Scheduled weekly dependency update for week 11 #675

coderabbitai · 2026-03-16T14:59:45Z

⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

#!/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/ # List all Sphinx configuration files for manual review fd -e py -e rst conf docs/

Repository: DagsHub/client

Length of output: 215

🌐 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 receives app; it now takes config and env.

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 = True to 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 *.app on these objects; use supported APIs/objects instead. (sphinx-doc.org)

5) Parser API deprecations

Parser.set_application() deprecated

Parser.config and Parser.env attributes 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.io classes. (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

🏁 Script executed:

# Get the previous version of Sphinx from the requirements file git diff HEAD~1 docs/requirements-docs.txt | head -20

Repository: DagsHub/client

Length of output: 244

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.

coderabbitai · 2026-03-16T14:59:45Z

⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash # Check for pytest configuration and common patterns that may break # Check pytest configuration files for deprecated settings fd -e ini -e cfg -e toml setup.cfg pytest.ini pyproject.toml tox.ini | xargs cat # Search for deprecated pytest imports or patterns rg -n 'pytest\.(yield_fixture|fixture.*\(scope.*\)|warns.*None)' --type py -g '!venv' -g '!.tox' # Check for --strict usage (removed in pytest 9) rg -n '\-\-strict[^-]' --type py --type toml --type ini

Repository: DagsHub/client

Length of output: 298

🌐 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

PytestRemovedIn9Warning is 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]

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 old path)

pytest_collect_file(file_path: pathlib.Path)

pytest_pycollect_makemodule(module_path: pathlib.Path)

pytest_report_header(start_path: pathlib.Path) (replaces old startdir)

pytest_report_collectionfinish(start_path: pathlib.Path) (replaces old startdir) [3]

4) pytest.importorskip() behavior tightening

In pytest 9.0, the previous warning about ImportError vs ModuleNotFoundError becomes an error unless you pass exc_type explicitly.

Fix: pass exc_type=ImportError if you really want to treat any ImportError as “skip”. [4]

5) Command-line collection semantics changed for overlapping/duplicate paths

pytest a/ a/b and pytest a/b a/ now behave like pytest a (prefix wins).

pytest x.py x.py now behaves like pytest x.py (no longer runs twice).

Use --keep-duplicates if you relied on the old behavior. [1]

6) Smaller but potentially breaking internals/behavior

config.args (non-public) now contains only strings (no pathlib.Path instances). [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.local hook args replaced with pathlib.Path. [3]

pytest docs: pytest.importorskip() warning→error timeline in 9.0. [4]

pytest changelog (9.0.2 note about config.inicfg compatibility shim + deprecation/removal plan). [5]

🏁 Script executed:

#!/bin/bash # Find pytest configuration files echo "=== Looking for pytest configuration files ===" find . -maxdepth 3 \( -name "pytest.ini" -o -name "pyproject.toml" -o -name "setup.cfg" -o -name "tox.ini" -o -name ".pytest.ini" \) -type f 2>/dev/null | head -20 echo "" echo "=== Checking Python version requirement ===" # Check for Python version in setup.py, pyproject.toml, setup.cfg find . -maxdepth 2 \( -name "setup.py" -o -name "pyproject.toml" -o -name "setup.cfg" \) -type f 2>/dev/null | xargs grep -l "python_requires\|Programming Language :: Python :: 3" 2>/dev/null | head -5

Repository: DagsHub/client

Length of output: 190

🏁 Script executed:

#!/bin/bash # Search for common deprecated pytest patterns that break in 9.0 echo "=== Searching for deprecated pytest patterns ===" # Check for deprecated hook signatures (py.path.local) rg 'py\.path\.local|pytest_ignore_collect.*path[^:]*:.*py\.path|pytest_collect_file.*path[^:]*:.*py\.path' --type py -n 2>/dev/null | head -10 # Check for pytest.importorskip usage echo "" echo "=== pytest.importorskip usage ===" rg 'pytest\.importorskip' --type py -A 2 -n 2>/dev/null | head -20 # Check for yield_fixture (deprecated) echo "" echo "=== Deprecated yield_fixture usage ===" rg '@pytest\.yield_fixture|@yield_fixture' --type py -n 2>/dev/null | head -10 # Check for --strict flag echo "" echo "=== Checking for --strict flag usage ===" rg '\-\-strict' --type py --type toml --type cfg --type ini -n 2>/dev/null | head -10

Repository: DagsHub/client

Length of output: 223

🏁 Script executed:

#!/bin/bash # Check plugin version compatibility echo "=== Checking pytest plugin versions from requirements-dev.txt ===" cat requirements-dev.txt echo "" echo "=== Checking for pytest-mock and pytest-env imports/usage ===" rg 'pytest_mock|mocker|pytest_env' --type py -n 2>/dev/null | head -15 echo "" echo "=== Checking pytest configuration in files ===" fd pyproject.toml -x cat {} \;

Repository: DagsHub/client

Length of output: 1573

🏁 Script executed:

#!/bin/bash echo "=== Content of pytest.ini ===" cat ./pytest.ini echo "" echo "=== Content of pyproject.toml ===" cat ./pyproject.toml echo "" echo "=== Checking setup.py for python_requires ===" head -50 ./setup.py | grep -A 5 -B 5 "python_requires"

Repository: DagsHub/client

Length of output: 296

🏁 Script executed:

#!/bin/bash echo "=== Full setup.py to check python_requires ===" grep -n "python_requires\|version\|author" ./setup.py | head -20

Repository: DagsHub/client

Length of output: 537

🌐 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==3.15.1 requires pytest>=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==1.6.0 declares pytest>=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:

1: https://pypi.org/pypi/pytest-mock/3.15.1/json

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.

-Original file line number
+Diff line change
@@ -1,7 +1,7 @@
-    sphinx==7.3.7
-    furo==2024.5.6
-    sphinx-autobuild==2024.4.16
+    sphinx==9.1.0
+    furo==2025.12.19
+    sphinx-autobuild==2025.8.25
     sphinx-copybutton==0.5.2
-    sphinx-sitemap==2.6.0
-    sphinx-click==5.0.1
-    sphinx-autodoc-typehints==2.3.0
+    sphinx-sitemap==2.9.0
+    sphinx-click==6.2.0
+    sphinx-autodoc-typehints==3.9.8

-Original file line number
+Diff line change
@@ -1,9 +1,9 @@
-    setuptools==80.9.0
-    pytest==8.3.5
+    setuptools==82.0.1
+    pytest==9.0.2
     respx==0.22.0
     pytest-git==1.8.0
-    pytest-env==1.1.5
-    pytest-mock==3.14.0
-    fiftyone==1.5.2
-    datasets==3.6.0
-    ultralytics==8.3.237
+    pytest-env==1.6.0
+    pytest-mock==3.15.1
+    fiftyone==1.13.4
+    datasets==4.7.0
+    ultralytics==8.4.22

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Scheduled weekly dependency update for week 11 #675

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coderabbitai Bot Mar 16, 2026

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Scheduled weekly dependency update for week 11 #675

Scheduled weekly dependency update for week 11 #675

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coderabbitai Bot Mar 16, 2026

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Sphinx 9.0 (released Nov 30, 2025): breaking/incompatible changes & how to migrate

Deprecations you should address during the upgrade (to avoid future breaks)

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coderabbitai Bot Mar 16, 2026

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pytest 9.0: breaking changes + migration checklist

1) Python support

2) “Removed-in-9” deprecations now fail

3) Plugin hook signature updates (py.path.local → pathlib.Path)

4) pytest.importorskip() behavior tightening

5) Command-line collection semantics changed for overlapping/duplicate paths

6) Smaller but potentially breaking internals/behavior

Uh oh!

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4) `pytest.importorskip()` behavior tightening