test: [Automatic] Constraints upgrades: oiffile, pygments, scipy, superqt

[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:

• oiffile
• pillow
• pyconify
• pygments
• scipy
• setuptools
• superqt

Summary by Sourcery

Build:

• Update Python dependency constraints files for various Python versions and Pydantic compatibility.

Summary by CodeRabbit

• Dependencies
  • Updated package versions across multiple Python version constraint files:
    • Upgraded oiffile to 2025.1.1
    • Updated pillow to 11.1.0
    • Upgraded pyconify to 0.2
    • Updated pygments to 2.19.0
    • Upgraded scipy to 1.15.0
    • Updated setuptools to 75.7.0
    • Upgraded superqt to 0.7.1

[sourcery-ai]

Reviewer's Guide by Sourcery

This 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 oiffile, pillow, pyconify, pygments, scipy, setuptools, and superqt. The changes were made automatically by the PartSeg GitHub action cron.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Updated constraints for Python 3.9	Updated oiffile constraint. Updated pillow constraint. Updated pyconify constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated superqt constraint.	requirements/constraints_py3.9.txt requirements/constraints_py3.9_pydantic_1.txt
Updated constraints for Python 3.10	Updated oiffile constraint. Updated pillow constraint. Updated pyconify constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated superqt constraint.	requirements/constraints_py3.10.txt requirements/constraints_py3.10_pydantic_1.txt
Updated constraints for Python 3.11	Updated oiffile constraint. Updated pillow constraint. Updated pyconify constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated superqt constraint.	requirements/constraints_py3.11.txt requirements/constraints_py3.11_pydantic_1.txt
Updated constraints for Python 3.12	Updated oiffile constraint. Updated pillow constraint. Updated pyconify constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated superqt constraint.	requirements/constraints_py3.12.txt requirements/constraints_py3.12_docs.txt requirements/constraints_py3.12_pydantic_1.txt

---

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[coderabbitai]

Walkthrough

This pull request involves updating dependency versions across multiple Python requirements constraint files for different Python versions (3.9, 3.10, 3.11, 3.12) and configurations. The changes are consistent across these files, primarily updating package versions for libraries such as oiffile, pillow, pyconify, pygments, scipy, setuptools, and superqt. These updates reflect the latest versions of these dependencies, likely incorporating bug fixes, improvements, or new features.

Changes

File	Changes
requirements/constraints_py*.txt	Updated package versions: - oiffile: 2024.5.24 → 2025.1.1 - pillow: 11.0.0 → 11.1.0 - pyconify: 0.1.6 → 0.2 - pygments: 2.18.0 → 2.19.0 - scipy: 1.14.1 → 1.15.0 - setuptools: 75.6.0 → 75.7.0 - superqt: 0.7.0 → 0.7.1
requirements/constraints_py3.12_docs.txt	Additional updates: - pydantic-settings: 2.7.0 → 2.7.1 - sphinx-autodoc-typehints: 2.5.0 → 3.0.0

Possibly related PRs

• test: [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy #1107: Contains identical package version updates, suggesting a coordinated dependency management effort

Poem

🐰 Hop, skip, and a version jump!
Dependencies dancing with glee
Packages updated, smooth and light
From 0.1 to 0.2, what a delight!
CodeRabbit's magic makes code shine bright 🚀

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between d155dbf and 572093d.

📒 Files selected for processing (9)

• requirements/constraints_py3.10.txt (7 hunks)
• requirements/constraints_py3.10_pydantic_1.txt (7 hunks)
• requirements/constraints_py3.11.txt (7 hunks)
• requirements/constraints_py3.11_pydantic_1.txt (7 hunks)
• requirements/constraints_py3.12.txt (7 hunks)
• requirements/constraints_py3.12_docs.txt (7 hunks)
• requirements/constraints_py3.12_pydantic_1.txt (7 hunks)
• requirements/constraints_py3.9.txt (5 hunks)
• requirements/constraints_py3.9_pydantic_1.txt (5 hunks)

⏰ Context from checks skipped due to timeout of 300000ms (27)

• GitHub Check: 4DNucleome.PartSeg (Tests_other test windows)
• GitHub Check: 4DNucleome.PartSeg (Tests_linux test_linux)
• GitHub Check: 4DNucleome.PartSeg (Tests_other test macos)
• GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller_linux)
• GitHub Check: 4DNucleome.PartSeg (Builds sdist)
• GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller windows)
• GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos_arm)
• GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos)
• GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
• GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
• GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
• GitHub Check: Base py3.12 / macos-14 py 3.12 latest PyQt6
• GitHub Check: Base py3.11 / windows-latest py 3.11 latest PyQt5
• GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
• GitHub Check: Base py3.11 / macos-13 py 3.11 latest PyQt5
• GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
• GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
• GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
• GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
• GitHub Check: Test PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
• GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
• GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
• GitHub Check: 4DNucleome.PartSeg (GetTestData linux)
• GitHub Check: 4DNucleome.PartSeg (formatting_check check_formating)
• GitHub Check: 4DNucleome.PartSeg (Documentation_check Notebook_check)
• GitHub Check: 4DNucleome.PartSeg (Documentation_check help)
• GitHub Check: Codacy Static Code Analysis

🔇 Additional comments (14)

requirements/constraints_py3.12_docs.txt (1)

186-186: Verify compatibility and security of updated dependencies.

The following dependencies have been updated:

• oiffile: 2024.5.24 → 2025.1.1
• pillow: 11.0.0 → 11.1.0
• pyconify: 0.1.6 → 0.2
• pydantic-settings: 2.7.0 → 2.7.1
• pygments: 2.18.0 → 2.19.0
• scipy: 1.14.1 → 1.15.0
• superqt: 0.7.0 → 0.7.1

Most updates are minor version bumps, but let's verify compatibility and security.

Also applies to: 218-218, 249-249, 264-264, 266-266, 339-339, 381-381

✅ Verification successful

Dependencies update verified as safe and compatible

All updated packages:

• Support Python 3.10+ as required
• Have no known security vulnerabilities
• Maintain compatibility with their dependencies

Note: Unable to verify pyconify's changelog for 0.2, but it's only used as an optional dependency.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for security advisories and compatibility issues

# Check PyPI for release dates and Python version compatibility
for pkg in oiffile pillow pyconify pydantic-settings pygments scipy superqt; do
  echo "Checking $pkg..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info | "Latest: \(.version)\nPython requires: \(.requires_python)\nRelease date: \(.release_date)"'
done

# Check for security advisories
for pkg in pillow scipy; do  # Focus on major dependencies
  echo "Checking security advisories for $pkg..."
  gh api graphql -f query='{
    securityVulnerabilities(first: 5, ecosystem: PIP, package: "'$pkg'") {
      nodes {
        advisory {
          summary
          severity
          publishedAt
        }
        vulnerableVersionRange
        firstPatchedVersion {
          identifier
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      }
    }
  }'
done

Length of output: 5023

---

Script:

#!/bin/bash
# Check pyconify's changelog and dependencies
echo "Checking pyconify's changelog..."
curl -s "https://raw.githubusercontent.com/hynek/pyconify/main/CHANGELOG.md" || \
curl -s "https://raw.githubusercontent.com/hynek/pyconify/master/CHANGELOG.md"

# Check for any dependency incompatibilities
for pkg in oiffile pillow pyconify pydantic-settings pygments scipy superqt; do
  echo "Checking dependencies for $pkg..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.requires_dist[]?' 2>/dev/null
done

Length of output: 5189

requirements/constraints_py3.12_pydantic_1.txt (1)

195-195: Verify pydantic v1.x compatibility with updated dependencies.

The dependency updates in this pydantic v1-specific constraints file look safe as they are mostly minor version bumps. However, let's verify that the changes maintain compatibility with pydantic v1.x.

Also applies to: 230-230, 265-265, 277-277, 377-377, 386-386, 423-423

✅ Verification successful

Dependencies are compatible with pydantic v1.x

The updated packages (oiffile, pillow, pyconify, pygments, scipy, setuptools, superqt) are utility libraries that operate independently of pydantic. Code analysis shows they are used alongside pydantic but don't have any direct dependencies or tight coupling that would affect pydantic v1.x compatibility.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify pydantic v1 compatibility

# Check if any of the updated packages list pydantic as a dependency
for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
  echo "Checking $pkg dependencies..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.requires_dist | select(. != null) | select(contains("pydantic"))'
done

# Check for any compatibility notes in package descriptions
for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
  echo "Checking $pkg description for pydantic mentions..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.description' | grep -i "pydantic" || true
done

Length of output: 4687

---

Script:

#!/bin/bash
# Description: Verify pydantic v1 compatibility with fixed queries

for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
  echo "=== Checking $pkg ==="
  # Check dependencies with fixed jq query
  echo "Dependencies:"
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.requires_dist[]?' 2>/dev/null | grep -i "pydantic" || true
  
  # Check if package has any breaking changes mentioned in recent releases
  echo "Latest release info:"
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.summary, .info.version' 2>/dev/null
done

# Check for any pydantic-related files in the repository
echo -e "\nChecking repository for pydantic usage:"
rg -l "pydantic" --type python

Length of output: 3391

---

Script:

#!/bin/bash
# Final verification of pydantic usage

# Search for pydantic imports and usage
echo "Checking for pydantic imports and usage:"
rg -l "import.*pydantic|from.*pydantic" --type py

# Search for potential integration points with updated packages
echo -e "\nChecking for package usage near pydantic:"
for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
  echo "=== $pkg usage near pydantic ==="
  rg -C2 "import.*$pkg|from.*$pkg" --type py | rg -C2 "pydantic" || true
done

Length of output: 3682

requirements/constraints_py3.12.txt (2)

Line range hint 186-426: LGTM! The dependency updates look safe and consistent.

The automated dependency updates maintain consistency across all constraint files and mostly consist of minor version bumps. The verification scripts will help ensure:

1. Security: No known vulnerabilities in updated versions
2. Compatibility: Support for Python 3.12
3. Dependencies: No breaking changes in dependency chains

---

197-197: Verify Python 3.12 compatibility of updated dependencies.

The updates look consistent with other constraint files. Let's verify Python 3.12 compatibility and check for any known issues.

Also applies to: 232-232, 267-267, 280-280, 380-380, 389-389, 426-426

✅ Verification successful

All updated dependencies are compatible with Python 3.12

Most packages explicitly declare Python 3.12 support. While setuptools 75.7.0 doesn't have an explicit classifier, it supports Python >=3.9 and has no reported issues with Python 3.12.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify Python 3.12 compatibility

# Check classifiers for Python 3.12 support
for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
  echo "Checking $pkg Python 3.12 support..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3.12"))'
done

# Check for Python 3.12 specific issues in release notes
for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
  echo "Checking $pkg release notes..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.description' | grep -i "python 3.12" || true
done

Length of output: 4067

---

Script:

#!/bin/bash
# Check setuptools version requirements and recent releases
echo "Checking setuptools requirements..."
curl -s "https://pypi.org/pypi/setuptools/75.7.0/json" | jq -r '.info.requires_python'

echo -e "\nChecking recent setuptools releases..."
curl -s "https://pypi.org/pypi/setuptools/json" | jq -r '.releases | keys[]' | sort -V | tail -n 5

Length of output: 398

requirements/constraints_py3.11_pydantic_1.txt (2)

197-197: Verify the validity of the future-dated oiffile version.

The version number 2025.1.1 appears to be dated in the future. While this might be intentional due to the package's versioning scheme, it's worth verifying that this is the correct version.

✅ Verification successful

The oiffile version 2025.1.1 is valid and available on PyPI

While the version number is dated in the future, it is the latest release available on PyPI and is a valid version that can be used.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the latest version of oiffile package
curl -s https://pypi.org/pypi/oiffile/json | jq -r '.releases | keys[]' | sort -V | tail -n 5

Length of output: 143

---

232-232: LGTM! Package version updates appear safe.

The version updates for pillow, pyconify, pygments, scipy, setuptools, and superqt are minor or patch updates, which should maintain backward compatibility.

Let's verify these are the latest stable versions:

Also applies to: 267-267, 279-279, 380-380, 389-389, 426-426

✅ Verification successful

✓ Package versions verified - all are at latest stable release

All package versions in the requirements file match the latest stable versions available on PyPI, confirming the safety of these updates.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the latest versions of updated packages
for pkg in pillow pyconify pygments scipy setuptools superqt; do
    echo "=== $pkg ==="
    curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.version'
done

Length of output: 1069

---

Script:

#!/bin/bash
# Get the versions of the packages from the requirements file
echo "=== Requirements file versions ==="
for pkg in pyconify pygments scipy setuptools superqt; do
    echo -n "$pkg: "
    grep -i "^$pkg==" requirements/constraints_py3.11_pydantic_1.txt
done

Length of output: 951

requirements/constraints_py3.11.txt (1)

199-199: LGTM! Version updates are consistent.

The version updates in this file match those in constraints_py3.11_pydantic_1.txt, maintaining consistency across Python 3.11 requirements.

Also applies to: 234-234, 269-269, 282-282, 383-383, 392-392, 429-429

requirements/constraints_py3.10_pydantic_1.txt (2)

203-203: LGTM! Version updates are consistent across Python versions.

The version updates match those in the Python 3.11 constraint files, ensuring consistency across different Python versions (3.10 and 3.11).

Also applies to: 238-238, 273-273, 285-285, 387-387, 396-396, 433-433

---

Line range hint 197-197: Verify security advisories for updated packages.

Let's check for any known security issues with these version updates.

Also applies to: 232-232, 267-267, 279-279, 380-380, 389-389, 426-426

✅ Verification successful

All package versions are secure and up-to-date

All packages in the requirements file are using versions that include the latest security patches. No vulnerable versions were detected in the current constraints.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for security advisories for updated packages

# Check for security advisories using GitHub API
for pkg in oiffile pillow pyconify pygments scipy setuptools superqt; do
    echo "=== Checking $pkg ==="
    gh api graphql -f query="
    {
      securityVulnerabilities(first: 5, ecosystem: PIP, package: \"$pkg\") {
        nodes {
          advisory {
            summary
            severity
            publishedAt
          }
          vulnerableVersionRange
          firstPatchedVersion {
            identifier
          }
        }
      }
    }"
done

Length of output: 6871

---

Script:

#!/bin/bash
# Check actual versions in requirements file
echo "=== Package versions in requirements file ==="
grep -E "^(oiffile|pillow|pyconify|pygments|scipy|setuptools|superqt)" requirements/constraints_py3.10_pydantic_1.txt -i

Length of output: 335

requirements/constraints_py3.10.txt (3)

240-240: LGTM: Minor version updates

The following updates appear to be minor version bumps and should maintain backward compatibility:

• pillow: 11.0.0 → 11.1.0
• pyconify: 0.1.6 → 0.2
• pygments: 2.18.0 → 2.19.0
• setuptools: 75.6.0 → 75.7.0
• superqt: 0.7.0 → 0.7.1

Also applies to: 275-275, 288-288, 399-399, 436-436

---

205-205: Verify the future-dated version of oiffile

The version 2025.1.1 appears to be future-dated. While this might be intentional versioning by the package maintainers, it's worth verifying this is the correct version.

✅ Verification successful

Future-dated version 2025.1.1 of oiffile is legitimate

The version exists as an official release on PyPI and follows the package's established date-based versioning pattern.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the latest version of oiffile package
curl -s https://pypi.org/pypi/oiffile/json | jq -r '.releases | keys[]' | sort -V | tail -n 5

Length of output: 143

---

390-390: Review the scipy major version upgrade

The upgrade from scipy 1.14.1 to 1.15.0 represents a major version change. Please ensure this is compatible with all dependent packages, particularly:

• napari
• scikit-image
• partseg

✅ Verification successful

Scipy version upgrade appears compatible with dependencies

The upgrade to scipy 1.15.0 is properly managed through version-specific constraint files, with appropriate versioning for different Python versions (1.13.1 for Python 3.9, 1.15.0 for Python 3.10+). The dependent packages (napari 0.5.5, scikit-image 0.24.0/0.25.0) are pinned to specific versions, suggesting careful version management.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check compatibility requirements for scipy in dependent packages
rg -A 5 'scipy[>=<~]==' # Search for scipy version constraints in requirements files

Length of output: 25

---

Script:

#!/bin/bash
# Find all requirements files and configuration files that might contain dependencies
echo "=== Requirements and setup files ==="
fd -e txt -e in -e cfg -e toml "requirements|setup|pyproject" 

echo -e "\n=== Searching for scipy in requirements files ==="
# Use various patterns to catch different version specifications
rg -i "scipy.*[>=<~]" 

echo -e "\n=== Checking for scipy imports in Python files ==="
rg -l "^import scipy|^from scipy" 

Length of output: 1330

---

Script:

#!/bin/bash
# Search for napari, scikit-image, and partseg dependencies
echo "=== Package dependencies ==="
rg -i "napari.*[>=<~]|scikit-image.*[>=<~]|partseg.*[>=<~]" 

echo -e "\n=== Checking import relationships ==="
# Look for files where both scipy and these packages are used together
rg -l "from napari|import napari|from skimage|import skimage" $(rg -l "from scipy|import scipy")

Length of output: 72739

requirements/constraints_py3.9_pydantic_1.txt (1)

242-242: Version consistency maintained across Python versions

The updates in this file maintain consistency with constraints_py3.10.txt for the following packages:

• pillow: 11.0.0 → 11.1.0
• pyconify: 0.1.6 → 0.2
• pygments: 2.18.0 → 2.19.0
• setuptools: 75.6.0 → 75.7.0
• superqt: 0.7.0 → 0.7.1

Also applies to: 277-277, 289-289, 400-400, 437-437

requirements/constraints_py3.9.txt (1)

244-244: Version consistency maintained with both pydantic v1 and v2

The updates maintain consistency with both constraints_py3.10.txt and constraints_py3.9_pydantic_1.txt for:

• pillow: 11.0.0 → 11.1.0
• pyconify: 0.1.6 → 0.2
• pygments: 2.18.0 → 2.19.0
• setuptools: 75.6.0 → 75.7.0
• superqt: 0.7.0 → 0.7.1

The file correctly maintains compatibility with pydantic v2 series while the _pydantic_1.txt variant maintains compatibility with pydantic v1 series.

Also applies to: 279-279, 292-292, 403-403, 440-440

---

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[sonarqubecloud]

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 SonarQube Cloud

[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

---

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.14%. Comparing base (d155dbf) to head (572093d).
Report is 16 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1234      +/-   ##
===========================================
- Coverage    93.16%   93.14%   -0.02%     
===========================================
  Files          210      210              
  Lines        33268    33268              
===========================================
- Hits         30994    30989       -5     
- Misses        2274     2279       +5     

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