Scheduled weekly dependency update for week 11#675
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📝 WalkthroughWalkthroughUpdated multiple documentation and development dependencies in two requirements files. Sphinx ecosystem packages upgraded to newer versions, and core dev dependencies including pytest, setuptools, and machine learning libraries bumped to latest compatible versions. Changes
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docs/requirements-docs.txtrequirements-dev.txt
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- GitHub Check: build (3.12)
- GitHub Check: build (3.10)
- GitHub Check: build (3.11)
- GitHub Check: build (3.13)
🔇 Additional comments (4)
requirements-dev.txt (3)
5-6: pytest-env and pytest-mock are compatible with pytest 9.0.2. pytest-env 1.6.0 requires pytest>=9.0.2, and pytest-mock 3.15.1 requires pytest>=6.2.5 — both support the target pytest version without compatibility issues.
7-9: Verify compatibility of ML library updates.Three machine learning libraries are being updated with significant version jumps:
- fiftyone: 1.5.2 → 1.13.4 (8 minor versions)
- datasets: 3.6.0 → 4.7.0 (major version)
- ultralytics: 8.3.237 → 8.4.22 (minor version)
All three are mocked in the documentation build (
autodoc_mock_importsin conf.py). Most are imported underTYPE_CHECKINGguards for lazy loading, but fiftyone has actual runtime usage indagshub/data_engine/annotation/voxel_conversion.py(imports and instantiatesDetections,Detection,Label,Classification). Verify that this runtime usage remains compatible with fiftyone 1.13.4.
8-8: No action needed — datasets 4.7.0 upgrade is safe for this codebase.While datasets 4.0 introduced breaking changes (script removal, Sequence→List migration, audio/video decoding changes), the codebase uses only
Dataset.from_pandas(), which is a stable API unaffected by these changes. No usage ofload_dataset(),trust_remote_code, Sequence schemas, or datasets library audio/video decoding was found. Audio/video processing relies on TensorFlow, torchaudio, and torchvision instead.> Likely an incorrect or invalid review comment.docs/requirements-docs.txt (1)
1-7: All Sphinx extensions are compatible with Sphinx 9.1.0.Verification confirms sphinx-click 6.2.0 and sphinx-autodoc-typehints 3.9.8 both support Sphinx 9.1.0 without issues. No further action needed.
| sphinx==7.3.7 | ||
| furo==2024.5.6 | ||
| sphinx-autobuild==2024.4.16 | ||
| sphinx==9.1.0 |
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🧩 Analysis chain
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#!/bin/bash
# Verify Sphinx configuration and check for other deprecated settings
# Check if autodoc_default_flags is still used
rg -n 'autodoc_default_flags' docs/
# Check for other common deprecated Sphinx settings removed in 9.0
rg -n 'add_stylesheet|add_javascript|autodoc_default_flags' docs/
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fd -e py -e rst conf docs/Repository: DagsHub/client
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🌐 Web query:
Sphinx 9.0 breaking changes migration guide
💡 Result:
Sphinx 9.0 (released Nov 30, 2025): breaking/incompatible changes & how to migrate
1) Extension API: create_source_parser() signature changed
- Breaking change:
SphinxComponentRegistry.create_source_parser()no longer receivesapp; it now takesconfigandenv. - Migration: Update any custom source-parser registration code to match the new signature. (sphinx-doc.org)
2) Source file decoding is now strict
- Breaking change: Non-decodable bytes in source files now raise an error (previously replaced with
?plus a warning). - Migration: Ensure sources are valid text (typically UTF-8) and fix/convert any files with invalid bytes. (sphinx-doc.org)
3) sphinx.ext.autodoc rewrite (edge-case incompatibilities)
- Breaking change: autodoc was substantially rewritten, and extensions relying on autodoc internals may break in edge cases.
- Migration options:
- Prefer updating your extension(s) to current autodoc behavior.
- If you need a temporary bridge, set
autodoc_use_legacy_class_based = Trueto use the pre-9.0 implementation. (sphinx-doc.org)
Deprecations you should address during the upgrade (to avoid future breaks)
4) Remaining public .app attributes deprecated
- Includes
builder.app,env.app,events.app,SphinxTransform.app. - Migration: Stop accessing
*.appon these objects; use supported APIs/objects instead. (sphinx-doc.org)
5) Parser API deprecations
Parser.set_application()deprecatedParser.configandParser.envattributes deprecated- Migration: Update custom parsers to avoid these and follow the newer parser integration patterns. (sphinx-doc.org)
6) Non‑UTF‑8 source encodings deprecated (planned removal in Sphinx 10)
- Migration: Move projects to UTF‑8 source files now. (sphinx-doc.org)
7) sphinx.io deprecated (planned removal in Sphinx 10)
- Sphinx has moved to standard Python I/O internally.
- Migration: Stop importing/depending on
sphinx.ioclasses. (sphinx-doc.org)
8) “tags” kwarg will be required in Sphinx 11 for certain environment methods
- From Sphinx 9 onward it can be passed optionally; Sphinx 11 will require it for:
sphinx.environment.adapters.toctree.global_toctree_for_doc()sphinx.environment.BuildEnvironment.get_and_resolve_doctree()
- Migration: Start passing
tags=where you call these methods. (sphinx-doc.org)
If you share your current Sphinx version (8.x? earlier?) and any custom extensions you use, I can turn this into a step-by-step upgrade checklist for your specific project.
Citations:
- 1: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 2: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 3: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 4: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 5: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 6: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 7: https://www.sphinx-doc.org/en/master/changes/9.0.html
- 8: https://www.sphinx-doc.org/en/master/changes/9.0.html
🌐 Web query:
autodoc_default_flags Sphinx removed deprecated when
💡 Result:
autodoc_default_flags was deprecated in Sphinx 1.8 (released Sep 13, 2018) in favor of autodoc_default_options.[1]
It was slated to be removed in Sphinx 4.0 (the Sphinx autodoc code notes “this option will be removed in Sphinx-4.0”).[2] Sphinx 4.0.0 was released May 9, 2021, so that’s when the removal happened.[3]
Sources: [1] (sphinx-doc.org) [2] (jinjaapidoc.readthedocs.io) [3] (sphinx-doc.org)
Citations:
- 1: https://www.sphinx-doc.org/en/master/changes/1.8.html
- 2: https://jinjaapidoc.readthedocs.io/en/master/_modules/sphinx/ext/autodoc.html
- 3: https://www.sphinx-doc.org/en/master/changes/4.0.html
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CRITICAL: autodoc_default_flags is incompatible with Sphinx 9.1.0 — documentation build will fail.
The upgrade to Sphinx 9.1.0 requires fixing a deprecated configuration. The setting autodoc_default_flags was removed in Sphinx 4.0 and has been non-functional for years. The configuration file docs/source/conf.py (line 68) still uses this setting, which will cause the documentation build to fail with Sphinx 9.1.0.
Replace autodoc_default_flags with autodoc_default_options (a dictionary):
# In docs/source/conf.py, replace line 68:
- autodoc_default_flags = ["inherited-members"]
+ autodoc_default_options = {
+ "inherited-members": True,
+ }Verify the documentation builds successfully after this change.
| setuptools==80.9.0 | ||
| pytest==8.3.5 | ||
| setuptools==82.0.1 | ||
| pytest==9.0.2 |
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🌐 Web query:
pytest 9.0 breaking changes migration guide
💡 Result:
pytest 9.0: breaking changes + migration checklist
1) Python support
- Python 3.9 is no longer supported → upgrade to Python ≥ 3.10. [1]
2) “Removed-in-9” deprecations now fail
PytestRemovedIn9Warningis now an error by default in pytest 9.0, so code/plugins still using APIs slated for removal will start failing. [2]- Temporary stopgap (only for the 9.0.x series): add to
pytest.ini:filterwarnings = ignore::pytest.PytestRemovedIn9Warning[2]
- Temporary stopgap (only for the 9.0.x series): add to
3) Plugin hook signature updates (py.path.local → pathlib.Path)
If you implement these hooks, update signatures to the new pathlib.Path params (old py.path.local params were deprecated and are now effectively enforced by the “RemovedIn9” errors): [3]
pytest_ignore_collect(collection_path: pathlib.Path)(replaces oldpath)pytest_collect_file(file_path: pathlib.Path)pytest_pycollect_makemodule(module_path: pathlib.Path)pytest_report_header(start_path: pathlib.Path)(replaces oldstartdir)pytest_report_collectionfinish(start_path: pathlib.Path)(replaces oldstartdir) [3]
4) pytest.importorskip() behavior tightening
- In pytest 9.0, the previous warning about
ImportErrorvsModuleNotFoundErrorbecomes an error unless you passexc_typeexplicitly.- Fix: pass
exc_type=ImportErrorif you really want to treat anyImportErroras “skip”. [4]
- Fix: pass
5) Command-line collection semantics changed for overlapping/duplicate paths
pytest a/ a/bandpytest a/b a/now behave likepytest a(prefix wins).pytest x.py x.pynow behaves likepytest x.py(no longer runs twice).- Use
--keep-duplicatesif you relied on the old behavior. [1]
6) Smaller but potentially breaking internals/behavior
config.args(non-public) now contains only strings (nopathlib.Pathinstances). [1]- If you rely on the private
config.inicfg, it was broken in 9.0.0 and later restored via a compatibility shim in 9.0.2—but it’s slated for deprecation/removal (avoid using it). [5]
Primary docs to review while migrating
- pytest 9.0.0 changelog (breaking changes + removals) [1]
- Deprecations and removals reference (what the “RemovedIn9” errors are pointing at) [4]
Sources
- pytest changelog (9.0.0 “Removals and backward incompatible breaking changes”). [1]
- pytest changelog (PytestRemovedIn9Warning now errors by default + temporary filterwarnings stopgap). [2]
- pytest docs:
py.path.localhook args replaced withpathlib.Path. [3] - pytest docs:
pytest.importorskip()warning→error timeline in 9.0. [4] - pytest changelog (9.0.2 note about
config.inicfgcompatibility shim + deprecation/removal plan). [5]
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🌐 Web query:
pytest-mock 3.15.1 pytest 9.0 compatibility pytest-env 1.6.0 pytest 9.0 compatibility
💡 Result:
-
pytest-mock 3.15.1 → pytest 9.0.x: Compatible by declared requirements:
pytest-mock==3.15.1requirespytest>=6.2.5(no upper bound), so it can be installed alongside pytest 9.0.x. [1] -
pytest-env 1.6.0 → pytest 9.0.x: Compatible only with pytest ≥ 9.0.2:
pytest-env==1.6.0declarespytest>=9.0.2, so it will not install with pytest 9.0.0 or 9.0.1, but will with 9.0.2+. [2]
Sources: [1] [3] [2] (pypi.org)
Citations:
Update python_requires in setup.py to >=3.10 — pytest 9.0 requires Python 3.10 or higher.
The upgrade to pytest 9.0.2 introduces a hard requirement for Python 3.10+. Your setup.py currently specifies python_requires=">=3.9", which creates a constraint conflict. This must be updated to python_requires=">=3.10" to ensure compatibility.
The pytest plugin dependencies (pytest-mock 3.15.1 and pytest-env 1.6.0) are compatible with pytest 9.0.2, and your test code contains no deprecated pytest patterns (no yield_fixture, py.path.local hooks, or other breaking changes). However, the Python version constraint is the blocking issue.
1 participant
Update sphinx from 7.3.7 to 9.1.0.
Changelog
9.1.0
Links
Update furo from 2024.5.6 to 2025.12.19.
The bot wasn't able to find a changelog for this release. Got an idea?
Links
Update sphinx-autobuild from 2024.4.16 to 2025.8.25.
Changelog
2025.08.25
2024.10.03
2024.10.02
2024.09.19
2024.09.18
2024.09.17
2024.09.03
Links
Update sphinx-sitemap from 2.6.0 to 2.9.0.
Changelog
2.9.0
2.8.0
2.7.2
2.7.1
2.7.0
Links
Update sphinx-click from 5.0.1 to 6.2.0.
Changelog
Links
Update sphinx-autodoc-typehints from 2.3.0 to 3.9.8.
Changelog
3.9.8
3.9.7
3.9.6
3.9.5
3.9.4
3.9.3
3.9.1
3.9.0
3.8.0
3.7.0
3.6.3
3.6.2
3.6.1
3.6.0
3.5.2
3.5.1
3.5.0
3.4.0
3.3.0
3.2.0
3.1.0
3.0.1
3.0.0
2.5.0
2.4.4
2.4.3
2.4.2
2.4.1
2.4.0
Links
Update setuptools from 80.9.0 to 82.0.1.
Changelog
82.0.1
82.0.0
81.0.0
80.10.2
80.10.1
80.10.0
Links
Update pytest from 8.3.5 to 9.0.2.
Changelog
9.0.2
9.0.1
9.0.0
8.4.2
8.4.1
8.4.0