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chore: Modernize tox configuration and workflows - #1494
As napari dropped pyqt5 the tests start failing we need to modernize test definition
Summary by Sourcery
Modernize test and packaging automation for current Python, Qt, and napari versions while improving tox environment coverage and diagnostics.
New Features:
Expand automated napari compatibility testing to cover PyQt6 and PySide6 across supported Python versions and napari 0.9.2.
Bug Fixes:
Exclude the PySide6 release with a known reference-counting crash on older Python versions.
Update test workflows and dependency constraints to use current Python and Qt backend combinations.
Enhancements:
Modernize the tox configuration with tox 4 syntax, consolidated environments, configurable work directories, and updated napari version coverage.
Build:
Run PyInstaller packaging with Python 3.14 and its corresponding dependency constraints.
CI:
Update Azure and GitHub Actions test matrices, reporting, failure diagnostics, and workflow environment configuration for current Python, Qt, and napari versions.
Summary by CodeRabbit
Tests
Automated test runs now cover Python 3.10–3.14 with PyQt6 and PySide6 across configured napari versions.
Test configurations now include napari 0.9.2 and updated Python and Qt combinations.
Azure tests now run with Python 3.13 and PyQt6.
Failure reports now include the Qt backend, making test failures easier to identify.
Chores
The PyInstaller build pipeline now uses Python 3.14.
Modernizes tox 4 configuration and CI workflows by updating Python and napari targets, replacing PyQt5-oriented test environments with current Qt backends, centralizing environment-specific dependencies and reporting, and propagating backend/work-directory settings through Azure and GitHub Actions.
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Walkthrough
The PR revises tox test environments and updates Azure Pipelines and GitHub Actions to use new Python, Qt backend, and napari selections. It also configures tox work directories, adds backend details to failure reports, and constrains a PySide6 dependency for Python versions below 3.12.
Changes: CI test matrix and tox updates
Layer / File(s)
Summary
Define tox environments and commands tox.ini, pyproject.toml
tox now lists explicit Python, backend, and napari combinations. It consolidates test selections and updates dependencies, report options, and paths. The PySide6 optional dependency excludes version 6.12.0 when Python is below 3.12.
Configure GitHub test workflows .github/workflows/base_test_workflow.yml, .github/workflows/test_napari_repo.yml, .github/workflows/test_napari_widgets.yml, .github/workflows/test_prereleases.yml, .github/TEST_FAIL_TEMPLATE.md
The workflows set tox work directories, add PyQt6 and PySide6 to the napari repository matrix, and select napari 0.9.2 for the latest-release job. Failure reports include backend details.
Update Azure Python test pipelines .azure-pipelines/pyinstaller.yaml, .azure-pipelines/tests.yaml
The PyInstaller pipeline uses Python 3.14 and its constraints file. The test pipeline uses Python 3.13, its constraints file, and the PyQt6 tox environment.
4DNucleome/PartSeg#1481: This issue reports a PyInstaller bundle test failure in the pre-release workflow, which this PR also updates; the failure cause is not specified.
4DNucleome/PartSeg#1460: This issue reports a pip install --pre failure in the pre-release workflow, which this PR updates; the failure cause is not specified.
4DNucleome/PartSeg#1484: This PR adds PySide6 to the napari repository workflow matrix, which relates to the issue’s PySide6 workflow failure; the failure cause is not specified.
Possibly related PRs
4DNucleome/PartSeg#1493: Both PRs change tox environment selections and PyInstaller Python 3.14 setup.
4DNucleome/PartSeg#1492: This PR adds PySide6 test environments, which exercise the signal compatibility changes in PR #1492.
Merge Risk: Minimal · up to d6250
The revised test combinations are consistent with their workflow callers. No actionable merge-blocking issue was identified; merge after normal checks pass.
Pre-merge checks: 5
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Title check
The title "chore: Modernize tox configuration and workflows" matches the main change. The changeset updates tox.ini (Python/backend/napari matrix, removed testenv blocks, path changes), the GitHub Act…
Docstring Coverage
No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentat…
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Full details: Title check
Explanation
The title "chore: Modernize tox configuration and workflows" matches the main change. The changeset updates tox.ini (Python/backend/napari matrix, removed testenv blocks, path changes), the GitHub Actions workflows (TOX_WORK_DIR, PyQt6 and PySide6 backend matrix, napari version updates), and the Azure pipelines (Python 3.13 and 3.14 with new constraints files). The title is concise, specific, and follows the conventional commit style. It does not mention the napari 0.9.2 support or the PyQt5 removal, but it does not need to cover every detail.
Full details: Docstring Coverage
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No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 0 functions across 0 files. (1 skipped: 1 unsupported.)
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Reviewing files that changed from the base of the PR and between 0c7c922 and d625072.
Files selected for processing: 1
pyproject.toml
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Hey - I've found 1 issue
Prompt for AI Agents
Please address the comments from this code review:
## Individual Comments### Comment 1
<locationpath="tox.ini"line_range="14" />
<code_context>
+ py{311,312,313,314}-{PyQt6,PySide6}-napari_repo
+ py{310,311,312,313}-{PyQt5,PyQt6}-napari_62
+ py{310,311,312,313,314}-{PyQt5,PyQt6}-napari_70
+ py{311,312,313,314}-{PyQt5,PyQt6}-napari_92
+ py{312,313}-PySide6-napari_62
+ py{312,313,314}-PySide6-napari_{70,92}
</code_context>
<issue_to_address>
**PyQt5 napari tests remain enabled**
When running the default tox environment list, tox creates these environments with `napari==0.9.2`, so the default test matrix still exercises the backend combination napari dropped and those environments fail instead of providing a runnable test suite.
Remove PyQt5 from the napari_92 environment expansion, keeping it only for napari versions that support that backend.
</issue_to_address>
Sourcery assessment
Approval pending. 1 finding to address first.
Blocking findings: tox.ini:14
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✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.61%. Comparing base (ea55379) to head (d625072). ⚠️ Report is 1 commits behind head on develop.
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Czaki
changed the title
As napari dropped pyqt5 the tests start failing we need to modernize test definition
Summary by Sourcery
Modernize test and packaging automation for current Python, Qt, and napari versions while improving tox environment coverage and diagnostics.
New Features:
Bug Fixes:
Enhancements:
Build:
CI:
Summary by CodeRabbit
Tests
Chores