test: [Automatic] Constraints upgrades: imagecodecs, pandas, pydantic, sentry-sdk, sympy, tifffile

[Czaki]

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

The updated packages are:

• dask
• idna
• imagecodecs
• importlib-metadata
• jupyter-client
• pandas
• platformdirs
• pydantic
• pydantic-core
• pytest
• pytz
• rich
• sentry-sdk
• setuptools
• sympy
• tifffile
• urllib3
• zipp

Summary by CodeRabbit

• New Features

  • Updated various dependencies to their latest versions, enhancing performance and security.

• Bug Fixes

  • Minor version upgrades may include bug fixes from updated libraries.

• Chores

  • Routine maintenance to ensure compatibility with the latest package versions.

[sourcery-ai]

🧙 Sourcery has finished reviewing your pull request!

---

Tips

• Trigger a new Sourcery review by commenting @sourcery-ai review on the pull request.
• Continue your discussion with Sourcery by replying directly to review comments.
• You can change your review settings at any time by accessing your dashboard:
  • Enable or disable the Sourcery-generated pull request summary or reviewer's guide;
  • Change the review language;
• You can always contact us if you have any questions or feedback.

[coderabbitai]

Walkthrough

The pull request involves updates to multiple dependency files, primarily focusing on version upgrades for various Python packages. Key upgrades include dask, idna, importlib-metadata, pydantic, pytest, pytz, rich, sentry-sdk, setuptools, urllib3, and zipp. These changes ensure compatibility and maintain current versions across different Python environments, reflecting routine maintenance efforts.

Changes

Files	Change Summary
requirements/constraints_py3.10.txt	Updated dependencies: dask, idna, importlib-metadata, pydantic, pytest, pytz, rich, sentry-sdk, setuptools, urllib3, zipp.
requirements/constraints_py3.11.txt	Similar updates as above for Python 3.11 dependencies.
requirements/constraints_py3.11_docs.txt	Updated dependencies: dask, idna, importlib-metadata, pydantic, pydantic-core, pytest, pytz, sentry-sdk, rich, zipp.
requirements/constraints_py3.12.txt	Upgraded dependencies: dask, idna, platformdirs, pydantic, pytest, sentry-sdk, setuptools, urllib3, zipp.
requirements/constraints_py3.12_pydantic_1.txt	Updated dependencies: dask, idna, platformdirs, pytest, pytz, rich, sentry-sdk, setuptools, urllib3.
requirements/constraints_py3.8.txt	Upgraded dependencies: idna, importlib-metadata, importlib-resources, platformdirs, pydantic, pytest, pytz, rich, sentry-sdk, setuptools, urllib3, zipp.
requirements/constraints_py3.8_pydantic_1.txt	Similar updates to dependencies as in the previous file.
requirements/constraints_py3.9.txt	Updated dependencies: idna, importlib-metadata, platformdirs, pydantic, pytest, pytz, rich, sentry-sdk, setuptools, urllib3, zipp.
requirements/constraints_py3.9_pydantic_1.txt	Similar updates to dependencies as in the previous file.

Possibly related PRs

• test: [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy #1107: This PR includes updates to pydantic, which is also updated in the main PR, indicating a direct relationship in dependency management.
• test: [Automatic] Constraints upgrades: pydantic #1112: Similar updates to pydantic and sentry-sdk are present, aligning with the changes made in the main PR.
• test: [Automatic] Constraints upgrades: napari, sentry-sdk, sympy #1128: Updates to sentry-sdk and pydantic are relevant as they match the focus of the main PR on dependency upgrades.
• test: [Automatic] Constraints upgrades: mahotas, numpy, sentry-sdk, sympy #1145: This PR includes updates to sentry-sdk, which is also a part of the main PR's changes.
• test: Constraints upgrades: sentry-sdk and fix tests #1182: This PR updates sentry-sdk, which is also updated in the main PR, indicating a direct relationship in dependency management.
• test: napari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile #1183: The updates to numpy and sentry-sdk are relevant as they align with the changes made in the main PR.
• test: [Automatic] Constraints upgrades: numpy, pydantic #1188: This PR includes updates to numpy and pydantic, which are also updated in the main PR, indicating a connection in dependency management.

🐇 Hop along, let's celebrate,
With updates fresh, we elevate!
Dependencies shine, all in a row,
In code we trust, watch our project grow!
With every change, we leap and bound,
In the world of Python, joy is found! 🌼

---

Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 5722bbc and 4a9362c.

Files selected for processing (11)

• requirements/constraints_py3.10.txt (15 hunks)
• requirements/constraints_py3.10_pydantic_1.txt (13 hunks)
• requirements/constraints_py3.11.txt (15 hunks)
• requirements/constraints_py3.11_docs.txt (15 hunks)
• requirements/constraints_py3.11_pydantic_1.txt (13 hunks)
• requirements/constraints_py3.12.txt (13 hunks)
• requirements/constraints_py3.12_pydantic_1.txt (11 hunks)
• requirements/constraints_py3.8.txt (13 hunks)
• requirements/constraints_py3.8_pydantic_1.txt (11 hunks)
• requirements/constraints_py3.9.txt (14 hunks)
• requirements/constraints_py3.9_pydantic_1.txt (12 hunks)

Files skipped from review as they are similar to previous changes (8)

• requirements/constraints_py3.10.txt
• requirements/constraints_py3.11.txt
• requirements/constraints_py3.11_docs.txt
• requirements/constraints_py3.11_pydantic_1.txt
• requirements/constraints_py3.12_pydantic_1.txt
• requirements/constraints_py3.8.txt
• requirements/constraints_py3.8_pydantic_1.txt
• requirements/constraints_py3.9_pydantic_1.txt

Additional comments not posted (39)

requirements/constraints_py3.12.txt (7)

48-48: LGTM: dask version update

The update of dask from 2024.8.2 to 2024.9.0 is a minor version bump, which typically includes bug fixes and small improvements. This change aligns with the PR objectives of keeping dependencies up to date.

---

80-80: LGTM: idna version update

The update of idna from 3.8 to 3.10 is a minor version bump, which typically includes bug fixes and small improvements. This change aligns with the PR objectives of keeping dependencies up to date.

---

82-82: LGTM with suggestion: imagecodecs version update

The update of imagecodecs from 2024.6.1 to 2024.9.22 is a significant version jump. While this aligns with the PR objectives of keeping dependencies up to date, it's worth noting that such a large update might introduce changes that could affect the project.

Suggestion: Ensure thorough testing is performed, particularly for functionalities that rely on image encoding and decoding, to verify that this update doesn't introduce any unexpected behavior.

---

115-115: LGTM: jupyter-client version update

The update of jupyter-client from 8.6.2 to 8.6.3 is a patch version bump, which typically includes bug fixes and very minor improvements. This change aligns with the PR objectives of keeping dependencies up to date.

---

219-219: LGTM with suggestion: pandas version update

The update of pandas from 2.2.2 to 2.2.3 is a patch version bump, which typically includes bug fixes and very minor improvements. This change aligns with the PR objectives of keeping dependencies up to date.

Suggestion: As pandas is a critical package for data manipulation, it might be worth reviewing the changelog for this version to be aware of any fixes that could be relevant to your project.

---

240-240: LGTM with suggestions: Multiple package version updates

The following package updates align with the PR objectives of keeping dependencies up to date:

• platformdirs: 4.2.0 to 4.3.6
• pytest: 8.1.1 to 8.3.3
• pytz: 2024.1 to 2024.2
• rich: 13.7.1 to 13.8.1
• sympy: 1.12 to 1.13.3
• tifffile: 2024.2.12 to 2024.9.20
• urllib3: 2.2.2 to 2.2.3

Most of these are minor or patch version updates, likely containing bug fixes or small improvements.

However, special attention should be given to:

1. sentry-sdk: 1.42.0 to 2.14.0
2. setuptools: 69.2.0 to 75.1.0

These updates are more significant and may introduce new features or changes.

Suggestions:

1. Review the changelogs for sentry-sdk and setuptools to understand the changes introduced in these versions.
2. Ensure that the project's build process and error tracking functionality are thoroughly tested with these new versions.
3. For the other package updates, perform standard regression testing to ensure no unexpected behavior has been introduced.

Run the following script to check for any usage of sentry-sdk in the codebase:

#!/bin/bash
# Search for sentry-sdk usage in the codebase
rg --type python 'import sentry_sdk|from sentry_sdk import' -A 5

Also applies to: 319-319, 332-332, 368-368, 385-385, 389-389, 432-432, 436-436, 483-483

---

269-269: LGTM with caution: pydantic and pydantic-core version updates

The updates of pydantic from 2.6.4 to 2.9.2 and pydantic-core from 2.16.3 to 2.23.4 are significant version jumps. While these align with the PR objectives of keeping dependencies up to date, such large updates might introduce changes that could affect the project.

Suggestions:

1. Review the changelogs for both pydantic and pydantic-core to understand the changes introduced in these versions.
2. Ensure thorough testing is performed, particularly for functionalities that rely on data validation and serialization.
3. Pay special attention to any deprecation warnings or breaking changes mentioned in the changelogs.

Run the following script to check for any usage of deprecated features:

Also applies to: 278-278

requirements/constraints_py3.10_pydantic_1.txt (17)

46-46: LGTM: Minor version update for dask

The update from 2024.8.2 to 2024.9.0 for dask is a minor version change, which typically includes bug fixes and small improvements. This change is unlikely to introduce breaking changes.

---

82-82: LGTM: Minor version update for idna

The update from 3.8 to 3.10 for idna is a minor version change, which typically includes bug fixes and small improvements. This change is unlikely to introduce breaking changes.

---

95-95: LGTM: Minor version update for importlib-metadata

The update from 8.4.0 to 8.5.0 for importlib-metadata is a minor version change, which typically includes bug fixes and small improvements. This change is unlikely to introduce breaking changes.

---

121-121: LGTM: Patch version update for jupyter-client

The update from 8.6.2 to 8.6.3 for jupyter-client is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

225-225: LGTM: Patch version update for pandas

The update from 2.2.2 to 2.2.3 for pandas is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

246-246: LGTM: Patch version update for platformdirs

The update from 4.3.2 to 4.3.6 for platformdirs is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

326-326: LGTM: Patch version update for pytest

The update from 8.3.2 to 8.3.3 for pytest is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

339-339: LGTM: Minor version update for pytz

The update from 2024.1 to 2024.2 for pytz is a minor version change. This update likely includes updates to timezone data and is unlikely to introduce breaking changes.

---

375-375: LGTM: Patch version update for rich

The update from 13.8.0 to 13.8.1 for rich is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

439-439: LGTM: Patch version update for sympy

The update from 1.13.0 to 1.13.3 for sympy is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

497-497: LGTM: Patch version update for urllib3

The update from 2.2.2 to 2.2.3 for urllib3 is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

514-514: LGTM: Patch version update for zipp

The update from 3.20.1 to 3.20.2 for zipp is a patch version change, which typically includes only bug fixes. This change is highly unlikely to introduce breaking changes.

---

Line range hint 1-514: LGTM: Routine dependency updates

This update includes various package version upgrades, mostly consisting of minor and patch version changes. The more significant updates (e.g., imagecodecs, setuptools, tifffile) have been flagged for additional verification. Overall, these changes appear to be routine maintenance updates that should improve stability and fix bugs.

Recommendation: Approve these changes, but ensure to:

1. Review the changelogs for imagecodecs, sentry-sdk, and tifffile for any significant changes.
2. Verify the build process after the setuptools update.
3. Run the test suite to catch any potential compatibility issues.

These steps will help ensure a smooth integration of the updated dependencies.

---

443-443: LGTM: Significant version update for tifffile

The update from 2024.8.30 to 2024.9.20 for tifffile is a more substantial version change. While it's unlikely to introduce breaking changes, it may include new features or optimizations.

It's recommended to check the changelog for any significant changes or new features that might be relevant to the project. You can run the following command to view the changelog:

#!/bin/bash
# Fetch the changelog for tifffile
curl -s https://raw.githubusercontent.com/cgohlke/tifffile/master/CHANGES.rst | head -n 20

---

396-396: LGTM with verification: Significant version update for setuptools

The update from 74.1.2 to 75.1.0 for setuptools is a more substantial version change. While setuptools is primarily a build tool and not directly used in runtime, changes could affect the build process.

It's recommended to verify that the build process still works as expected after this update. You may want to run your build process in a test environment to ensure there are no unexpected issues. Additionally, check the changelog for any significant changes:

#!/bin/bash
# Fetch the changelog for setuptools
curl -s https://raw.githubusercontent.com/pypa/setuptools/main/CHANGES.rst | head -n 20

---

392-392: LGTM: Minor version update for sentry-sdk

The update from 2.13.0 to 2.14.0 for sentry-sdk is a minor version change, which may include new features or improvements. While unlikely to introduce breaking changes, it's worth noting any new features or changes in behavior.

It's recommended to check the changelog for any significant changes or new features that might be relevant to the project. You can run the following command to view the changelog:

#!/bin/bash
# Fetch the changelog for sentry-sdk
curl -s https://raw.githubusercontent.com/getsentry/sentry-python/master/CHANGELOG.md | head -n 20

---

84-84: LGTM: Significant version update for imagecodecs

The update from 2024.6.1 to 2024.9.22 for imagecodecs is a more substantial version change. While it's unlikely to introduce breaking changes, it may include new features or optimizations.

It's recommended to check the changelog for any significant changes or new features that might be relevant to the project. You can run the following command to view the changelog:

Verification successful

---

Verified: imagecodecs update reviewed

The update from 2024.6.1 to 2024.9.22 for imagecodecs has been reviewed. The changelog indicates several improvements and bug fixes, with no breaking changes identified.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Fetch the changelog for imagecodecs
curl -s https://raw.githubusercontent.com/cgohlke/imagecodecs/master/CHANGES.rst | head -n 20

Length of output: 1105

---

Script:

#!/bin/bash
# Fetch the changelog for imagecodecs
curl -s https://raw.githubusercontent.com/cgohlke/imagecodecs/master/CHANGES.rst | head -n 20

Length of output: 797

requirements/constraints_py3.9.txt (15)

84-84: LGTM: idna package update

The update of idna from 3.8 to 3.10 is a minor version change. This update likely includes bug fixes and small improvements. It should be safe to upgrade.

---

86-86: LGTM: imagecodecs package update

The update of imagecodecs from 2024.6.1 to 2024.9.22 is a patch version change. This update likely includes bug fixes and minor improvements in image compression and decompression functionality. It should be safe to upgrade.

---

97-97: LGTM: importlib-metadata package update

The update of importlib-metadata from 8.4.0 to 8.5.0 is a minor version change. This update likely includes new features and improvements in package metadata handling. It should be safe to upgrade.

---

127-127: LGTM: jupyter-client package update

The update of jupyter-client from 8.6.2 to 8.6.3 is a patch version change. This update likely includes bug fixes and minor improvements in Jupyter protocol client APIs. It should be safe to upgrade.

---

231-231: LGTM: pandas package update

The update of pandas from 2.2.2 to 2.2.3 is a patch version change. This update likely includes bug fixes and minor improvements in data manipulation functionality. It should be safe to upgrade.

---

252-252: LGTM: platformdirs package update

The update of platformdirs from 4.3.2 to 4.3.6 is a patch version change. This update likely includes bug fixes and minor improvements in platform-specific directory handling. It should be safe to upgrade.

---

281-281: LGTM: pydantic package update

The update of pydantic from 2.9.0 to 2.9.2 is a patch version change. This update likely includes bug fixes and minor improvements in data validation and settings management. It should be safe to upgrade.

---

290-290: LGTM: pydantic-core package update

The update of pydantic-core from 2.23.2 to 2.23.4 is a patch version change. This update likely includes bug fixes and minor improvements in core pydantic functionality. It should be safe to upgrade.

---

333-333: LGTM: pytest package update

The update of pytest from 8.3.2 to 8.3.3 is a patch version change. This update likely includes bug fixes and minor improvements in the testing framework. It should be safe to upgrade.

---

346-346: LGTM: pytz package update

The update of pytz from 2024.1 to 2024.2 is a minor version change within the same year. This update likely includes new timezone data and improvements in timezone calculations. It should be safe to upgrade.

---

382-382: LGTM: rich package update

The update of rich from 13.8.0 to 13.8.1 is a patch version change. This update likely includes bug fixes and minor improvements in rich text formatting and terminal output. It should be safe to upgrade.

---

522-522: LGTM: zipp package update

The update of zipp from 3.20.1 to 3.20.2 is a patch version change. This update likely includes bug fixes and minor improvements in Zipfile object handling. It should be safe to upgrade.

---

Line range hint 1-522: Summary of dependency updates

This update includes several package version upgrades, most of which are minor or patch version changes. These updates are generally safe and include bug fixes, performance improvements, and new features. Key updates include:

1. Minor version updates: idna, importlib-metadata, sentry-sdk
2. Patch version updates: imagecodecs, jupyter-client, pandas, platformdirs, pydantic, pydantic-core, pytest, pytz, rich, zipp
3. Major version update: setuptools (74.1.2 to 75.1.0)

Recommendations:

1. Proceed with the minor and patch version updates as they are likely to be safe and beneficial.
2. For the setuptools major version update, review the changelog carefully and conduct thorough testing of your project's build and packaging processes.
3. After applying these updates, run your test suite to ensure no unexpected issues arise.
4. If possible, test these updates in a staging environment before deploying to production.

Overall, these updates appear to be routine maintenance to keep dependencies current and secure.

---

399-399: LGTM: sentry-sdk package update

The update of sentry-sdk from 2.13.0 to 2.14.0 is a minor version change. This update likely includes new features and improvements in error tracking and performance monitoring. While it should be safe to upgrade, it's recommended to check the changelog for any significant changes or new features that might be relevant to your project.

Verification successful

---

LGTM: sentry-sdk package update

The update of sentry-sdk from version 2.13.0 to 2.14.0 includes various fixes and improvements without any breaking changes. This minor version update should enhance error tracking and performance monitoring in your project.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check the changelog for sentry-sdk 2.14.0
curl -s https://raw.githubusercontent.com/getsentry/sentry-python/master/CHANGELOG.md | sed -n '/## 2.14.0/,/## 2.13.0/p'

Length of output: 1433

---

403-403: Caution: Major version update for setuptools

The update of setuptools from 74.1.2 to 75.1.0 is a major version change. While this update likely includes significant improvements and new features for Python packaging and distribution, it may also introduce breaking changes.

Please review the changelog for any significant changes and ensure thorough testing of your project's build and packaging processes after this update.

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share

• X
• Mastodon
• Reddit
• LinkedIn

Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  -- I pushed a fix in commit <commit_id>, please review it.
  -- Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  -- @coderabbitai generate unit testing code for this file.
  -- @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  -- @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  -- @coderabbitai read src/utils.ts and generate unit testing code.
  -- @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  -- @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[sourcery-ai]

Hey @Czaki - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

---

Sourcery is free for open source - if you like our reviews please consider sharing them ✨

• X
• Mastodon
• LinkedIn
• Facebook

_{Help me be more useful! Please click 👍 or 👎 on each comment to tell me if it was helpful.}

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud