chore: Drop python 3.9 tests for napari repository

[Czaki]

Ss napari drop python 3.9 stop testing i against napari repo

closes #1243

Summary by Sourcery

CI:

• Remove Python 3.9 from the napari repository test matrix

Summary by CodeRabbit

• Tests
  • Updated our automated testing configuration to focus on Python 3.10, 3.11, and 3.12 for enhanced compatibility and performance.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request removes Python 3.9 from the test matrix in the test_napari_repo.yml workflow. This streamlines the testing process by focusing on actively supported Python versions.

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

File-Level Changes

Change	Details	Files
Removed Python 3.9 from the test matrix.	Removed '3.9' from the python matrix in the test_napari_repo.yml workflow.	.github/workflows/test_napari_repo.yml

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#1243	Fix the failing tests on ubuntu-24.04 py3.9 in the napari repo workflow.	✅

Possibly linked issues

• [test-bot] napari repos test fail #1243: The PR removes python 3.9 tests, addressing the issue of failing python 3.9 tests in the napari repo workflow.
• [test-bot] napari repos test fail #1243: The PR removes python 3.9 tests, addressing the issue of failing python 3.9 tests.

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[coderabbitai]

Walkthrough

This pull request updates the CI workflow configuration for the napari repository. In the workflow file (.github/workflows/test_napari_repo.yml), the Python version matrix for the test_napari job is modified by removing Python 3.9. Only Python versions 3.10, 3.11, and 3.12 are now used for testing, while the remainder of the workflow remains unchanged.

Changes

File	Change Summary
.github/workflows/test_napari_repo.yml	Removed Python 3.9 from the test matrix; now testing on Python 3.10, 3.11, and 3.12.

Poem

I'm a rabbit with a joyful hop,
CI changes make my heart go pop!
Python 3.9 has hopped away,
Leaving room for a brighter day.
Carrots and code—hip hip hooray!

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📜 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 cc63206 and 9a7ea84.

📒 Files selected for processing (1)

• .github/workflows/test_napari_repo.yml (1 hunks)

⏰ Context from checks skipped due to timeout of 300000ms (31)

• 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 pyinstaller_linux)
• GitHub Check: 4DNucleome.PartSeg (Builds sdist)
• 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 / macos-13 py 3.11 latest PyQt5
• GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
• GitHub Check: repo py3.12
• GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
• GitHub Check: repo py3.11
• GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
• GitHub Check: repo py3.10
• 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 PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
• GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
• GitHub Check: Test PartSeg conda
• GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
• GitHub Check: 4DNucleome.PartSeg (GetTestData linux)
• 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: Codacy Static Code Analysis

🔇 Additional comments (1)

.github/workflows/test_napari_repo.yml (1)

37-37:

❓ Verification inconclusive

LGTM! Verify Python version support policy.

The removal of Python 3.9 from the test matrix aligns with the PR objective. However, please ensure this change is documented in:

• Project's minimum Python version requirements
• Release notes/changelog
• Documentation about supported Python versions

Let's check the project's Python version requirements:

---

🏁 Script executed:

#!/bin/bash
# Check Python version requirements in key files
echo "Checking pyproject.toml..."
rg "python_requires|python_version" pyproject.toml

echo -e "\nChecking README..."
rg "python|Python" README.md

echo -e "\nChecking setup.py/setup.cfg if they exist..."
fd -e py -e cfg -x rg "python|Python" {} \;

Length of output: 1972

---

LGTM, with one note: The removal of Python 3.9 from the testing matrix meets the PR objective. However, please verify that the project’s Python version support policy and related documentation (e.g., minimum Python version in dependency configurations, release notes, and any user-facing docs) reflect this change. The search in the pyproject.toml shows conditional dependency declarations based on Python versions, but there's no explicit documentation update confirming the drop of Python 3.9 support. Could you please double-check or update the docs to confirm that Python 3.9 is no longer supported?

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[sourcery-ai]

Hey @Czaki - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider updating the minimum supported python version in setup.py and other relevant files.

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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[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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.15%. Comparing base (cc63206) to head (9a7ea84).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1244      +/-   ##
===========================================
- Coverage    93.16%   93.15%   -0.02%     
===========================================
  Files          210      210              
  Lines        33288    33288              
===========================================
- Hits         31014    31009       -5     
- Misses        2274     2279       +5     

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