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test: [Automatic] Constraints upgrades: imageio, ipykernel, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk #1035

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merged 1 commit into from
Dec 4, 2023

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Czaki
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@Czaki Czaki commented Nov 6, 2023

This PR is automatically created and updated by PartSeg GitHub
action cron to keep bundle dependencies modules up to date.

The updated packages are:

  • certifi
  • charset-normalizer
  • comm
  • dask
  • exceptiongroup
  • fsspec
  • idna
  • imageio
  • importlib-metadata
  • ipykernel
  • ipython
  • jsonschema
  • jsonschema-specifications
  • jupyter-client
  • jupyter-core
  • numpy
  • pandas
  • pexpect
  • pillow
  • platformdirs
  • prompt-toolkit
  • psygnal
  • pygments
  • pyinstaller
  • pyqt6
  • pyqt6-qt6
  • qtconsole
  • referencing
  • rich
  • rpds-py
  • scipy
  • sentry-sdk
  • setuptools
  • simpleitk
  • tornado
  • traitlets
  • urllib3
  • wcwidth
  • wrapt

Summary by CodeRabbit

  • Documentation

    • Updated the list of package versions to ensure compatibility and stability across Python versions 3.8, 3.9, 3.10, and 3.11.
  • Chores

    • Performed routine updates to dependencies to include the latest bug fixes, performance improvements, and new features.
  • Bug Fixes

    • Addressed potential security vulnerabilities by updating packages to their more secure versions.

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coderabbitai bot commented Nov 6, 2023

Walkthrough

The updates reflect a broad upgrade of package versions across Python 3.8, 3.9, 3.10, and 3.11 environments. These changes likely introduce bug fixes, performance enhancements, and new features, which could affect the behavior of dependent software.

Changes

File Path Change Summary
requirements/constraints_py3.8.txt Updated packages such as certifi, charset-normalizer, comm, fsspec, and others.
requirements/constraints_py3.9.txt Similar updates to constraints_py3.8.txt with additional changes to packages like dask, exceptiongroup, numpy, pandas, and more.
requirements/constraints_py3.10.txt Package version updates including certifi, charset-normalizer, dask, exceptiongroup, and others.
requirements/constraints_py3.11.txt Updates to packages such as certifi, charset-normalizer, comm, dask, fsspec, and more.

🐇✨

In the garden of the code, where the Python packages grow,

We've tended to the versions, with updates in a row.

Bugs hop away, performance blooms, features ripe and sweet,

A rabbit's work is never done, but oh, these changes are neat!

🌱📦🚀🌟


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Review Status

Actionable comments generated: 0

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between b301c39 and ed7b915.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (11 hunks)
  • requirements/constraints_py3.11.txt (11 hunks)
  • requirements/constraints_py3.8.txt (9 hunks)
  • requirements/constraints_py3.9.txt (11 hunks)
Additional comments: 40
requirements/constraints_py3.9.txt (10)
  • 23-28: babel has been updated. Ensure that this does not affect any localization or internationalization features in your application.

  • 32-38: charset-normalizer has been updated. This could potentially affect how text is processed in your application, so make sure to test any features that rely on text processing.

  • 86-92: imageio has been updated. This could potentially affect how images are processed in your application, so make sure to test any features that rely on image processing.

  • 111-136: Several packages related to Jupyter and IPython have been updated, including ipython, jupyter-client, and jupyter-core. If your application uses Jupyter notebooks or IPython, make sure to test these features thoroughly.

  • 243-248: pillow has been updated. This could potentially affect how images are processed in your application, so make sure to test any features that rely on image processing.

  • 313-321: pyqt6 and related packages have been updated. This could potentially affect the GUI of your application, so make sure to test all GUI features thoroughly.

  • 388-394: rpds-py has been updated. This could potentially affect data structures used in your application, so make sure to test any features that rely on these data structures.

  • 401-407: sentry-sdk has been updated. This could potentially affect error reporting in your application, so make sure to test error reporting features thoroughly.

  • 475-481: traitlets has been updated. This could potentially affect configuration management in your application, so make sure to test any features that rely on configuration management.

  • 508-514: wcwidth has been updated. This could potentially affect how text is displayed in your application, so make sure to test any features that rely on text display.

requirements/constraints_py3.8.txt (9)
  • 34-40: The charset-normalizer package has been updated from 3.3.1 to 3.3.2. Ensure that this update does not introduce any breaking changes.

  • 86-92: The imageio package has been updated from 2.31.6 to 2.32.0. Ensure that this update does not introduce any breaking changes.

  • 120-140: The jsonschema package has been updated from 4.19.1 to 4.19.2 and jupyter-core has been updated from 5.4.0 to 5.5.0. Ensure that these updates do not introduce any breaking changes.

  • 322-330: The pyqt6 package and its related packages have been updated from 6.5.3 to 6.6.0. Ensure that this update does not introduce any breaking changes.

  • 376-382: The qtconsole package has been updated from 5.4.4 to 5.5.0. Ensure that this update does not introduce any breaking changes.

  • 401-407: The rpds-py package has been updated from 0.10.6 to 0.12.0. Ensure that this update does not introduce any breaking changes.

  • 414-420: The sentry-sdk package has been updated from 1.32.0 to 1.34.0. Ensure that this update does not introduce any breaking changes.

  • 488-494: The traitlets package has been updated from 5.12.0 to 5.13.0. Ensure that this update does not introduce any breaking changes.

  • 521-527: The wcwidth package has been updated from 0.2.8 to 0.2.9. Ensure that this update does not introduce any breaking changes.

requirements/constraints_py3.11.txt (11)
  • 23-28: The versions of these packages have been updated. Ensure that these updates do not introduce breaking changes or incompatibilities.

  • 32-38: The version of charset-normalizer has been updated from 3.3.1 to 3.3.2. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 82-88: The version of imageio has been updated from 2.31.6 to 2.32.0. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 102-127: The versions of these packages have been updated. Ensure that these updates do not introduce breaking changes or incompatibilities.

  • 234-239: The version of pillow has been updated from 10.0.1 to 10.0.1. This seems to be a mistake as the version number has not changed. Please verify.

  • 304-312: The version of pyqt6 and its related packages have been updated from 6.5.3 to 6.6.0. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 354-360: The version of qtconsole has been updated from 5.4.4 to 5.5.0. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 379-385: The version of rpds-py has been updated from 0.10.6 to 0.12.0. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 392-398: The version of sentry-sdk has been updated from 1.32.0 to 1.34.0. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 459-465: The version of traitlets has been updated from 5.12.0 to 5.13.0. Ensure that this update does not introduce breaking changes or incompatibilities.

  • 491-497: The version of wcwidth has been updated from 0.2.8 to 0.2.9. Ensure that this update does not introduce breaking changes or incompatibilities.

requirements/constraints_py3.10.txt (10)
  • 23-28: babel version is updated. Ensure that this does not introduce any localization or internationalization issues.

  • 32-38: charset-normalizer version is updated. This is used by requests, so ensure that it does not introduce any issues with HTTP requests.

  • 86-92: imageio version is updated. This is used for reading and writing a wide range of image data, including animated images, volumetric data, and scientific formats. Ensure that it does not introduce any issues with image handling.

  • 106-131: ipython, jupyter-core, and jsonschema versions are updated. These are used for interactive computing and validation of JSON schemas, respectively. Ensure that these updates do not introduce any issues with interactive computing or JSON schema validation.

  • 238-243: pillow version is updated. This is used for handling images. Ensure that it does not introduce any issues with image handling.

  • 308-316: > Note: This review was outside of the patch, so it was mapped to the patch with the greatest overlap. Original lines [308-364]

pyqt6 and related packages are updated. These are used for creating the graphical user interface. Ensure that these updates do not introduce any issues with the user interface.

  • 383-389: rpds-py version is updated. This is used by jsonschema and referencing. Ensure that it does not introduce any issues with JSON schema validation or referencing.

  • 396-402: sentry-sdk version is updated. This is used for error tracking and monitoring. Ensure that it does not introduce any issues with error tracking or monitoring.

  • 470-476: traitlets version is updated. This is used for configuring applications. Ensure that it does not introduce any issues with application configuration.

  • 502-508: wcwidth version is updated. This is used by prompt-toolkit, which is used by ipython. Ensure that it does not introduce any issues with interactive computing.

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, ipython, qtconsole, sentry-sdk test: [Automatic] Constraints upgrades: imageio, ipython, numpy, pandas, pyinstaller, qtconsole, sentry-sdk, simpleitk Nov 13, 2023
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Review Status

Actionable comments generated: 0

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between b301c39 and af7ccb9.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (15 hunks)
  • requirements/constraints_py3.11.txt (15 hunks)
  • requirements/constraints_py3.8.txt (13 hunks)
  • requirements/constraints_py3.9.txt (15 hunks)
Files skipped from review due to trivial changes (2)
  • requirements/constraints_py3.8.txt
  • requirements/constraints_py3.9.txt

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, ipython, numpy, pandas, pyinstaller, qtconsole, sentry-sdk, simpleitk test: [Automatic] Constraints upgrades: imageio, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk Nov 20, 2023
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Review Status

Actionable comments generated: 0

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between b301c39 and bd81032.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (16 hunks)
  • requirements/constraints_py3.11.txt (16 hunks)
  • requirements/constraints_py3.8.txt (17 hunks)
  • requirements/constraints_py3.9.txt (16 hunks)
Files skipped from review due to trivial changes (1)
  • requirements/constraints_py3.10.txt
Additional comments: 49
requirements/constraints_py3.9.txt (16)
  • 23-54: The update of certifi and charset-normalizer versions seems consistent and should not cause any issues if they are backward compatible. However, the update of dask to 2023.11.0 should be checked for compatibility with the rest of the codebase, as major version updates can sometimes introduce breaking changes.

  • 86-92: The update of imageio to 2.33.0 is noted. Ensure that this version is compatible with the image processing functionalities used in the project, as imageio is a critical library for handling image files.

  • 111-136: The update of ipython to 8.17.2, jsonschema to 4.20.0, jupyter-client to 8.6.0, and jupyter-core to 5.5.0 are significant and should be tested thoroughly to ensure that they do not introduce any regressions, especially in interactive environments and data validation processes.

  • 189-195: The update of numpy to 1.26.2 is crucial as it is a foundational package for numerical computations. It is important to verify that all numerical operations and dependencies that rely on numpy are still functioning correctly after this update.

  • 229-235: The update of pandas to 2.1.3 should be carefully reviewed to ensure that all data manipulation and analysis functionalities are still working as expected, as pandas is a core library for handling data frames.

  • 243-270: The update of pillow to 10.1.0, platformdirs to 4.0.0, and psygnal to 0.9.5 should be checked for compatibility with image processing and signal handling functionalities within the project.

  • 284-290: The update of pygments to 2.17.1 should be checked to ensure that syntax highlighting and code formatting functionalities are not affected.

  • 296-299: The update of pyinstaller to 6.2.0 and pyinstaller-hooks-contrib to 2023.10 should be verified to ensure that the application packaging process is still working correctly and that all necessary hooks are included.

  • 313-321: The update of pyqt6 and related packages to 6.6.0 and 13.6.0 respectively should be carefully tested to ensure that the GUI components of the project are functioning correctly with these new versions.

  • 363-369: The update of qtconsole to 5.5.1 should be tested to ensure that the console functionality within the application is not affected.

  • 376-382: The update of referencing to 0.31.0 should be verified to ensure that any functionality related to JSON schema referencing is still working as intended.

  • 386-407: The update of rich to 13.7.0, rpds-py to 0.13.0, and sentry-sdk to 1.35.0 should be checked for compatibility with the project's logging, data structure handling, and error reporting functionalities.

  • 412-418: The update of simpleitk to 2.3.1 should be verified to ensure that medical image processing functionalities are not affected.

  • 475-481: The update of traitlets to 5.13.0 should be checked to ensure that configuration management and event handling in the application are still functioning correctly.

  • 500-505: The update of urllib3 to 2.1.0 should be verified to ensure that all HTTP communications within the application are still secure and functioning correctly.

  • 508-516: The update of wcwidth to 0.2.10 and wrapt to 1.16.0 should be checked for compatibility with the project's text processing and decorator functionalities.

requirements/constraints_py3.8.txt (17)
  • 29-47: The update of certifi to 2023.11.17 and charset-normalizer to 3.3.2 is consistent across all Python versions as mentioned in the summary. This is good for maintaining consistency in dependency management. However, ensure that these updates do not introduce any compatibility issues with the rest of the codebase or other dependencies.

  • 86-92: The update of imageio to 2.33.0 is consistent with the summary. Ensure that this version of imageio is compatible with the current codebase, especially if imageio is used extensively for image processing tasks.

  • 102-108: The update of importlib-resources to 6.1.1 is a minor version bump. Verify that this update does not affect any dynamic resource loading that may be happening in the codebase.

  • 120-140: The updates to ipython to 8.12.3, jsonschema to 4.20.0, jupyter-client to 8.6.0, and jupyter-core to 5.5.0 are consistent with the summary. Ensure that these updates are tested for compatibility with the interactive environments and data validation processes used in the project.

  • 250-256: The update of pillow to 10.1.0 is consistent with the summary. Since pillow is a critical library for image manipulation, ensure that this update does not break any image processing functionality in the project.

  • 259-279: The updates to platformdirs to 4.0.0, prompt-toolkit to 3.0.41, and psygnal to 0.9.5 are consistent with the summary. Verify that these updates do not introduce any breaking changes, especially prompt-toolkit which is often used for command-line interfaces and could affect the user experience if there are compatibility issues.

  • 293-299: The update of pygments to 2.17.1 is consistent with the summary. Verify that syntax highlighting and code formatting features are still functioning correctly after this update.

  • 305-308: The update of pyinstaller to 6.2.0 is consistent with the summary. Ensure that the application's packaging process is still working as expected after this update, as pyinstaller is critical for creating standalone executables.

  • 322-330: The updates to pyqt6 and related packages are consistent with the summary. These updates are important for GUI-related functionality, so thorough testing is required to ensure that the graphical interface of the application remains stable and performs well.

  • 377-382: The update of qtconsole to 5.5.1 is consistent with the summary. Verify that the console functionality within the application, if utilized, is still working as expected after this update.

  • 392-395: The update of referencing to 0.31.0 is consistent with the summary. Since referencing is related to jsonschema, ensure that the data validation and referencing mechanisms are still functioning correctly.

  • 402-407: The update of rich to 13.7.0 is consistent with the summary. Verify that the console rendering and logging functionalities that may use rich are still working as expected after this update.

  • 417-420: The update of sentry-sdk to 1.35.0 is consistent with the summary. Ensure that error reporting and logging to Sentry are still functioning correctly after this update.

  • 428-431: The update of simpleitk to 2.3.1 is consistent with the summary. Since simpleitk is used for medical image analysis, ensure that the update does not affect any image processing or analysis functionality.

  • 488-494: The update of traitlets to 5.13.0 is consistent with the summary. Verify that this update does not affect configuration management or event handling in the application.

  • 515-518: The update of urllib3 to 2.1.0 is consistent with the summary. Since urllib3 is a fundamental library for HTTP communication, ensure that all network requests and related functionality are still working as expected after this update.

  • 524-529: The update of wcwidth to 0.2.10 is consistent with the summary. Verify that this update does not affect text rendering in terminal interfaces, as wcwidth is used to determine the printable width of characters.

requirements/constraints_py3.11.txt (16)
  • 23-54: The updates to the package versions in this hunk are consistent with the summary provided. It's important to ensure that the updated versions do not introduce any breaking changes or incompatibilities with the existing codebase. It would be advisable to run a full suite of tests to verify that the updates do not cause any regressions.

  • 82-88: The update to imageio from 2.31.6 to 2.33.0 should be checked for any deprecated functions or changes in the API that might affect the codebase. Running tests that involve image processing would be a good way to ensure compatibility.

  • 102-127: The updates to ipython, jupyter-client, and jupyter-core are significant as they are core components of interactive computing environments. It's crucial to verify that the new versions work well with the project's Jupyter notebooks or any other interactive environments used.

  • 180-186: The update to numpy from 1.26.1 to 1.26.2 is a minor version bump. However, given the central role of numpy in scientific computing, it's important to ensure that this update does not affect any numerical computations or data processing pipelines.

  • 220-226: The update to pandas from 2.1.2 to 2.1.3 is also a minor version bump. Similar to numpy, it's important to verify that the update does not introduce any issues with data manipulation or analysis functionalities.

  • 234-261: The updates to pillow, platformdirs, and psygnal should be checked for compatibility with the project's image handling and file system interactions. Special attention should be given to pillow due to its extensive use in image processing.

  • 275-281: The update to pygments from 2.16.1 to 2.17.1 should be checked for any changes in syntax highlighting or code formatting features that might be used in documentation or in the project's user interface.

  • 284-290: The update to pyinstaller from 6.1.0 to 6.2.0 is important for the project's packaging and distribution. It's essential to ensure that the new version does not affect the build process or the generation of executables.

  • 304-312: The updates to pyqt6 and related packages are significant as they are likely to affect the project's user interface. Thorough testing of the UI should be conducted to ensure that all elements are functioning as expected after the update.

  • 354-360: The update to qtconsole from 5.4.4 to 5.5.1 should be checked for any changes in the console interface used by the project. If the project relies on custom console widgets or integration, these should be tested to ensure they work with the new version.

  • 367-373: The update to referencing from 0.30.2 to 0.31.0 should be checked for any changes in the way references are handled within the project, especially if the project uses JSON schema references extensively.

  • 377-398: The updates to rich and sentry-sdk are important for the project's logging and error reporting. It's crucial to verify that the logging output and error reporting functionalities are not affected by these updates.

  • 403-409: The update to simpleitk from 2.3.0 to 2.3.1 should be checked for compatibility with the project's medical image processing functionalities. Any changes in the API or behavior should be thoroughly tested.

  • 459-465: The update to traitlets from 5.12.0 to 5.13.0 should be checked for any changes in configuration management or component interaction patterns, as traitlets is often used for these purposes in Jupyter and IPython-related projects.

  • 482-488: The update to urllib3 from 2.0.7 to 2.1.0 is important for network communications. It's essential to ensure that the update does not affect any HTTP requests or other network interactions within the project.

  • 491-499: The update to wcwidth from 0.2.8 to 0.2.10 should be checked for any changes in the way terminal output is formatted, as wcwidth is used to determine the printable width of characters. Additionally, the update to wrapt from 1.12.1 to 1.16.0 should be checked for compatibility with any decorators used in the project.

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Review Status

Actionable comments generated: 0

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between b301c39 and 8e02b8b.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (18 hunks)
  • requirements/constraints_py3.11.txt (17 hunks)
  • requirements/constraints_py3.8.txt (19 hunks)
  • requirements/constraints_py3.9.txt (18 hunks)
Files skipped from review due to trivial changes (1)
  • requirements/constraints_py3.10.txt
Additional comments: 41
requirements/constraints_py3.11.txt (17)
  • 23-54: The updates to package versions in the requirements file appear to be part of routine maintenance. Ensure that the updated versions are tested for compatibility with the project.

  • 78-88: The version updates for idna and imageio are noted. It's important to verify that these updates do not introduce any compatibility issues with the existing codebase.

  • 102-127: The updates to ipython, jupyter-client, and jupyter-core are significant as they are core components of interactive computing in Python. Ensure thorough testing to confirm that the interactive environments function as expected after these updates.

  • 180-186: The update to numpy is critical due to its foundational role in numerical computing in Python. Compatibility with other scientific packages that depend on numpy should be verified.

  • 220-226: The update to pandas is important for data manipulation tasks. Verify that the new version does not affect any data processing workflows in the project.

  • 232-261: The updates to pillow, platformdirs, and psygnal should be checked for compatibility, especially since pillow is a widely used imaging library and changes could impact image processing functionality.

  • 275-281: The update to pygments is noted. Since it's used for syntax highlighting, ensure that documentation or UI components that rely on this functionality are still displaying correctly.

  • 287-290: The update to pyinstaller is crucial as it affects the packaging of the application. Verify that the application builds and runs correctly with the new version.

  • 307-312: The updates to pyqt6 and related packages are significant due to their role in the GUI of the application. Ensure that the GUI components work as expected with these new versions.

  • 357-360: The update to qtconsole is important for projects that use Jupyter environments. Testing should confirm that the console interactions remain stable.

  • 370-373: The update to referencing should be verified to ensure that JSON schema validations, if used in the project, are still functioning correctly.

  • 380-398: The updates to rich, rpds-py, and sentry-sdk are noted. Since rich is used for rendering rich text and formatting in the terminal, and sentry-sdk is used for error tracking, their functionality should be tested.

  • 406-409: The update to simpleitk is relevant for projects involving medical image processing. Ensure that image processing pipelines are unaffected by this update.

  • 462-465: The update to traitlets is important for configuration management in IPython and Jupyter. Verify that configurations and command-line interfaces are working as intended.

  • 485-488: The update to urllib3 is critical as it's widely used for HTTP client functionality. Ensure that network communications and data fetching are functioning correctly after the update.

  • 494-499: The update to wcwidth and wrapt should be verified, especially since wcwidth affects the way text is displayed in terminals and wrapt is used for function wrappers and decorators.

  • 506-507: The update to setuptools is crucial for the build and distribution process of the project. Verify that the project's setup process works correctly with the new version.

requirements/constraints_py3.8.txt (19)
  • 29-47: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 66-72: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 82-92: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 102-108: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 120-140: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 246-256: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 259-279: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 293-299: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 305-308: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 322-330: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 376-382: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 389-395: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 399-407: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 414-420: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 425-431: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 488-494: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 512-518: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 521-529: The updates to package versions in this hunk are part of routine maintenance. Ensure that the updated versions are tested for compatibility and do not introduce any breaking changes or known vulnerabilities.

  • 535-539: The update to setuptools in this hunk is part of routine maintenance. Ensure that the updated version is tested for compatibility and does not introduce any breaking changes or known vulnerabilities.

requirements/constraints_py3.9.txt (5)
  • 23-54: The updates to the package versions in constraints_py3.9.txt appear to be minor version updates or patches. Ensure that the updated packages are tested for compatibility with the existing codebase.

  • 111-136: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [64-125]

The package version updates continue throughout the file. As with the previous hunk, ensure compatibility with the existing codebase through thorough testing.

  • 111-136: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [82-263]

The pattern of updating package versions to newer minor or patch versions is consistent throughout the file. Continue to verify compatibility and functionality with the existing codebase.

  • 386-407: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [284-513]

The updates to package versions are consistent with the rest of the file, focusing on minor and patch version increments. Ensure that these updates do not introduce any breaking changes by conducting appropriate testing.

  • 520-524: The update to setuptools is noteworthy due to its central role in Python package management. Verify that this update does not affect build or deployment processes.

@Czaki Czaki changed the title test: [Automatic] Constraints upgrades: imageio, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk test: [Automatic] Constraints upgrades: imageio, ipykernel, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk Dec 4, 2023
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Review Status

Actionable comments generated: 4

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between b301c39 and 02f5c86.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (18 hunks)
  • requirements/constraints_py3.11.txt (17 hunks)
  • requirements/constraints_py3.8.txt (18 hunks)
  • requirements/constraints_py3.9.txt (19 hunks)
Additional comments: 62
requirements/constraints_py3.10.txt (18)
  • 23-54: The updates to certifi, charset-normalizer, comm, and dask align with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 64-70: The update to exceptiongroup is consistent with the PR's objective and is correctly reflected in the constraints file.

  • 74-92: The updates to fsspec, idna, and imageio are consistent with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 95-131: The updates to importlib-metadata, ipykernel, ipython, jupyter-client, and jupyter-core are consistent with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 184-190: The update to numpy is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 224-230: The update to pandas is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 236-265: The updates to partsegcore-compiled-backend, pexpect, pillow, platformdirs, and psygnal are consistent with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 279-285: The update to pygments is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 288-294: The update to pyinstaller is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 308-316: The updates to pyqt6, pyqt6-qt6, and pyqt6-sip are consistent with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 358-364: The update to qtconsole is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 371-377: The update to referencing is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 384-402: The updates to rich, rpds-py, scikit-image, scipy, and sentry-sdk are consistent with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 410-413: The update to simpleitk is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 465-476: The update to tornado and traitlets is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 494-499: The update to urllib3 is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

  • 505-510: The updates to wcwidth and wrapt are consistent with the PR's objective to update dependencies and are correctly reflected in the constraints file.

  • 517-518: The update to setuptools is consistent with the PR's objective to update dependencies and is correctly reflected in the constraints file.

requirements/constraints_py3.11.txt (17)
  • 23-54:
    The updates to certifi, charset-normalizer, comm, and dask align with the PR's objective to update dependencies to newer versions.

  • 70-88:
    The updates to fsspec and imageio are consistent with the PR's goal of keeping dependencies current.

  • 94-127:
    The updates to importlib-metadata, ipykernel, ipython, jupyter-client, and jupyter-core are in line with the PR's objective to update dependencies.

  • 180-186:
    The update to numpy version is consistent with the PR's goal of updating dependencies.

  • 232-261: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [220-246]

The update to pandas version is in line with the PR's objective to keep the project's dependencies up-to-date.

  • 232-261:
    The updates to pexpect, pillow, platformdirs, and psygnal align with the PR's goal of updating dependencies.

  • 275-281:
    The update to pygments version is consistent with the PR's objective to maintain current dependencies.

  • 287-290:
    The update to pyinstaller version aligns with the PR's goal of updating dependencies.

  • 304-312:
    The updates to pyqt6, pyqt6-qt6, and pyqt6-sip are consistent with the PR's objective to update dependencies.

  • 354-360:
    The update to qtconsole version is in line with the PR's objective to keep dependencies up-to-date.

  • 370-373:
    The update to referencing version aligns with the PR's goal of updating dependencies.

  • 377-398:
    The updates to rich, rpds-py, scipy, and sentry-sdk are consistent with the PR's objective to maintain current dependencies.

  • 403-409:
    The update to simpleitk version is in line with the PR's objective to update dependencies.

  • 451-465:
    The updates to tornado and traitlets align with the PR's goal of keeping dependencies current.

  • 482-488:
    The update to urllib3 version is consistent with the PR's objective to update dependencies.

  • 491-497:
    The updates to wcwidth and wrapt are in line with the PR's objective to maintain current dependencies.

  • 503-507:
    The update to setuptools version aligns with the PR's goal of updating dependencies.

requirements/constraints_py3.8.txt (18)
  • 29-47:
    The updates to certifi, charset-normalizer, and comm versions are consistent with the PR's objective to keep dependencies current.

  • 66-89:
    The updates to fsspec, idna, and imageio versions align with the PR's goal of updating dependencies.

  • 95-116:
    The updates to importlib-metadata, importlib-resources, and ipykernel versions are in accordance with the PR's objective to maintain up-to-date dependencies.

  • 120-140:
    The updates to jsonschema, jsonschema-specifications, jupyter-client, and jupyter-core versions are appropriate for the PR's aim of dependency version management.

  • 246-256:
    The update to pillow version is consistent with the PR's goal of keeping dependencies up-to-date.

  • 259-279:
    The updates to prompt-toolkit and psygnal versions align with the PR's objective of updating dependencies.

  • 293-299:
    The update to pygments version is in line with the PR's goal of maintaining current dependencies.

  • 305-308:
    The update to pyinstaller version is consistent with the PR's objective to update dependencies.

  • 322-330:
    The updates to pyqt6, pyqt6-qt6, and pyqt6-sip versions are appropriate for the PR's aim of keeping dependencies current.

  • 376-382:
    The update to qtconsole version aligns with the PR's goal of updating dependencies.

  • 389-395:
    The update to referencing version is consistent with the PR's objective to maintain up-to-date dependencies.

  • 399-407:
    The updates to rich and rpds-py versions are in line with the PR's goal of updating dependencies.

  • 414-420:
    The update to sentry-sdk version aligns with the PR's objective of keeping dependencies current.

  • 425-431:
    The update to simpleitk version is appropriate for the PR's aim of updating dependencies.

  • 480-494:
    The update to tornado version is consistent with the PR's goal of maintaining up-to-date dependencies.

  • 512-518:
    The update to urllib3 version aligns with the PR's objective of updating dependencies.

  • 521-527:
    The updates to wcwidth and wrapt versions are in line with the PR's goal of keeping dependencies current.

  • 535-539:
    The update to setuptools version is consistent with the PR's objective to update dependencies and ensure compatibility across different Python versions.

requirements/constraints_py3.9.txt (9)
  • 98-101: The version 7.0.0 for importlib-metadata is correctly updated and follows the semantic versioning format.

  • 313-321: The updates to pyqt5-sip, pyqt6, pyqt6-qt6, and pyqt6-sip are consistent with the PR's objective to update dependencies and do not show any apparent issues.

  • 363-369: The update to qtconsole version 5.5.1 is consistent with the PR's objective to update dependencies and follows the semantic versioning format.

  • 379-382: The package referencing is updated to version 0.31.1. Ensure that this version is correct and compatible with the jsonschema and jsonschema-specifications packages it is associated with.

  • 415-416: The update to simpleitk version 2.3.1 is consistent with the PR's objective to update dependencies and follows the semantic versioning format.

  • 470-473: The update to tornado version 6.4 is consistent with the PR's objective to update dependencies and follows the semantic versioning format.

  • 502-505: The update to urllib3 version 2.1.0 is consistent with the PR's objective to update dependencies and follows the semantic versioning format.

  • 511-513: The update to wcwidth version 0.2.12 is consistent with the PR's objective to update dependencies and follows the semantic versioning format.

  • 523-524: The update to setuptools version 69.0.2 is consistent with the PR's objective to update dependencies and follows the semantic versioning format.

Comment on lines 23 to 54
# referencing
babel==2.13.1
# via sphinx
backcall==0.2.0
# via ipython
build==1.0.3
# via npe2
cachey==0.2.1
# via napari
certifi==2023.7.22
certifi==2023.11.17
# via
# napari
# requests
# sentry-sdk
charset-normalizer==3.3.1
charset-normalizer==3.3.2
# via requests
click==8.1.7
# via
# dask
# typer
cloudpickle==3.0.0
# via dask
comm==0.1.4
comm==0.2.0
# via ipykernel
coverage==7.3.2
# via
# coverage
# pytest-cov
czifile==2019.7.2
# via PartSeg (setup.cfg)
dask==2023.10.1
dask==2023.12.0
# via
# dask
# napari
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The update to dask version 2023.12.0 seems to be a future version considering the current date is December 2023. Please verify that this is the correct version and not a typo or placeholder.

Comment on lines 87 to 92
imagecodecs==2023.9.18
# via PartSeg (setup.cfg)
imageio==2.31.6
imageio==2.33.0
# via
# -r requirements/version_denylist.txt
# PartSeg (setup.cfg)
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The version 2023.9.18 for imagecodecs seems to be a future version. Please check if this is the intended version.

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Review Status

Actionable comments generated: 4

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between fd6e1b8 and 07cc0f9.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (18 hunks)
  • requirements/constraints_py3.11.txt (17 hunks)
  • requirements/constraints_py3.8.txt (18 hunks)
  • requirements/constraints_py3.9.txt (19 hunks)
Files skipped from review as they are similar to previous changes (1)
  • requirements/constraints_py3.8.txt
Additional comments: 37
requirements/constraints_py3.10.txt (18)
  • 23-54: The updates to package versions in this hunk are consistent with the PR's objective to keep dependencies current. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 64-70: The addition of exceptiongroup is consistent with the PR's objective. Verify that this new dependency is compatible with the existing codebase and does not introduce any breaking changes.

  • 74-92: The updates to package versions in this hunk are consistent with the PR's objective. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 95-131: The updates to package versions in this hunk are consistent with the PR's objective. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 184-190: The update to numpy version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 224-230: The update to pandas version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 236-265: The updates to package versions in this hunk are consistent with the PR's objective. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 279-285: The update to pygments version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 288-294: The update to pyinstaller version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 308-316: The updates to pyqt6 and related packages are consistent with the PR's objective. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 358-364: The update to qtconsole version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 371-377: The addition of referencing is consistent with the PR's objective. Verify that this new dependency is compatible with the existing codebase and does not introduce any breaking changes.

  • 381-402: The updates to package versions in this hunk are consistent with the PR's objective. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 407-413: The update to simpleitk version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 462-476: The update to tornado version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 493-499: The update to urllib3 version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

  • 502-510: The updates to package versions in this hunk are consistent with the PR's objective. Ensure that these updates do not introduce compatibility issues with the PartSeg project.

  • 514-518: The update to setuptools version is consistent with the PR's objective. Ensure that this update does not introduce compatibility issues with the PartSeg project.

requirements/constraints_py3.11.txt (17)
  • 23-54:
    The updates to certifi, charset-normalizer, comm, and dask align with the PR's objective to update package versions.

  • 70-88:
    The updates to fsspec and imageio are consistent with the PR's objective to keep dependencies current.

  • 94-127:
    The updates to importlib-metadata, ipykernel, ipython, jupyter-client, and jupyter-core are in line with the PR's goal of updating dependencies.

  • 180-186:
    The update to numpy version is consistent with the PR's objective of maintaining up-to-date dependencies.

  • 220-226:
    The update to pandas version is in line with the PR's goal of updating dependencies.

  • 232-261:
    The updates to pexpect, pillow, platformdirs, and psygnal align with the PR's objective to update package versions.

  • 275-281:
    The update to pygments version is consistent with the PR's objective of maintaining up-to-date dependencies.

  • 287-290:
    The update to pyinstaller version is in line with the PR's goal of updating dependencies.

  • 304-312:
    The updates to pyqt6, pyqt6-qt6, and pyqt6-sip are consistent with the PR's objective to keep dependencies current.

  • 354-360:
    The update to qtconsole version is in line with the PR's goal of updating dependencies.

  • 367-373:
    The update to referencing version is consistent with the PR's objective of maintaining up-to-date dependencies.

  • 377-398:
    The updates to rich, rpds-py, scikit-image, scipy, and sentry-sdk align with the PR's objective to update package versions.

  • 403-409:
    The update to simpleitk version is in line with the PR's goal of updating dependencies.

  • 451-465:
    The updates to tornado and traitlets are consistent with the PR's objective to keep dependencies current.

  • 482-488:
    The update to urllib3 version is in line with the PR's goal of updating dependencies.

  • 491-499:
    The updates to wcwidth and wrapt align with the PR's objective to update package versions.

  • 503-507:
    The update to setuptools version is consistent with the PR's objective of maintaining up-to-date dependencies.

requirements/constraints_py3.9.txt (2)
  • 23-26: The package referencing is mentioned in the comment for attrs but it is not present in the list of dependencies. This could be an error or an outdated comment. Please verify.

  • 520-524: The setuptools package is listed as unsafe in the requirements file, yet it is included with a specific version. Ensure that including setuptools with a version number is intentional and safe for the project's dependency management.

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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

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Review Status

Actionable comments generated: 4

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between f253a37 and c8a0186.
Files selected for processing (4)
  • requirements/constraints_py3.10.txt (18 hunks)
  • requirements/constraints_py3.11.txt (17 hunks)
  • requirements/constraints_py3.8.txt (18 hunks)
  • requirements/constraints_py3.9.txt (19 hunks)
Files skipped from review as they are similar to previous changes (1)
  • requirements/constraints_py3.8.txt
Additional comments: 41
requirements/constraints_py3.10.txt (18)
  • 23-54:
    The updates to certifi, charset-normalizer, comm, and dask align with the PR's objective to update dependencies to newer versions.

  • 64-70:
    The update to exceptiongroup is consistent with the PR's objective and is correctly reflected in the hunk.

  • 74-92:
    The updates to fsspec, idna, and imageio are in line with the PR's objective to keep dependencies current.

  • 95-131:
    The updates to importlib-metadata, ipykernel, ipython, jupyter-client, and jupyter-core are consistent with the PR's objective to update dependencies.

  • 184-190:
    The update to numpy is consistent with the PR's objective to update dependencies to newer versions.

  • 224-230:
    The update to pandas is consistent with the PR's objective to update dependencies to newer versions.

  • 236-265:
    The updates to partsegcore-compiled-backend, pexpect, pillow, platformdirs, and psygnal are consistent with the PR's objective to update dependencies.

  • 279-285:
    The update to pygments is consistent with the PR's objective to update dependencies to newer versions.

  • 288-294:
    The update to pyinstaller is consistent with the PR's objective to update dependencies to newer versions.

  • 308-316:
    The updates to pyqt6, pyqt6-qt6, and pyqt6-sip are consistent with the PR's objective to update dependencies to newer versions.

  • 358-364:
    The update to qtconsole is consistent with the PR's objective to update dependencies to newer versions.

  • 371-377:
    The update to referencing is consistent with the PR's objective to update dependencies to newer versions.

  • 381-402:
    The updates to rich, rpds-py, scipy, and sentry-sdk are consistent with the PR's objective to update dependencies.

  • 407-413:
    The update to simpleitk is consistent with the PR's objective to update dependencies to newer versions.

  • 462-476:
    The update to tornado is consistent with the PR's objective to update dependencies to newer versions.

  • 493-499:
    The update to urllib3 is consistent with the PR's objective to update dependencies to newer versions.

  • 502-510:
    The updates to vispy, wcwidth, and wrapt are consistent with the PR's objective to update dependencies.

  • 514-518:
    The update to setuptools is consistent with the PR's objective to update dependencies to newer versions.

requirements/constraints_py3.11.txt (4)
  • 304-306: The summary mentions an update to pyqt5-sip, but there is no such update in the constraints_py3.11.txt file. Please verify if this was an oversight in the summary or if the update to pyqt5-sip is missing from the file.

  • 43-44: The summary mentions an update to comm, which is correctly reflected in the hunk.

  • 91-127: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [23-506]

The summary mentions an update to exceptiongroup, but this package is not present in the constraints_py3.11.txt file. Please verify if this was an oversight in the summary or if the update to exceptiongroup is missing from the file.

  • 91-127: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [30-507]

The updates to pillow, numpy, scipy, imageio, requests, urllib3, charset-normalizer, idna, certifi, pyinstaller, rich, prompt-toolkit, platformdirs, pygments, ipykernel, ipython, jupyter-client, jupyter-core, importlib-metadata, tornado, traitlets, wrapt, simpleitk, sentry-sdk, rpds-py, referencing, qtconsole, pyzmq, pyqt6-sip, pyqt6-qt6, pyqt6, fsspec, dask, and comm are correctly reflected in the constraints_py3.11.txt file as per the PR objectives and the summary.

requirements/constraints_py3.9.txt (19)
  • 23-54: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 74-92: > Note: This review was outside the patches, so it was mapped to the patch with the greatest overlap. Original lines [64-101]

The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 74-92: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 95-101: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 106-136: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 189-195: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 229-235: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 241-270: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 284-290: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 293-299: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 313-321: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 363-369: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 376-382: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 386-407: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 412-418: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 467-481: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 499-505: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 508-516: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

  • 520-524: The updates to package versions in this hunk are consistent with the PR objectives to keep dependencies current.

Comment on lines +51 to 54
dask==2023.12.0
# via
# dask
# napari
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The version 2023.12.0 for dask is flagged as a future version. Please confirm the accuracy of this version number.

Comment on lines +77 to 78
fsspec==2023.12.0
# via dask
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The version 2023.12.0 for fsspec also appears to be a future version. Please confirm the accuracy of this version number.

Comment on lines 87 to 88
imagecodecs==2023.9.18
# via PartSeg (setup.cfg)
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The version 2023.9.18 for imagecodecs seems to be a future version. Please check if this is the intended version.

Comment on lines 298 to 299
pyinstaller-hooks-contrib==2023.10
# via pyinstaller
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The package pyinstaller-hooks-contrib is updated to version 2023.10, which seems to be a future version. Please confirm this version number.

@Czaki Czaki added this to the 0.15.3 milestone Dec 4, 2023
@Czaki Czaki merged commit 43c0be1 into develop Dec 4, 2023
51 checks passed
@Czaki Czaki deleted the auto-dependency-upgrades branch December 4, 2023 14:25
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