fix: general tooling fixes in support of quil-rs

[antalsz]

This PR is probably unnecessary but I'm leaving it up as draft until I confirm that

Description

When working on quil-rs, I uncovered some errors when quil-rs is checked with Mypy or Ruff; this PR fixes those small issues.

Checklist

• The PR targets the master branch
• The above description motivates these changes.
• The change is atomic and can be described by a single commit (your PR will be squashed on merge).
• All changes to code are covered via unit tests.
• Parameters and return values have type hints with PEP 484 syntax.
• Functions and classes have useful Sphinx-style docstrings.
• (New Feature) The docs have been updated accordingly.
• (Bugfix) The associated issue is referenced above using auto-close keywords.

[github-actions]

Bencher Report

Branch	quil-rs-ci-fixes
Testbed	ci-runner-linux

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Benchmark	Latency	seconds (s)
test/benchmarks/test_program.py::test_copy_everything_except_instructions	📈 view plot ⚠️ NO THRESHOLD	9.32
test/benchmarks/test_program.py::test_instructions	📈 view plot ⚠️ NO THRESHOLD	4.11
test/benchmarks/test_program.py::test_iteration	📈 view plot ⚠️ NO THRESHOLD	4.21

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[antalsz]

Confirmed, this is unnecessary – I was misled by some broken CI in quil-rs. Sorry!