chore: Drop test against pyside2 in napari repo workflow #1352
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Reviewer's guide (collapsed on small PRs)Reviewer's GuideUpdates tox environments and CI workflow to stop running full napari-repo tests with PySide2 and to add Python 3.13 coverage for napari-repo, while keeping widget-only tests for released napari versions across all backends. Flow diagram for updated tox environments and backend coverageflowchart TD
start["Start tox invocation"] --> select_env["Select tox environment"]
subgraph released_napari["Widget tests for released napari"]
select_env --> env_widgets
env_widgets --> choose_py_version["Python version py39, py310, py311, py312, py313"]
choose_py_version --> choose_backend["Qt backend PyQt5, PySide2, PyQt6, PySide6"]
choose_backend --> choose_napari_version["napari version 0.4.19 or 0.5.4"]
choose_napari_version --> install_released["Install napari from PyPI"]
install_released --> run_widgets_pytest["Run pytest on test_napari_widgets with JSON report"]
end
subgraph napari_repo["Full tests for napari repo"]
select_env --> env_repo
env_repo --> choose_py_version_repo["Python version py310, py311, py312, py313"]
choose_py_version_repo --> choose_backend_repo["Qt backend PyQt5, PyQt6, PySide6"]
choose_backend_repo --> install_repo["Install napari from GitHub napari/napari"]
install_repo --> run_full_pytest["Run pytest on package/tests with JSON report"]
end
run_widgets_pytest --> end_widgets["End widget test env"]
run_full_pytest --> end_repo["End repo test env"]
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📝 WalkthroughWalkthroughUpdates CI and test configuration: adds Python 3.13 to the napari test matrix, splits napari repo tests into a dedicated tox environment, and defers showing the napari Viewer until after initialization in one GUI module. Changes
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~20 minutes Possibly related PRs
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Hey - I've found 1 issue, and left some high level feedback:
- In the new
[testenv:py{310,311,312,313}-{PyQt5,PyQt6,PySide6}-napari_repo]you dropped the-vflag from the pytest invocation compared to the other napari testenvs; if that wasn’t intentional, consider adding-vfor consistent output across environments. - The pytest command and JSON report options are now duplicated between the napari widget env and the new
napari_repoenv; consider extracting the common command into a factor or a sharedcommandssnippet to keep the tox config DRY and easier to maintain.
Prompt for AI Agents
Please address the comments from this code review:
## Overall Comments
- In the new `[testenv:py{310,311,312,313}-{PyQt5,PyQt6,PySide6}-napari_repo]` you dropped the `-v` flag from the pytest invocation compared to the other napari testenvs; if that wasn’t intentional, consider adding `-v` for consistent output across environments.
- The pytest command and JSON report options are now duplicated between the napari widget env and the new `napari_repo` env; consider extracting the common command into a factor or a shared `commands` snippet to keep the tox config DRY and easier to maintain.
## Individual Comments
### Comment 1
<location> `tox.ini:84` </location>
<code_context>
+ 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]
+deps =
+ {[testenv]deps}
</code_context>
<issue_to_address>
**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.
</issue_to_address>Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
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| [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.
Czaki
changed the title
Czaki
changed the title
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Actionable comments posted: 1
🤖 Fix all issues with AI agents
In `@tox.ini`:
- Around line 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).
| [testenv:py{310,311,312,313}-{PyQt5,PyQt6,PySide6}-napari_repo] | ||
| 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} |
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🧩 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-abi3wheels for Windows (x86/x64), macOS (x86_64/arm64), and Linux x86_64 (manylinux glibc ≥ 2.17). Because they’reabi3wheels, 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-siphas 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-abi3wheels, 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:
- 1: https://pypi.org/project/PyQt5/
- 2: https://pypi.org/project/pyqt5-sip/?utm_source=openai
- 3: https://pypi.org/project/pyqt5-sip/?utm_source=openai
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).
There was a problem hiding this comment.
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`.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #1352 +/- ##
===========================================
- Coverage 93.17% 93.15% -0.02%
===========================================
Files 210 210
Lines 33253 33254 +1
===========================================
- Hits 30983 30979 -4
- Misses 2270 2275 +5 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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1 participant
Add testing napari repo against python 3.13
Summary by Sourcery
Update napari testing configuration to separate repo-based tests from pinned napari versions and expand CI coverage to Python 3.13.
Enhancements:
CI:
Summary by CodeRabbit