chore(deps): upgrade myst-parser to v5, sphinx <10, swagger-plugin-for-sphinx to v7#596
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Pull request overview
This PR consolidates multiple dependency update efforts by upgrading the documentation toolchain to support newer Sphinx releases while keeping compatibility with the repo’s supported Python versions.
Changes:
- Bump
myst-parserto>=5,<6(pulls inmarkdown-it-pyv4 via lockfile update). - Relax
sphinxupper bound to<10to allow Sphinx 9 when the Python version permits it. - Upgrade
swagger-plugin-for-sphinxto>=7,<8.
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| File | Description |
|---|---|
pyproject.toml |
Updates dependency-group pins for MyST, Sphinx, and Swagger Sphinx plugin to allow newer compatible versions. |
uv.lock |
Refreshes the lockfile to reflect the upgraded packages (including transitive updates like markdown-it-py v4). |
Codecov Report✅ All modified and coverable lines are covered by tests. |
…r-sphinx to v7 - myst-parser: >=4.0.1,<5 → >=5,<6 (v5.0.0 adds Sphinx 9 support, requires Python >=3.11) - sphinx: >=8.2.3,<9 → >=8.2.3,<10 (opens door to Sphinx 9 on Python >=3.12; stays at 8.x while Python 3.11 is supported) - swagger-plugin-for-sphinx: >=6.1.0,<7 → >=7,<8 (v7 drops Sphinx 7 support, aligns with Sphinx 8/9) Validated locally: uv sync resolves cleanly, make docs and make lint both pass. Closes #388, #416, #483. Supersedes #368 (sphinx v9 upper bound now open; full v9 adoption follows Python 3.11 EOL). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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…inx 9 #596 widened the sphinx constraint to <10 but main's lock still resolved to 8.2.3 (no upgrade triggered), so docs CI passed there. The lock-file maintenance refresh on this branch upgraded sphinx to 9.0.4/9.1.0 and docs build broke with: sphinx.errors.ExtensionError: Could not import extension sphinx_toolbox.collapse (cannot import name 'logger' from 'sphinx.ext.autodoc') sphinx-toolbox 4.1.2 (latest) declares sphinx>=3.2.0 but its code imports `logger` from `sphinx.ext.autodoc`, which Sphinx 9 removed. Tighten our upper bound until sphinx-toolbox ships Sphinx 9 support. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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* chore(deps): lock file maintenance
* test(application): add --force to mapping validation integration tests to prevent health check timeout
The two tests testing invalid mapping formats were calling `run execute`
without `--force`, causing `_abort_if_system_unhealthy()` to make a
network call before reaching the argument validation. On slower CI
runners (Python 3.11) this exceeded the 10-second test timeout.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(lint): resolve ruff 0.15.11 lint violations introduced by lock file update
New ruff version introduces several previously-undetected rules:
- RUF067: ignore for __init__.py (intentional conditional imports for optional deps)
- RUF069: ignore float equality in tests (intentional exact value assertions)
- RUF071: noqa for os.path.commonprefix (character-by-character comparison is intended for S3 key prefixes)
- D420: reorder Returns before Raises in docstrings (application, platform, qupath)
- ISC004: parenthesize implicit string concatenations in collections
- PYI034: use Self return type for __enter__ methods; noqa for __new__ (returns subclass instance)
- RUF070: remove unnecessary intermediate assignment before yield
Also applies ruff format auto-fixes to markdown code blocks and removes
duplicate __all__ entries in platform/__init__.py.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(test): rewrite test_serve_notebook to use async NiceGUI test client
NiceGUI 3.10.0 broke the TestClient(app) approach because /notebook/{run_id}
is a @ui.page route (NiceGUI-managed, removed during nicegui_reset_globals())
rather than a plain FastAPI @app.get() route that survives resets.
Replace the synchronous TestClient usage with the async user.open() / user.find()
pattern consistent with all other GUI tests in the project. The user fixture
runs tests/main.py which re-registers all @ui.page routes, making them
accessible to the NiceGUI async test client.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(deps): bump nicegui lower bound to 3.10.0 and pin coverage <7.13
Two related dependency fixes for CI:
1. nicegui >= 3.10.0: required by CVE-2026-39844 (already noted in the
prior comment as "not yet merged"). The lock file maintenance bumps
the resolved version to 3.10.0+, and the test rewrite in the previous
commit relies on 3.10.0 behaviour, so users installing the SDK should
not be allowed to fall back to 3.9.x.
2. coverage < 7.13: coverage 7.13.x introduced a regression where
pytest-cov fails with "INTERNALERROR: Expected current collector to
be ..." when tests spawn subprocesses (e.g., the marimo server in
notebook integration tests). Reproduced on both 7.13.4 and 7.13.5;
7.12.0 works. Re-evaluate when coverage releases a fix.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(deps): pin sphinx <9 — sphinx-toolbox 4.1.2 incompatible with Sphinx 9
#596 widened the sphinx constraint to <10 but main's lock still resolved
to 8.2.3 (no upgrade triggered), so docs CI passed there. The lock-file
maintenance refresh on this branch upgraded sphinx to 9.0.4/9.1.0 and
docs build broke with:
sphinx.errors.ExtensionError: Could not import extension
sphinx_toolbox.collapse (cannot import name 'logger' from
'sphinx.ext.autodoc')
sphinx-toolbox 4.1.2 (latest) declares sphinx>=3.2.0 but its code
imports `logger` from `sphinx.ext.autodoc`, which Sphinx 9 removed.
Tighten our upper bound until sphinx-toolbox ships Sphinx 9 support.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(gui): extract dark-mode theme sync helpers — fix Sonar S3358
Two `ui.timer(callback=lambda: ...)` blocks each contained an outer
ternary (`grid.classes(...) if grid else None`) wrapping inner ternaries
on `app.storage.general.get("dark_mode", False)`. Sonar S3358 flags
those as nested conditional expressions.
Both lambdas were originally single-line and only became multi-line
after ruff 0.15's reformatter ran (commit c4bba3c). Replace each lambda
with a named helper function that pulls `dark_mode` out once and
guards the grid existence with an early return.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---------
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Helmut Hoffer von Ankershoffen né Oertel <helmut@aignostics.com>
Co-authored-by: Helmut Hoffer von Ankershoffen <helmuthva@googlemail.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Consolidates and supersedes four stalled dependency PRs (#368, #388, #416, #483) into a single validated change.
>=4.0.1,<5→>=5,<6: v5.0.0 (released 2026-01-15) adds Sphinx 9 support and requires Python ≥3.11. This was the blocker Oliver identified in chore(deps): update dependency sphinx to v9 #368.>=8.2.3,<9→>=8.2.3,<10: Opens the upper bound to allow Sphinx 9. Stays at 8.x while Python 3.11 is in the support matrix (Sphinx 9.1 requires Python ≥3.12); will self-upgrade to 9.x once Python 3.11 is dropped.>=6.1.0,<7→>=7,<8: v7 drops Sphinx 7 support, consistent with our Sphinx 8/9 direction.Closes #388, #416, #483. Supersedes #368 (the
<10upper bound is now open; full Sphinx 9 adoption follows when Python 3.11 reaches EOL and is dropped fromrequires-python).Test plan
uv sync --all-extrasresolves cleanly — myst-parser 5.0.0, swagger-plugin-for-sphinx 7.0.0 installedmake docspasses — html, singlehtml, latex all build with zero warningsmake lintpasses — ruff, pyright, mypy all clean