py(deps[dev]): Require ruff>=0.16.0

[tony]

Summary

• Pin a ruff>=0.16.0 floor in the dev and lint dependency groups so contributors and CI see the same diagnostics instead of splitting on whatever ruff each machine resolved.
• Relock uv.lock onto ruff 0.16.0.
• Reformat the Python snippets embedded in AGENTS.md and README.md — 0.16.0 formats Python and pycon code blocks inside Markdown by default, so ruff format --check now reaches documentation it previously ignored.
• Adopt ruff's default rule set. [tool.ruff.lint] select replaces the default set rather than extending it, so this project was silently opting out of every default rule its list did not name. Renaming the key to extend-select layers the project's linters on top of the defaults instead of in place of them. Enabled rules go from 351 to 565.
• Triage the four new findings — three fixed in code, one scoped to an ignore with its reason in the config.

Changes

pyproject.toml — ruff becomes ruff>=0.16.0 in both the dev and lint groups. [tool.ruff.lint] select becomes extend-select, with the same entries, one per line, each carrying the name of the linter it selects, and a comment recording why select stays unset.

uv.lock — relocked, ruff 0.15.22 to 0.16.0.

AGENTS.md, README.md — ruff format normalized the quotes in the conf.py example for linkify_issues. CLAUDE.md is a symlink to AGENTS.md, so it follows.

src/doctest_docutils.py, tests/test_doctest_docutils.py — return-in-init (PLE0101). Three exception classes ended their constructor with return super().__init__(...). __init__ returns None by contract, so the return carried no value and no control flow; it is now a plain statement.

CHANGES — development entries recording the ruff floor, why Markdown snippets are now in scope for ruff format, and the default rule set adoption.

Ignores added

exec-builtin (S102), scoped to docs/conf.py. The Sphinx config reads __title__, __version__, and the project URLs by exec'ing src/gp_libs.py into a dict — the standard idiom for reading package metadata without importing the package, which keeps a docs build from pulling in gp-libs' runtime dependencies. The input is a file in this repository, not untrusted data. The ignore is per-file rather than global so exec anywhere else still trips the rule.

Design decisions

The config change lands by itself, before any fix or ignore, so the rule-set delta is reviewable independently of the code it turned up. Each fix and each ignore is then its own commit carrying the rule's documentation link.

The Markdown reformat is likewise its own commit so a reviewer can confirm at a glance that the documentation churn is ruff's quote normalization and nothing else.

select cannot name the default set — ruff's selector syntax has no token for it — so leaving select unset and layering with extend-select is the only way to get defaults-plus-extras. Expanding to whole linter prefixes instead was considered and rejected: it drags in all of D, PL, S, and friends rather than the curated subset ruff recommends.

Test plan

• uv run ruff check . — all checks passed
• uv run ruff format . --check — all files already formatted
• uv run mypy . — no issues found
• uv run py.test — full suite green, including the doctests collected from docs/ and src/

codecov/patch reports 0% of the diff hit. The only executable lines this branch touches are the three exception constructors, and those constructor bodies were already outside coverage — project coverage is unchanged at 76.32% (+0.00%). The rule fix neither adds nor removes covered lines; earlier commits on this branch touched no Python source at all, which is why the check was previously reported as "coverage not affected".

[codecov]

Codecov Report

❌ Patch coverage is 90.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 76.68%. Comparing base (14807d3) to head (c1ca2f5).

Files with missing lines	Patch %	Lines
tests/test_doctest_docutils.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #82      +/-   ##
==========================================
+ Coverage   76.32%   76.68%   +0.35%     
==========================================
  Files          15       15              
  Lines        1018     1025       +7     
==========================================
+ Hits          777      786       +9     
+ Misses        241      239       -2     

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