likely including bug fixes or small improvements. Ensure that all dependencies and integrations withdaskare still functioning as expected.
84-84: Minor update forimageio.The update from
2.35.0to2.35.1is a minor version change, which typically includes bug fixes. Verify that image handling functionalities remain stable.
315-315: Minor update forpyzmq.The update from
26.1.0to26.1.1is a minor version change. Ensure that message queuing functionalities continue to operate smoothly.
373-373: Minor update forsimpleitk.The update from
2.3.1to2.4.0is a minor version change. Check that image processing functionalities usingsimpleitkare unaffected.
447-447: Minor update fortyper.The update from
0.12.3to0.12.4is a minor version change. Verify that command-line interface functionalities usingtyperremain stable.
172-172: Major update fornumpy.The update from
1.26.4to2.1.0is a major version change. This could introduce breaking changes or new features. Ensure that all numerical computations and integrations withnumpyare tested thoroughly.requirements/constraints_py3.11_pydantic_1.txt (6)
46-46: Minor update fordask.The update from
2024.8.0to2024.8.1is a minor version change, likely including bug fixes or small improvements. Ensure that all dependencies and integrations withdaskare still functioning as expected.
82-82: Minor update forimageio.The update from
2.35.0to2.35.1is a minor version change, which typically includes bug fixes. Verify that image handling functionalities remain stable.
339-339: Minor update forpyzmq.The update from
26.1.0to26.1.1is a minor version change. Ensure that message queuing functionalities continue to operate smoothly.
403-403: Minor update forsimpleitk.The update from
2.3.1to2.4.0is a minor version change. Check that image processing functionalities usingsimpleitkare unaffected.
468-468: Minor update fortyper.The update from
0.12.3to0.12.4is a minor version change. Verify that command-line interface functionalities usingtyperremain stable.
178-178: Major update fornumpy.The update from
1.26.4to2.1.0is a major version change. This could introduce breaking changes or new features. Ensure that all numerical computations and integrations withnumpyare tested thoroughly.requirements/constraints_py3.10_pydantic_1.txt (6)
46-46: Minor update fordask.The update from
2024.8.0to2024.8.1is a minor version change, likely including bug fixes or small improvements. Ensure that all dependencies and integrations withdaskare still functioning as expected.
86-86: Minor update forimageio.The update from
2.35.0to2.35.1is a minor version change, which typically includes bug fixes. Verify that image handling functionalities remain stable.
346-346: Minor update forpyzmq.The update from
26.1.0to26.1.1is a minor version change. Ensure that message queuing functionalities continue to operate smoothly.
410-410: Minor update forsimpleitk.The update from
2.3.1to2.4.0is a minor version change. Check that image processing functionalities usingsimpleitkare unaffected.
482-482: Minor update fortyper.The update from
0.12.3to0.12.4is a minor version change. Verify that command-line interface functionalities usingtyperremain stable.
184-184: Major update fornumpy.The update from
1.26.4to2.1.0is a major version change. This could introduce breaking changes or new features. Ensure that all numerical computations and integrations withnumpyare tested thoroughly.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #1183 +/- ##
===========================================
- Coverage 93.09% 93.07% -0.02%
===========================================
Files 209 209
Lines 32895 32897 +2
===========================================
- Hits 30622 30619 -3
- Misses 2273 2278 +5 ☔ View full report in Codecov by Sentry. |
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imageio, numpy, simpleitkimageio, numpy, scipy, simpleitk, tifffile
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Files selected for processing (11)
- requirements/constraints_py3.10.txt (10 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (11 hunks)
- requirements/constraints_py3.11.txt (10 hunks)
- requirements/constraints_py3.11_docs.txt (9 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (11 hunks)
- requirements/constraints_py3.12.txt (9 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (10 hunks)
- requirements/constraints_py3.8.txt (7 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (8 hunks)
- requirements/constraints_py3.9.txt (7 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (8 hunks)
Files skipped from review due to trivial changes (3)
- requirements/constraints_py3.11_docs.txt
- requirements/constraints_py3.12_pydantic_1.txt
- requirements/constraints_py3.8.txt
Files skipped from review as they are similar to previous changes (5)
- requirements/constraints_py3.10.txt
- requirements/constraints_py3.10_pydantic_1.txt
- requirements/constraints_py3.11.txt
- requirements/constraints_py3.11_pydantic_1.txt
- requirements/constraints_py3.12.txt
Additional comments not posted (23)
requirements/constraints_py3.9_pydantic_1.txt (9)
82-82: LGTM!The
idnaversion update from 3.7 to 3.8 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
86-86: LGTM!The
imageioversion update from 2.35.0 to 2.35.1 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
95-95: LGTM!The
importlib-metadataversion update from 8.2.0 to 8.4.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
279-279: LGTM!The
pydanticversion update from 1.10.17 to 1.10.18 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
350-350: LGTM!The
pyzmqversion update from 26.1.0 to 26.2.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
401-401: LGTM!The
setuptoolsversion update from 72.2.0 to 73.0.1 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
414-414: LGTM!The
simpleitkversion update from 2.3.1 to 2.4.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
448-448: LGTM!The
tifffileversion update from 2024.8.10 to 2024.8.24 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
486-486: LGTM!The
typerversion update from 0.12.3 to 0.12.5 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
requirements/constraints_py3.9.txt (8)
84-84: LGTM!The
idnaversion update from 3.7 to 3.8 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
88-88: LGTM!The
imageioversion update from 2.35.0 to 2.35.1 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
97-97: LGTM!The
importlib-metadataversion update from 8.2.0 to 8.4.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
353-353: LGTM!The
pyzmqversion update from 26.1.0 to 26.2.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
404-404: LGTM!The
setuptoolsversion update from 72.2.0 to 73.0.1 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
417-417: LGTM!The
simpleitkversion update from 2.3.1 to 2.4.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
451-451: LGTM!The
tifffileversion update from 2024.8.10 to 2024.8.24 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
489-489: LGTM!The
typerversion update from 0.12.3 to 0.12.5 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
requirements/constraints_py3.8_pydantic_1.txt (6)
77-77: LGTM!The
idnaversion update from 3.7 to 3.8 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
81-81: LGTM!The
imageioversion update from 2.35.0 to 2.35.1 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
90-90: LGTM!The
importlib-metadataversion update from 8.2.0 to 8.4.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
98-98: LGTM!The
importlib-resourcesversion update from 6.4.0 to 6.4.4 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
286-286: LGTM!The
pydanticversion update from 1.10.17 to 1.10.18 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
358-358: LGTM!The
pyzmqversion update from 26.1.0 to 26.2.0 is a minor update, likely involving bug fixes or minor improvements.The code changes are approved.
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imageio, numpy, scipy, simpleitk, tifffileimageio, ipython, napari, numpy, qtconsole, scipy, simpleitk, tifffile
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Files selected for processing (11)
- requirements/constraints_py3.10.txt (17 hunks)
- requirements/constraints_py3.10_pydantic_1.txt (18 hunks)
- requirements/constraints_py3.11.txt (17 hunks)
- requirements/constraints_py3.11_docs.txt (16 hunks)
- requirements/constraints_py3.11_pydantic_1.txt (18 hunks)
- requirements/constraints_py3.12.txt (15 hunks)
- requirements/constraints_py3.12_pydantic_1.txt (16 hunks)
- requirements/constraints_py3.8.txt (12 hunks)
- requirements/constraints_py3.8_pydantic_1.txt (13 hunks)
- requirements/constraints_py3.9.txt (13 hunks)
- requirements/constraints_py3.9_pydantic_1.txt (14 hunks)
Files skipped from review as they are similar to previous changes (7)
- requirements/constraints_py3.10.txt
- requirements/constraints_py3.11.txt
- requirements/constraints_py3.11_pydantic_1.txt
- requirements/constraints_py3.12.txt
- requirements/constraints_py3.8.txt
- requirements/constraints_py3.8_pydantic_1.txt
- requirements/constraints_py3.9_pydantic_1.txt
Additional comments not posted (77)
requirements/constraints_py3.11_docs.txt (19)
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29-33: LGTM: certifi update approvedThe update of certifi from 2024.7.4 to 2024.8.30 is a minor version change, likely containing security fixes or small improvements. This update is beneficial for maintaining up-to-date security certificates.
46-48: LGTM: dask update approvedThe update of dask from 2024.8.0 to 2024.8.2 is a patch version change, likely containing bug fixes or minor improvements. This update should enhance the stability of the dask library used in the project.
80-82: LGTM: idna update approvedThe update of idna from 3.7 to 3.8 is a minor version change, likely containing improvements or bug fixes. This update should enhance the functionality of the idna library used in the project.
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84-90: LGTM: imageio update approvedThe update of imageio from 2.35.0 to 2.35.1 is a patch version change, likely containing bug fixes or minor improvements. This update should enhance the stability of the imageio library used in the project.
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102-106: LGTM: ipython update approvedThe update of ipython from 8.26.0 to 8.27.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial for development and debugging purposes. It's worth checking the changelog for any new features that could enhance the development experience.
315-319: LGTM: pyzmq update approvedThe update of pyzmq from 26.1.0 to 26.2.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial for ZeroMQ functionality in the project. It's worth checking the changelog for any new features or improvements that could be utilized.
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321-329: LGTM: qtconsole update approvedThe update of qtconsole from 5.5.2 to 5.6.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial for the Qt console functionality in the project. It's recommended to check the changelog for any new features or improvements that could enhance the user experience.
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354-359: LGTM: scipy update approvedThe update of scipy from 1.14.0 to 1.14.1 is a patch version change, likely containing bug fixes or minor improvements. This update should enhance the stability and performance of the scipy library used in the project.
388-389: LGTM: sphinx-autodoc-typehints update approvedThe update of sphinx-autodoc-typehints from 2.2.3 to 2.3.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial for documentation generation. It's worth checking the changelog for any new features that could improve the project's documentation, especially regarding type hints.
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446-458: LGTM: typer update approvedThe update of typer from 0.12.3 to 0.12.5 is a patch version change, likely containing bug fixes or minor improvements. This update should enhance the stability of the typer library used in the project for command-line interface functionality.
Line range hint
480-482: LGTM: zipp update approvedThe update of zipp from 3.20.0 to 3.20.1 is a patch version change, likely containing bug fixes or minor improvements. This update should enhance the stability of the zipp library used in the project for working with Python zip files and import-related functionality.
93-94: LGTM: importlib-metadata update approvedThe update of importlib-metadata from 8.2.0 to 8.4.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial, but it's worth checking the changelog for any new features that could be utilized in the project.
Verification successful
No direct usage of
importlib-metadatafoundThe
importlib-metadatapackage is not directly imported in the codebase outside of test files. This suggests that the update from version 8.2.0 to 8.4.0 is unlikely to have a direct impact. However, since it is listed as a dependency viadask, it is advisable to check ifdaskor any other dependencies might be affected by this update.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any usage of the importlib-metadata package and potential impacts of the update. rg --type python -g '!test_*' 'import importlib_metadata' -A 5Length of output: 95
Script:
#!/bin/bash # Description: Check for any usage of the importlib-metadata package and potential impacts of the update. rg --type py -g '!test_*' 'import importlib_metadata' -A 5Length of output: 60
70-71: LGTM: freetype-py update approvedThe update of freetype-py from 2.4.0 to 2.5.1 is a minor version change with a patch, which may introduce new features and bug fixes. This update is likely beneficial, but it's important to verify that it doesn't introduce any breaking changes that could affect the project.
344-347: LGTM: rich update approvedThe update of rich from 13.7.1 to 13.8.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial for enhanced console output formatting. It's worth checking the changelog for any new features that could improve the project's console output or logging capabilities.
Verification successful
No direct usage of
richfoundThe search did not reveal any direct imports of the
richpackage in the non-test Python files. This suggests that the update from version 13.7.1 to 13.8.0 is unlikely to have a direct impact on the codebase. However, it may still be used indirectly through other dependencies. The update appears safe.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any usage of the rich package and potential impacts of the update. rg --type python -g '!test_*' 'from rich import' -A 5Length of output: 86
Script:
#!/bin/bash # Description: Check for any usage of the rich package and potential impacts of the update. rg --type py -g '!test_*' 'from rich import' -A 5Length of output: 51
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172-189: Caution: Major numpy version updateThe update of numpy from 1.26.4 to 2.1.0 is a major version change, which may introduce breaking changes and new features. This update could potentially impact various parts of the project that rely on numpy.
Please ensure thorough testing is performed, especially for numpy-dependent functionalities. Review the numpy 2.0 and 2.1 release notes for any breaking changes or deprecations that might affect the project.
It's crucial to verify that all numpy-dependent code in the project is compatible with this new major version.
Verification successful
Caution: Major numpy version update
The update of numpy from 1.26.4 to 2.1.0 is a major version change, which may introduce breaking changes and new features. Given the extensive usage of numpy across the project, this update could potentially impact various parts of the project that rely on numpy.
- Please ensure thorough testing is performed, especially for numpy-dependent functionalities.
- Review the numpy 2.0 and 2.1 release notes for any breaking changes or deprecations that might affect the project.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for numpy usage and potential impacts of the major version update. rg --type python -g '!test_*' 'import numpy' -A 5Length of output: 82
Script:
#!/bin/bash # Description: Check for numpy usage and potential impacts of the major version update. rg --type py -g '!test_*' 'import numpy' -A 5Length of output: 29263
62-63: LGTM: executing update approvedThe update of executing from 2.0.1 to 2.1.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial, but it's worth checking the changelog for any new features that could be utilized in the project.
Verification successful
No direct usage of the
executingpackage foundThe search did not find any direct imports of the
executingpackage in the non-test Python files. This suggests that the package might not be used directly in the codebase. However, it could still be used indirectly through another dependency. Given the minor version update from 2.0.1 to 2.1.0, the risk of breaking changes is low, but it is advisable to check the changelog for any new features or changes that might be relevant.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any usage of the executing package and potential impacts of the update. rg --type python -g '!test_*' 'import executing' -A 5Length of output: 86
Script:
#!/bin/bash # Description: Check for any usage of the executing package and potential impacts of the update. rg --type py -g '!test_*' 'import executing' -A 5Length of output: 51
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154-158: LGTM: napari update approvedThe update of napari from 0.5.2 to 0.5.3 is a patch version change, likely containing bug fixes or minor improvements. This update should enhance the stability of the napari library used in the project. It's recommended to check the changelog for any specific bug fixes that might be relevant to your use case.
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1-482: Summary of package updatesThis update includes various minor and patch version updates for multiple packages, which should improve stability and potentially add new features to the project. Most updates are straightforward and should not cause any issues.
However, special attention should be given to the following update:
- numpy: Updated from 1.26.4 to 2.1.0 (major version change)
Given the major version update of numpy, it's crucial to thoroughly test all numpy-dependent functionalities in the project. Review the numpy 2.0 and 2.1 release notes for any breaking changes or deprecations that might affect the project.
Consider running the project's test suite with extra attention to numpy-related tests. If there are no dedicated numpy tests, it may be worthwhile to add some to ensure compatibility with the new major version.
372-373: LGTM: simpleitk update approvedThe update of simpleitk from 2.3.1 to 2.4.0 is a minor version change, which may introduce new features or improvements. This update is likely beneficial for image processing functionality in the project. It's recommended to check the changelog for any new features or improvements that could enhance the project's image processing capabilities.
requirements/constraints_py3.12_pydantic_1.txt (20)
27-30: Approved: certifi update to 2024.8.30This minor version update for certifi likely includes important security fixes or updates to the certificate bundle.
Please verify if there are any significant security-related changes in this update by checking the package's changelog or release notes.
46-48: Approved: dask update to 2024.8.2This patch version update for dask likely includes bug fixes or minor improvements.
60-62: Approved: executing update to 2.1.0This minor version update for executing may include new features or improvements.
Please check the package's changelog for any new features or potential breaking changes that might affect the project.
68-70: Approved with caution: freetype-py update to 2.5.1This is a more significant version update for freetype-py, which may include new features, improvements, or potential breaking changes.
Please thoroughly test font rendering functionality in the project to ensure compatibility with this new version. Check the package's changelog for any breaking changes that might require code adjustments.
78-80: Approved: idna update to 3.8This minor version update for idna likely includes bug fixes or minor improvements.
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82-88: Approved: imageio update to 2.35.1This patch version update for imageio likely includes bug fixes or minor improvements.
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100-105: Approved: ipython update to 8.27.0This minor version update for ipython may include new features, improvements, or bug fixes.
Please check the ipython changelog for any new features or improvements that could benefit the project, especially in development and debugging workflows.
138-140: Approved: lxml-html-clean update to 0.2.2This patch version update for lxml-html-clean likely includes bug fixes or minor improvements.
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158-162: Approved: napari update to 0.5.3This patch version update for napari likely includes bug fixes or minor improvements.
Please verify that the image viewing functionality in the project works as expected with this new version, especially for any custom integrations or plugins using napari.
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176-194: Approved with caution: numpy update to 2.1.0This is a major version update for numpy, which likely includes significant new features, improvements, and potential breaking changes.
Please take the following actions:
- Thoroughly review the numpy 2.1.0 changelog for breaking changes and new features.
- Conduct comprehensive testing of all numpy-dependent functionality in the project.
- Update any code that may be affected by breaking changes.
- Consider leveraging new features or optimizations introduced in this version to improve performance or functionality.
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267-276: Approved: pydantic update to 1.10.18This patch version update for pydantic likely includes bug fixes or minor improvements.
336-340: Approved: pyzmq update to 26.2.0This minor version update for pyzmq may include new features, improvements, or bug fixes.
Please verify that any ZeroMQ-related functionality in the project, especially in areas involving inter-process communication or networking, works as expected with this new version.
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342-353: Approved: qtconsole update to 5.6.0This minor version update for qtconsole may include new features, improvements, or bug fixes.
Please check the qtconsole changelog for any new features or improvements that could enhance the console functionality in the project. Ensure that any custom integrations with qtconsole continue to work as expected.
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365-369: Approved: rich update to 13.8.0This minor version update for rich may include new features, improvements, or bug fixes.
Please review the rich changelog for any new formatting options or features that could enhance the terminal output in the project. Consider updating any custom rich formatting to leverage new capabilities if applicable.
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377-382: Approved: scipy update to 1.14.1This patch version update for scipy likely includes bug fixes or minor improvements.
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386-390: Approved with caution: setuptools update to 74.0.0This major version update for setuptools may include significant changes, new features, or potential breaking changes.
Please take the following actions:
- Review the setuptools changelog for any breaking changes or new features that might affect the project's packaging process.
- Verify that the project's packaging and distribution processes still work as expected with this new version.
- Update any packaging scripts or configurations if necessary.
399-401: Approved: simpleitk update to 2.4.0This minor version update for simpleitk may include new features, improvements, or bug fixes.
Please verify that all image analysis functionality using simpleitk in the project works as expected with this new version. Check the simpleitk changelog for any new features or improvements that could benefit the project's image processing capabilities.
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433-440: Approved: tifffile update to 2024.8.30This patch version update for tifffile likely includes bug fixes or minor improvements.
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464-474: Approved: typer update to 0.12.5This patch version update for typer likely includes bug fixes or minor improvements.
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1-494: Summary of dependency updatesThis update includes various package version upgrades, mostly minor and patch versions, with a few significant updates:
Major version updates:
- numpy (1.26.4 to 2.1.0)
- setuptools (72.2.0 to 74.0.0)
Notable minor version updates:
- freetype-py (2.4.0 to 2.5.1)
- ipython (8.26.0 to 8.27.0)
- simpleitk (2.3.1 to 2.4.0)
Several patch version updates for various packages.
General recommendations:
- Thoroughly test the project, especially functionality related to numpy and setuptools, as these have major version updates.
- Review changelogs for all updated packages, particularly those with minor version changes, to leverage new features and ensure compatibility.
- Update any affected documentation or requirements files.
- Consider running the project's test suite with these new versions to catch any potential issues early.
- Monitor the application's performance after these updates, especially for any numpy-intensive operations.
requirements/constraints_py3.10_pydantic_1.txt (22)
27-30: LGTM: certifi update approvedThe update of certifi from 2024.7.4 to 2024.8.30 is a minor version change, likely containing security fixes or small improvements.
46-47: LGTM: dask update approvedThe update of dask from 2024.8.0 to 2024.8.2 is a patch version change, likely containing bug fixes or minor improvements.
82-83: LGTM: idna update approvedThe update of idna from 3.7 to 3.8 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
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86-91: LGTM: imageio update approvedThe update of imageio from 2.35.0 to 2.35.1 is a patch version change, likely containing bug fixes or minor improvements.
146-147: LGTM: lxml-html-clean update approvedThe update of lxml-html-clean from 0.2.0 to 0.2.2 is a patch version change, likely containing bug fixes or minor improvements.
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166-170: LGTM: napari update approvedThe update of napari from 0.5.2 to 0.5.3 is a patch version change, likely containing bug fixes or minor improvements.
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275-282: LGTM: pydantic update approvedThe update of pydantic from 1.10.17 to 1.10.18 is a patch version change, likely containing bug fixes or minor improvements.
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387-391: LGTM: scipy update approvedThe update of scipy from 1.14.0 to 1.14.1 is a patch version change, likely containing bug fixes or minor improvements.
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443-449: LGTM: tifffile update approvedThe update of tifffile from 2024.8.10 to 2024.8.30 is a patch version change, likely containing bug fixes or minor improvements.
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481-493: LGTM: typer update approvedThe update of typer from 0.12.3 to 0.12.5 is a patch version change, likely containing bug fixes or minor improvements.
514-515: LGTM: zipp update approvedThe update of zipp from 3.20.0 to 3.20.1 is a patch version change, likely containing bug fixes or minor improvements.
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1-515: Summary of package updatesAll package updates have been reviewed and approved. Most updates are minor or patch versions, which should not introduce breaking changes. However, special attention should be given to the following update:
- numpy: Updated from 1.26.4 to 2.1.0 (major version update)
Please ensure that:
- All parts of the project using numpy are thoroughly tested with the new version.
- The changelog for numpy 2.1.0 is carefully reviewed for any breaking changes or new features that may impact the project.
- Any necessary code adjustments are made to accommodate the numpy update.
For all other package updates, it's recommended to review their respective changelogs for any new features or improvements that could benefit the project.
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352-361: LGTM: qtconsole update approvedThe update of qtconsole from 5.5.2 to 5.6.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any new features or improvements that might be beneficial to the project.
Verification successful
Verification Successful: qtconsole update includes beneficial improvements
The update of qtconsole from 5.5.2 to 5.6.0 introduces improvements in syntax highlighting and ANSI color codes, consistent with a minor version update. The review comment's suggestion to check the changelog was valid and confirms the presence of these enhancements. No issues found with the update.
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#!/bin/bash # Description: Fetch the changelog for qtconsole package curl -s https://raw.githubusercontent.com/jupyter/qtconsole/main/docs/source/changelog.rst | head -n 20Length of output: 408
375-378: LGTM: rich update approvedThe update of rich from 13.7.1 to 13.8.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any new features or improvements that might be beneficial to the project.
Verification successful
Update of
richto 13.8.0 is safe and beneficialThe changelog for
richversion 13.8.0 includes several bug fixes and improvements without any breaking changes. This update is safe and beneficial for the project.
- Fixed
Tablerendering issues.- Improved
Panelstyles.- Enhanced progress tracking and thread handling.
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108-112: LGTM: ipython update approvedThe update of ipython from 8.26.0 to 8.27.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any new features or improvements that might be beneficial to the project.
Verification successful
LGTM: ipython update approved
The update of IPython from 8.26.0 to 8.27.0 includes important bug fixes and improvements, such as compatibility with Python 3.13. Ensure that
executingandstack_dataare updated if Python 3.13 is being used.Scripts executed
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64-65: LGTM: executing update approvedThe update of executing from 2.0.1 to 2.1.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any new features or improvements that might be beneficial to the project.
72-73: LGTM: freetype-py update approvedThe update of freetype-py from 2.4.0 to 2.5.1 is a minor version change with a patch, which may introduce new features or improvements and bug fixes.
It's recommended to check the changelog for any significant changes or improvements that might affect the project.
409-410: LGTM: simpleitk update approvedThe update of simpleitk from 2.3.1 to 2.4.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any new features or improvements that might be beneficial to the project.
Verification successful
Update Approved: simpleitk 2.4.0
The update of simpleitk from 2.3.1 to 2.4.0 introduces several new features and improvements, including:
- Update to ITK 5.4.0 with significant improvements.
- New methods added to
ThresholdImageFilter.- Improved Python support for
pathlib.Path.- Various bug fixes and documentation updates.
These changes are consistent with a minor version update and should maintain backward compatibility. It is recommended to review the full release notes for additional details.
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The following scripts were executed for the analysis:
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346-349: LGTM: pyzmq update approvedThe update of pyzmq from 26.1.0 to 26.2.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any new features or improvements that might be beneficial to the project.
396-399: LGTM: setuptools update approvedThe update of setuptools from 72.2.0 to 74.0.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any significant changes or improvements that might affect the project.
Verification successful
LGTM: setuptools update approved
The update of setuptools from 72.2.0 to 74.0.0 includes several new features, bug fixes, and deprecations. These changes are typical for minor version updates and generally maintain backward compatibility. It is recommended to review the changelog for any significant changes that might affect the project.
- Version 74.0.0: Introduces new features and deprecations.
- Version 73.0.0 and 73.0.1: Focus on bug fixes and minor feature updates.
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95-98: LGTM: importlib-metadata update approvedThe update of importlib-metadata from 8.2.0 to 8.4.0 is a minor version change, which may introduce new features or improvements while maintaining backwards compatibility.
It's recommended to check the changelog for any significant changes or improvements that might affect the project.
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184-201: LGTM with caution: numpy major version updateThe update of numpy from 1.26.4 to 2.1.0 is a major version change, which may introduce breaking changes and significant new features.
It's crucial to:
- Review the changelog for breaking changes and new features.
- Thoroughly test the project with this new version.
- Be prepared to make necessary code adjustments.
Please ensure that all numpy-dependent parts of the project are thoroughly tested with this new version.
Verification successful
LGTM with caution: numpy major version update
The update of numpy from 1.26.4 to 2.1.0 is a major version change, which may introduce breaking changes and significant new features. The changelog for numpy 2.1.0 includes numerous enhancements and bug fixes that could impact the project.
- Review the changelog for breaking changes and new features.
- Thoroughly test the project with this new version.
- Be prepared to make necessary code adjustments.
Please ensure that all numpy-dependent parts of the project are thoroughly tested with this new version.
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#!/bin/bash # Description: Search for release notes or changelog for numpy 2.1.0 in the numpy GitHub repository gh repo clone numpy/numpy -- -q cd numpy # Look for files that might contain release notes or changelog information fd 'release' --type f --exec grep -l '2.1.0' {} fd 'changelog' --type f --exec grep -l '2.1.0' {}Length of output: 670
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requirements/constraints_py3.9.txt (16)
382-382: Approved: rich update to 13.8.0The update of rich from 13.7.1 to 13.8.0 is a minor version bump, which may include new features or improvements.
Please review the changelog for any new features or important changes:
Verification successful
Approved: rich update to 13.8.0
The update of rich from 13.7.1 to 13.8.0 includes several bug fixes and improvements, such as rendering fixes for
TableandPanel, enhancements inprogress.track, and compatibility fixes for Python 3.13. These changes are beneficial and do not introduce breaking changes.Scripts executed
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88-88: Approved: imageio update to 2.35.1The update of imageio from 2.35.0 to 2.35.1 is a patch update, which likely includes bug fixes or minor improvements.
Please review the changelog for any bug fixes or improvements:
Verification successful
Verified: imageio update to 2.35.1
The update to imageio version 2.35.1 includes a fix for removing a pinned numpy regression, as noted in the changelog. This aligns with the typical nature of a patch update, focusing on bug fixes and minor improvements. No further action is required.
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359-359: Approved: qtconsole update to 5.6.0The update of qtconsole from 5.5.2 to 5.6.0 is a minor version bump, which may include new features or improvements.
Please check the changelog for any new features or important changes:
Verification successful
Approved: qtconsole update to 5.6.0
The update of qtconsole from 5.5.2 to 5.6.0 introduces improvements in syntax highlighting and ANSI color codes support, enhancing the user experience. This aligns with the expectations for a minor version update. No issues found.
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450-450: Approved: tifffile update to 2024.8.30The update of tifffile from 2024.8.10 to 2024.8.30 is a patch update, which likely includes bug fixes or minor improvements.
Please review the changelog for any bug fixes or improvements:
Verification successful
Verified: tifffile update to 2024.8.30
The update of tifffile to version 2024.8.30 includes support for writing OME Dataset and some StructuredAnnotations elements, along with passing 5096 tests, indicating improved functionality and reliability. There are no breaking changes in this version.
- Ensure to test the integration with your codebase to confirm compatibility.
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84-84: Approved: idna update to 3.8The update of idna from 3.7 to 3.8 is a minor version bump, which may include small improvements or bug fixes.
Please check the changelog for any notable changes:
Verification successful
Approved: idna update to 3.8
The update of idna from 3.7 to 3.8 includes a regression fix for IDNAError exceptions, support for Python 3.13, and the removal of support for Python 3.5. Documentation and testing improvements are also part of this release. These changes are beneficial for maintaining compatibility and improving package quality.
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152-152: Approved: lxml-html-clean update to 0.2.2The update of lxml-html-clean from 0.2.0 to 0.2.2 is a patch update, which likely includes bug fixes or minor improvements.
Please review the changelog or release notes for any bug fixes or improvements:
29-29: Approved: certifi update to 2024.8.30The update of certifi from 2024.7.4 to 2024.8.30 is a minor version bump, which likely includes security fixes or small improvements.
Please verify the changelog for any breaking changes or important updates:
74-74: Approved: freetype-py update to 2.5.1The update of freetype-py from 2.4.0 to 2.5.1 is a minor version bump with a patch, which may include new features and bug fixes.
Please review the changelog for any significant changes or improvements:
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1-522: Summary of package updatesThis update includes various minor version bumps and patch updates for multiple packages, with one major version update for setuptools (72.2.0 to 74.0.0). Most of these updates likely include bug fixes, performance improvements, and new features.
- Ensure that all package updates are compatible with your project's Python version and other dependencies.
- Pay special attention to the setuptools update, as it's a major version bump that might include breaking changes.
- After applying these updates, thoroughly test your project to ensure that all functionality remains intact.
- Consider updating your CI/CD pipeline to include tests with these new package versions.
- Keep an eye on the changelogs of these packages for any security updates or deprecation notices that might affect your project in the future.
To ensure that these updates don't introduce any compatibility issues, run your test suite and check for any deprecation warnings or errors:
If you encounter any issues, review the specific package changelog and consider rolling back the update or addressing the compatibility problem in your code.
66-66: Approved: executing update to 2.1.0The update of executing from 2.0.1 to 2.1.0 is a minor version bump, which may include new features or improvements.
Please check the changelog for any new features or important changes:
488-488: Approved: typer update to 0.12.5The update of typer from 0.12.3 to 0.12.5 is a patch update, which likely includes bug fixes or minor improvements.
Please check the changelog for any bug fixes or improvements:
Verification successful
Approved: Update to typer 0.12.5
The update to
typerversion 0.12.5 includes several enhancements and bug fixes, such as unifying the width of the Rich console, improving error messages, and fixing shell completion issues. These changes are consistent with a patch update and should improve the package's functionality without introducing breaking changes.
- Features: Unify Rich console width, improve error messages.
- Fixes: Address Rich formatting and shell completion issues.
- Refactors: Remove Python 3.6 specific code paths, clean up code.
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97-97: Approved: importlib-metadata update to 8.4.0The update of importlib-metadata from 8.2.0 to 8.4.0 is a minor version bump, which may include new features or improvements.
Please check the changelog for any new features or important changes:
172-172: Approved: napari update to 0.5.3The update of napari from 0.5.2 to 0.5.3 is a patch update, which likely includes bug fixes or minor improvements.
Please check the changelog for any bug fixes or improvements:
353-353: Approved: pyzmq update to 26.2.0The update of pyzmq from 26.1.0 to 26.2.0 is a minor version bump, which may include new features or improvements.
Please review the changelog for any new features or important changes:
Verification successful
Verified: pyzmq update to 26.2.0
The update to pyzmq version 26.2.0 addresses regressions from the new build system in version 26.0, restoring behaviors from version 25.1.2. Key changes include:
- Including libzmq location in rpath when building from source.
- Restoring libsodium randombytes_close fix for bundled libzmq.
- Disabling sometimes-broken IPC/EPOLL on Windows to prevent crashes.
These changes enhance stability, especially for Windows users. For more details, refer to issue #1981.
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403-403: Approved with caution: setuptools update to 74.0.0The update of setuptools from 72.2.0 to 74.0.0 is a major version bump, which may include breaking changes or significant new features.
Please carefully review the changelog for any breaking changes or significant new features:
Ensure that this update doesn't introduce any compatibility issues with your project.
416-416: Approved: simpleitk update to 2.4.0The update of simpleitk from 2.3.1 to 2.4.0 is a minor version bump, which may include new features or improvements.
Please check the release notes for any new features or important changes:
Verification successful
Verified: simpleitk update to 2.4.0
The update of simpleitk from 2.3.1 to 2.4.0 includes several new features, improvements, and bug fixes. Key changes include:
- Updated to ITK 5.4.0, benefiting from significant improvements.
- New methods added to
ThresholdImageFilter.- Improved Python support for
pathlib.Path.- Various bug fixes and documentation updates.
This update is beneficial and aligns with the expectations of a minor version bump.
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package/tests/test_PartSeg/conftest.py (1)
54-54: LGTM! The change disables thestartmethod ofStatusCheckerduring tests.The monkeypatch replaces the original functionality of the
startmethod with a no-operation lambda function. This effectively disables the execution of thestartmethod during tests, allowing for smoother test execution without triggering any side effects that the original method might have caused.The
raising=Falseargument ensures that no exceptions are raised if the method is called, further ensuring that the tests can proceed without interruption.This change is significant as it modifies the control flow during testing, potentially impacting how tests interact with the threading behavior of the application.
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package/PartSeg/launcher_main.py (4)
49-49: LGTM!The code change is approved.
50-50: LGTM!The code change is approved.
53-53: LGTM!The code change is approved.
58-58: LGTM!The code change is approved.
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Czaki
changed the title
imageio, ipython, napari, numpy, qtconsole, scipy, simpleitk, tifffilenapari==0.5.3 relesed fixes Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile
Czaki
changed the title
napari==0.5.3 relesed fixes Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffilenapari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile
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
StatusCheckerbehavior in tests to disable its execution during testing, allowing for smoother test execution.