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chore: Drop test against pyside2 in napari repo workflow #1352

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chore: Drop test against pyside2 in napari repo workflow #1352

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6f6b85f
Drop test against pyside2 in napari repo case
Czaki Feb 5, 2026
3eb6d6f
do not show viewer before add layers
Czaki Feb 6, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/test_napari_repo.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ jobs:
fail-fast: false
matrix:
platform: [ ubuntu-24.04 ]
python: ['3.10', '3.11', '3.12']
python: ['3.10', '3.11', '3.12', '3.13']
napari_version: ['repo']
steps:
- uses: actions/checkout@v6
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5 changes: 4 additions & 1 deletion package/PartSeg/common_gui/main_window.py
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Original file line number Diff line number Diff line change
Expand Up @@ -227,10 +227,13 @@ def get_colormaps(self) -> list[Optional[colormap.Colormap]]:
return [self.settings.colormap_dict[name][0] for name in colormaps_name]

def napari_viewer_show(self):
viewer = Viewer(title="Additional output", settings=self.settings, partseg_viewer_name=self.channel_info)
viewer = Viewer(
title="Additional output", settings=self.settings, partseg_viewer_name=self.channel_info, show=False
)
viewer.scale_bar.unit = "nm"
viewer.theme = self.settings.theme_name
viewer.create_initial_layers(image=True, roi=True, additional_layers=False, points=True)
viewer.show()
self.viewer_list.append(viewer)
viewer.window.qt_viewer.destroyed.connect(lambda _x: self.close_viewer(viewer))

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16 changes: 12 additions & 4 deletions tox.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -71,15 +71,23 @@ deps=
pytest-json-report
lxml_html_clean

[testenv:py{39,310,311,312,313}-{PyQt5,PySide2,PyQt6,PySide6}-napari_{419,54,repo}]

[testenv:py{39,310,311,312,313}-{PyQt5,PySide2,PyQt6,PySide6}-napari_{419,54}]
deps =
{[testenv]deps}
napari_419: napari==0.4.19.post1
napari_54: napari==0.5.4
napari_repo: git+https://github.com/napari/napari.git
commands =
!napari_repo: python -m pytest -v package/tests/test_PartSeg/test_napari_widgets.py --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json {posargs}
napari_repo: python -m pytest package/tests --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json {posargs}
python -m pytest -v package/tests/test_PartSeg/test_napari_widgets.py --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json {posargs}


[testenv:py{310,311,312,313}-{PyQt5,PyQt6,PySide6}-napari_repo]
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question (testing): The napari_repo env drops PySide2 and py39; confirm this reduction in matrix is intentional.

Previously, napari_repo ran on py{39,310,311,312,313}-{PyQt5,PySide2,PyQt6,PySide6}; now it’s only py{310,311,312,313}-{PyQt5,PyQt6,PySide6}. Unless this is due to an intentional upstream drop of py39/PySide2 support, consider keeping those combos so we don’t silently lose coverage for configurations users may still depend on.

deps =
{[testenv]deps}
git+https://github.com/napari/napari.git
commands =
python -m pytest package/tests --json-report --json-report-file={toxinidir}/report-{envname}-{sys_platform}.json {posargs}
Comment on lines +84 to +89
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@coderabbitai coderabbitai bot Feb 6, 2026 •
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⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🌐 Web query:

PyQt5 Python 3.13 wheels support

💡 Result:

PyQt5 does support Python 3.13 via wheels, but not as “cp313” wheels.

  • The latest PyQt5 release on PyPI (5.15.11, uploaded Jul 19, 2024) publishes cp38-abi3 wheels for Windows (x86/x64), macOS (x86_64/arm64), and Linux x86_64 (manylinux glibc ≥ 2.17). Because they’re abi3 wheels, they are usable on CPython 3.8+ (including 3.13). [1]
  • If your install pulls in Qt libraries via PyQt5-Qt5 / pyqt5-qt5, note that its wheels exist for Linux x86_64 and macOS, and (at least for recent versions like 5.15.18, Nov 9 2025) do not include Windows wheels. [2] (On Windows, PyQt5’s own wheel is the one you’ll typically rely on.)
  • On non-x86_64 Linux (e.g., Raspberry Pi), you may need platform-specific wheels from third parties (example: pyqt5-sip has cp313 wheels on piwheels), or build from source / use conda. [3]

What to do: on Python 3.13, try pip install PyQt5—if you’re on a supported platform above, pip should select the abi3 wheel automatically. [1]

Sources: PyQt5 on PyPI [1], pyqt5-qt5 on PyPI [2], piwheels pyqt5-sip builds [3].

🌐 Web query:

PyQt5 version 5.15 Python 3.13 compatibility

💡 Result:

PyQt5 5.15.x is compatible with Python 3.13, as long as you install a recent PyQt5 5.15 release and its current dependencies:

  • PyQt5 (latest 5.15.11) on PyPI declares “Requires: Python >=3.8” and ships cp38-abi3 wheels, which are intended to work on CPython 3.8+ (including 3.13). (pypi.org)
  • PyQt5-sip provides CPython 3.13 (cp313) wheels in recent releases (e.g., 12.18.0, uploaded Jan 13, 2026), which is important because PyQt5 depends on it. (pypi.org)

Practical guidance:

  • Use pip install PyQt5 (don’t pin an old PyQt5-sip), so pip can pick up a cp313 PyQt5-sip wheel automatically. (pypi.org)

Citations:

Pin the napari git dependency to a tag/commit for CI reproducibility.

Using an unpinned git+ dependency makes builds non-deterministic and can break on upstream changes. Pin to a specific tag or commit hash.

PyQt5 supports Python 3.13 via cp38-abi3 wheels (PyQt5 5.15.11+) and its pyqt5-sip dependency provides cp313 wheels, so py313-PyQt5 does not need exclusion on supported platforms (Windows x86/x64, macOS, Linux x86_64).

🔧 Suggested pinning for reproducibility 
 deps =
     {[testenv]deps}
-    git+https://github.com/napari/napari.git
+    git+https://github.com/napari/napari.git@<tag-or-commit>
🤖 Prompt for AI Agents 
In `@tox.ini` around lines 84 - 89, The napari git dependency in the testenv named
testenv:py{310,311,312,313}-{PyQt5,PyQt6,PySide6}-napari_repo is unpinned;
replace the deps entry git+https://github.com/napari/napari.git with a pinned
reference to a tag or commit (e.g.
git+https://github.com/napari/napari.git@vX.Y.Z or
git+https://github.com/napari/napari.git@<commit-hash>#egg=napari) to ensure CI
reproducibility, updating the deps line in that testenv block (keep the env name
and other deps identical).

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@Czaki Czaki Feb 6, 2026

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This workflow is intentionally to check if there is some napari incompatibility before the release of the next version

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@Czaki, thank you for the clarification! You're absolutely right—testing against the latest napari development version is a great practice for catching compatibility issues early. The unpinned dependency is appropriate for this pre-release testing workflow.

I appreciate the context and apologize for the noise on this one.

✏️ Learnings added 
Learnt from: Czaki
Repo: 4DNucleome/PartSeg PR: 1352
File: tox.ini:84-89
Timestamp: 2026-02-06T10:35:06.033Z
Learning: In the PartSeg repository, the testenv:py{310,311,312,313}-{PyQt5,PyQt6,PySide6}-napari_repo in tox.ini intentionally uses an unpinned git dependency (git+https://github.com/napari/napari.git) to test against the latest napari development version and catch incompatibilities before napari releases.

Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.

🧠 Learnings used 
Learnt from: Czaki
Repo: 4DNucleome/PartSeg PR: 1206
File: .github/workflows/test_napari_widgets.yml:30-30
Timestamp: 2024-10-17T12:19:43.905Z
Learning: In the CI configuration, `napari54` corresponds to napari version `0.5.4`.



[testenv:py{39,310,311,312,313}-PyQt5-coverage]
deps =
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