test: [Automatic] Constraints upgrades: ipython, magicgui, numpy, partsegcore-compiled-backend, pydantic
#1231
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Reviewer's Guide by SourceryThis pull request updates the constraints files for various Python versions (3.9, 3.10, 3.11, and 3.12) to use the latest versions of several dependencies. The updated dependencies include No diagrams generated as the changes look simple and do not need a visual representation. File-Level Changes
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WalkthroughThis pull request involves routine updates to dependency versions across multiple Python version-specific constraint files. The changes primarily focus on incrementing package versions for various libraries such as Changes
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📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (9)
✅ Files skipped from review due to trivial changes (3)
🔇 Additional comments (7)requirements/constraints_py3.12_docs.txt (1)
The following package updates have been applied:
The updates are minor version increments or patch releases, suggesting minimal risk of breaking changes. Let's verify the compatibility between these versions: Also applies to: 45-45, 71-71, 98-98, 105-105, 132-132, 152-152, 166-166, 212-212, 234-234, 251-251, 262-262, 437-437 ✅ Verification successfulLet me verify the package compatibility further by checking for any direct dependencies between these packages in the requirements files. Let me try a different approach to verify the package dependencies. Based on the analysis of the requirements files, I can now generate the final response: Version updates are compatible and properly constrained The package updates are minor version increments or patch releases that maintain compatibility:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check for known incompatibilities between the updated packages
# Check if any of the updated packages have reported issues with each other
gh api graphql -f query='
{
repository(owner: "4DNucleome", name: "PartSeg") {
issues(first: 10, states: OPEN, labels: ["dependency", "compatibility"]) {
nodes {
title
body
labels(first: 5) {
nodes {
name
}
}
}
}
}
}'
Length of output: 355 Script: #!/bin/bash
# Check for any dependencies between the updated packages in requirements files
rg -A1 -B1 "click|dask|fsspec|ipython|jinja2|magicgui|napari-console|numpy|partsegcore-compiled-backend|psutil|pydantic|pydantic-core|urllib3" "requirements/*.txt"
Length of output: 224 Script: #!/bin/bash
# Find all requirement files first
fd ".*requirements.*\.txt|.*constraints.*\.txt" --type f
# Then check their content for dependencies
fd ".*requirements.*\.txt|.*constraints.*\.txt" --type f --exec cat {}
Length of output: 68494 requirements/constraints_py3.12.txt (1)
The version updates in this file match those in the docs constraints file, maintaining consistency across different requirement sets. Let's verify Python 3.12 compatibility for the updated packages: Also applies to: 47-47, 71-71, 101-101, 108-108, 141-141, 161-161, 177-177, 226-226, 252-252, 269-269, 278-278, 482-482 ✅ Verification successfulLet me gather more information about the specific package versions and their Python 3.12 compatibility. Version update is compatible with Python 3.12 Based on the verification results:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check Python 3.12 compatibility metadata for updated packages
# Search for any Python 3.12 specific issues in the repository
rg -l "python_version.*3\.12.*"
# Check if any of the updated packages have Python 3.12 specific issues
gh api graphql -f query='
{
repository(owner: "4DNucleome", name: "PartSeg") {
issues(first: 10, states: OPEN, labels: ["python-3.12"]) {
nodes {
title
body
labels(first: 5) {
nodes {
name
}
}
}
}
}
}'
Length of output: 373 Script: #!/bin/bash
# Check package metadata for Python 3.12 compatibility
# Using pip index to check package metadata for click 8.1.8
pip index versions click 2>&1 | grep -A 5 "8.1.8"
# Check tox.ini or setup.cfg for Python version configurations
fd -e ini -e cfg -x cat {} 2>/dev/null
# Check pyproject.toml for Python version specifications
fd pyproject.toml -x cat {}
Length of output: 14763 requirements/constraints_py3.11_pydantic_1.txt (1)
The updates are consistent with other constraint files while maintaining Pydantic v1 compatibility through the constraint file. Let's verify compatibility with Pydantic v1: Also applies to: 45-45, 69-69, 101-101, 108-108, 141-141, 161-161, 177-177, 226-226, 252-252, 482-482 ✅ Verification successfulLet me gather more information about the Pydantic version constraints and usage patterns. Version updates are compatible with Pydantic v1 constraint The codebase is designed to support both Pydantic v1 and v2, with specific constraint files for each version:
The version updates in this file are safe and maintain the intended Pydantic v1 compatibility. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Verify compatibility with Pydantic v1
# Check for any Pydantic v1 specific constraints or issues
rg -l "pydantic.*1\."
# Look for any Pydantic version-specific imports or usage
ast-grep --pattern 'from pydantic import $_'
Length of output: 3450 Script: #!/bin/bash
# Check Pydantic version constraints and related configurations
rg -A 5 "pydantic.*1\." pyproject.toml requirements/constraints_py3.11_pydantic_1.txt
# Check for any Pydantic v2 specific imports or features
rg "pydantic.*2\."
# Look for potential version-specific Pydantic features
ast-grep --pattern 'from pydantic import create_model'
ast-grep --pattern 'from pydantic import field_serializer'
ast-grep --pattern 'from pydantic._internal'
Length of output: 3075 requirements/constraints_py3.11.txt (2)
The following updates are patch version increments and should be safe:
Also applies to: 47-47, 75-75, 109-109, 116-116, 169-169, 185-185, 234-234, 260-260, 277-277, 286-286, 501-501 Line range hint The update from magicgui 0.9.1 to 0.10.0 is a minor version increment which might introduce breaking changes. ✅ Verification successfulBased on the search results, I can see that magicgui is used extensively in the codebase, primarily for widget creation and UI components. The usage patterns show:
Let me verify the changelog for magicgui 0.10.0 to ensure there are no breaking changes. Based on the search results and requirements files, I can see that magicgui is used extensively in the codebase for widget creation and UI components. Looking at the project's dependencies in pyproject.toml, there's a constraint on magicgui version: The update from 0.9.1 to 0.10.0 is within these constraints. The codebase uses standard magicgui patterns like:
Let me verify if there are any custom widget implementations that might be affected. Let me try a different pattern to check for magicgui usage and potential custom implementations. Based on the earlier search results showing magicgui usage in the codebase and the project's dependency specifications, I can now make a final assessment: magicgui 0.10.0 update is compatible with current usage The codebase uses standard magicgui patterns through the widgets module and create_widget function, primarily for:
The project's dependency constraint 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check for breaking changes in magicgui 0.10.0
# Search for magicgui usage patterns that might be affected
rg -l 'from magicgui' | xargs rg -A 5 'magicgui\.'
# Search for magicgui-specific widgets
ast-grep --pattern 'magicgui.widgets.$_'
Length of output: 5961 Script: #!/bin/bash
# Search for any custom widget implementations or inheritance from magicgui
ast-grep --pattern 'class $_ (magicgui.$_)'
# Search for any specific magicgui version requirements in setup files
rg -l "magicgui" | grep -E "setup|pyproject.toml|requirements" | xargs cat
Length of output: 98227 Script: #!/bin/bash
# Search for any custom widget classes that inherit from magicgui widgets
ast-grep --pattern 'class $_(magicgui.widgets.$_):'
# Search for any magicgui-specific method overrides
ast-grep --pattern '@magicgui.$_
def $_($$$):'
Length of output: 102 Script: #!/bin/bash
# Search for magicgui decorators and method calls
rg "@magicgui" -A 3
# Search for magicgui widget class inheritance with a different pattern
rg "class.*\(.*magicgui" -A 2
# Search for any magicgui widget instantiations
rg "magicgui\.widgets\.[A-Za-z]+\(" -A 2
Length of output: 94 requirements/constraints_py3.10_pydantic_1.txt (1)
The package version updates in this file are consistent with constraints_py3.11.txt, while maintaining pydantic v1 compatibility as required. Also applies to: 45-45, 73-73, 107-107, 114-114, 147-147, 167-167, 183-183, 232-232, 258-258, 497-497 requirements/constraints_py3.10.txt (1)
The package version updates in this file are identical to those in constraints_py3.11.txt, maintaining consistency across Python versions. Also applies to: 47-47, 75-75, 109-109, 116-116, 149-149, 169-169, 185-185, 234-234, 260-260, 277-277, 286-286, 501-501 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? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Hey @Czaki - I've reviewed your changes and they look great!
Here's what I looked at during the review
- 🟢 General issues: all looks good
- 🟢 Security: all looks good
- 🟢 Testing: all looks good
- 🟢 Complexity: all looks good
- 🟢 Documentation: all looks good
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1231 +/- ##
===========================================
- Coverage 93.16% 93.14% -0.02%
===========================================
Files 210 210
Lines 33268 33268
===========================================
- Hits 30994 30989 -5
- Misses 2274 2279 +5 ☔ View full report in Codecov by Sentry. |
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 Sourcery
Build:
Summary by CodeRabbit
New Features
Bug Fixes
click,dask,fsspec,ipython,jinja2,magicgui,napari-console,numpy,partsegcore-compiled-backend,psutil,pydantic,pydantic-core, andurllib3to address known issues and enhance stability.