test: [Automatic] Constraints upgrades: partsegcore-compiled-backend, pydantic, pygments, scipy, 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:

• partsegcore-compiled-backend
• pydantic
• pygments
• scipy
• setuptools
• tifffile
• wrapt

Summary by Sourcery

Build:

• Update Python dependency constraints for all supported Python versions (3.9, 3.10, 3.11, and 3.12).

Summary by CodeRabbit

• Dependency Updates
  • Updated versions for multiple Python packages across different Python versions:
    • partsegcore-compiled-backend updated to 0.15.9
    • pydantic updated to 2.10.5 (or 1.10.20)
    • pygments updated to 2.19.1
    • scipy updated to 1.15.1
    • setuptools updated to 75.8.0
    • tifffile updated to 2025.1.10
    • wrapt updated to 1.17.1
  • Additional updates for Python 3.12 including shiboken6, pyside6, and related packages

[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) and Pydantic versions. The updated packages include partsegcore-compiled-backend, pydantic, pygments, scipy, setuptools, tifffile, and wrapt.

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 partsegcore-compiled-backend constraint. Updated pydantic constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated tifffile constraint. Updated wrapt constraint.	requirements/constraints_py3.9.txt requirements/constraints_py3.9_pydantic_1.txt
Updated constraints for Python 3.10	Updated partsegcore-compiled-backend constraint. Updated pydantic constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated tifffile constraint. Updated wrapt constraint.	requirements/constraints_py3.10.txt requirements/constraints_py3.10_pydantic_1.txt
Updated constraints for Python 3.11	Updated partsegcore-compiled-backend constraint. Updated pydantic constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated tifffile constraint. Updated wrapt constraint.	requirements/constraints_py3.11.txt requirements/constraints_py3.11_pydantic_1.txt
Updated constraints for Python 3.12	Updated partsegcore-compiled-backend constraint. Updated pydantic constraint. Updated pygments constraint. Updated scipy constraint. Updated setuptools constraint. Updated tifffile constraint. Updated wrapt 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 systematic updates to dependency versions across multiple Python version-specific constraint files. The changes are consistent across different Python version configurations (3.9, 3.10, 3.11, 3.12) and include both Pydantic version 1 and version 2 constraint files. The updates primarily involve minor version increments for packages like partsegcore-compiled-backend, pydantic, pygments, scipy, setuptools, tifffile, and wrapt. Some Python 3.12 specific files also include updates to shiboken6, pyside6, and related packages.

Changes

File	Changes
requirements/constraints_py3.*.txt	Updated versions for multiple packages: - partsegcore-compiled-backend: 0.15.8 → 0.15.9 - pydantic: 2.10.4 → 2.10.5 - pygments: 2.19.0 → 2.19.1 - scipy: 1.15.0 → 1.15.1 - setuptools: 75.7.0 → 75.8.0 - tifffile: 2024.12.12 → 2025.1.10 - wrapt: 1.17.0 → 1.17.1
requirements/constraints_py3.12.txt requirements/constraints_py3.12_pydantic_1.txt	Additional updates for: - shiboken6: 6.8.1 → 6.8.1.1 - pyside6: 6.8.1 → 6.8.1.1 - pyside6-addons: 6.8.1 → 6.8.1.1 - pyside6-essentials: 6.8.1 → 6.8.1.1

Possibly related PRs

• test: [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy #1107: Updates to similar dependencies like pydantic, scipy, tifffile, and wrapt
• test: [Automatic] Constraints upgrades: oiffile, pygments, scipy, superqt #1234: Updates to pygments and scipy

Poem

🐰 Dependency Dance, a Rabbit's Delight

Versions bump up, oh so light
Packages twirl, a semantic flight
From 0.15.8 to 0.15.9 we go
Constraints updated, ready to grow! 🚀

---

📜 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 a1c5879 and a697eea.

📒 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 (8 hunks)
• requirements/constraints_py3.12_docs.txt (6 hunks)
• requirements/constraints_py3.12_pydantic_1.txt (8 hunks)
• requirements/constraints_py3.9.txt (5 hunks)
• requirements/constraints_py3.9_pydantic_1.txt (5 hunks)

✅ Files skipped from review due to trivial changes (1)

• requirements/constraints_py3.9_pydantic_1.txt

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

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

🔇 Additional comments (8)

requirements/constraints_py3.12_docs.txt (1)

212-212: Review of dependency updates

The following package versions have been updated:

• partsegcore-compiled-backend: 0.15.8 → 0.15.9
• pydantic: 2.10.4 → 2.10.5
• pygments: 2.19.0 → 2.19.1
• scipy: 1.15.0 → 1.15.1
• tifffile: 2024.12.12 → 2025.1.10
• wrapt: 1.17.0 → 1.17.1

These are minor version updates that typically include bug fixes and improvements. The changes are consistent across all Python version constraint files.

Let's verify the compatibility and any breaking changes:

Also applies to: 251-251, 266-266, 339-339, 390-390, 448-448

✅ Verification successful

Dependency updates verified successfully

The updates are consistent across all relevant constraint files, with intentional version differences maintained for Python 3.9 compatibility and pydantic v1.x support. All packages are well above their last known vulnerable versions.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for breaking changes in the updated packages

# Check release notes and changelogs
echo "Checking release notes and changelogs for breaking changes..."

# Check PyPI for package metadata
for pkg in partsegcore-compiled-backend pydantic pygments scipy tifffile wrapt; do
  echo "Checking $pkg..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.version, .info.requires_python'
done

# Check for security advisories
for pkg in partsegcore-compiled-backend pydantic pygments scipy tifffile wrapt; do
  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
        }
      }
    }
  }'
done

Length of output: 7620

---

Script:

#!/bin/bash
# Verify consistency across Python version constraint files and check changelog
echo "Checking consistency across Python version files..."
for pkg in partsegcore-compiled-backend pydantic pygments scipy tifffile wrapt; do
  echo "=== $pkg ==="
  rg "^$pkg==" requirements/
done

echo -e "\nChecking for changelog..."
fd -g CHANGELOG.md -g CHANGES.md -g HISTORY.md -x cat {}

Length of output: 4680

requirements/constraints_py3.12_pydantic_1.txt (1)

224-224: Review of Pydantic v1 constraint updates

The updates in the Pydantic v1 constraint file are consistent with the main constraint files, with the exception of Pydantic being updated to v1.10.20 instead of v2.10.5. This is expected as this file specifically constrains to Pydantic v1.

Also applies to: 267-267, 277-277, 377-377, 432-432, 489-489

requirements/constraints_py3.12.txt (1)

226-226: Review of PySide6 updates

Additional updates in this file include PySide6 and related packages:

• pyside6: 6.8.1 → 6.8.1.1
• pyside6-addons: 6.8.1 → 6.8.1.1
• pyside6-essentials: 6.8.1 → 6.8.1.1
• shiboken6: 6.8.1 → 6.8.1.1

These are patch version updates that typically include bug fixes.

Also applies to: 269-269, 280-280, 380-380, 435-435, 493-493

requirements/constraints_py3.11_pydantic_1.txt (1)

226-226: Consistent updates across Python versions

The updates in the Python 3.11 Pydantic v1 constraint file match the Python 3.12 version, ensuring consistency across Python versions.

Also applies to: 269-269, 279-279, 380-380, 435-435, 493-493

requirements/constraints_py3.11.txt (1)

228-228: Consistent updates with different PySide6 version

The updates in this file match the other constraint files, with the exception of PySide6 which remains at version 6.4.2. This appears intentional as indicated by the version denylist.

Also applies to: 271-271, 282-282, 383-383, 438-438, 497-497

requirements/constraints_py3.10_pydantic_1.txt (1)

232-232: Version updates look good!

All package updates are either patch versions or minor increments, which should maintain backward compatibility:

• partsegcore-compiled-backend: 0.15.8 → 0.15.9
• pydantic: 1.10.19 → 1.10.20
• pygments: 2.19.0 → 2.19.1
• scipy: 1.15.0 → 1.15.1
• setuptools: 75.7.0 → 75.8.0
• tifffile: 2024.12.12 → 2025.1.10
• wrapt: 1.17.0 → 1.17.1

Also applies to: 275-275, 285-285, 387-387, 396-396, 442-442, 508-508

requirements/constraints_py3.10.txt (1)

234-234: Version updates look good!

All package updates are either patch versions or minor increments, maintaining backward compatibility:

• partsegcore-compiled-backend: 0.15.8 → 0.15.9
• pydantic: 2.10.4 → 2.10.5
• pygments: 2.19.0 → 2.19.1
• scipy: 1.15.0 → 1.15.1
• setuptools: 75.7.0 → 75.8.0
• tifffile: 2024.12.12 → 2025.1.10
• wrapt: 1.17.0 → 1.17.1

Also applies to: 277-277, 288-288, 390-390, 399-399, 445-445, 512-512

requirements/constraints_py3.9.txt (1)

238-238: Version updates look good, but verify Python 3.9 specific versions.

Most package updates maintain consistency with Python 3.10 constraints:

• partsegcore-compiled-backend: 0.15.8 → 0.15.9
• pydantic: 2.10.4 → 2.10.5
• pygments: 2.19.0 → 2.19.1
• setuptools: 75.7.0 → 75.8.0
• wrapt: 1.17.0 → 1.17.1

However, some packages have different versions for Python 3.9:

• scipy remains at 1.13.1 (vs 1.15.1 in Python 3.10)
• tifffile remains at 2024.8.30 (vs 2025.1.10 in Python 3.10)

Run the following script to verify if newer versions are available for Python 3.9:

Also applies to: 281-281, 292-292, 403-403, 516-516

✅ Verification successful

Python 3.9 specific versions are correct and up-to-date

The current versions in Python 3.9 constraints are the latest available versions that maintain compatibility:

• scipy 1.13.1 (newer versions require Python >=3.10)
• tifffile 2024.8.30 (newer versions require Python >=3.10)

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if newer versions of scipy and tifffile are available for Python 3.9

# Check PyPI for latest versions compatible with Python 3.9
curl -s https://pypi.org/pypi/scipy/json | jq '.releases | keys_unsorted | .[]' | grep -E '^"1\.' | sort -V
curl -s https://pypi.org/pypi/tifffile/json | jq '.releases | keys_unsorted | .[]' | grep -E '^"202[45]\.' | sort -V

# Check Python version compatibility in package metadata
for pkg in scipy tifffile; do
  echo "Checking $pkg..."
  curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.releases | to_entries[] | select(.key | contains("1.15.1")) | .value[].requires_python'
done

Length of output: 1751

---

Script:

#!/bin/bash
# Check Python version requirements for recent tifffile versions
curl -s https://pypi.org/pypi/tifffile/2025.1.10/json | jq -r '.info.requires_python'
curl -s https://pypi.org/pypi/tifffile/2024.12.12/json | jq -r '.info.requires_python'
curl -s https://pypi.org/pypi/tifffile/2024.8.30/json | jq -r '.info.requires_python'

Length of output: 278

---

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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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