feat: Drop support for Python 3.8, update dependencies

[MarquessV]

Description

Closes #1779 and #1776, since ruff has lints to help bring the codebase up to standards with the minimum supported Python version.

This also closes #1780 by adding a new CI check that uses osv-scanner to find vulnerabilities in our dependencies.

The updated dependencies will also close #1764, #1736,

Note: The CI checks for Python 3.8 have been removed as part of this PR, and since they are required checks, CI will remain yellow. When this PR otherwise passes CI, and is approved, I will remove the 3.8 required checks.

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.

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
7214	6326	88%	87%	🟢

New Files

No new covered files...

Modified Files

File	Coverage	Status
pyquil/init.py	100%	🟢
pyquil/_version.py	100%	🟢
pyquil/api/init.py	100%	🟢
pyquil/api/_abstract_compiler.py	94%	🟢
pyquil/api/_benchmark.py	92%	🟢
pyquil/api/_compiler.py	57%	🟢
pyquil/api/_compiler_client.py	94%	🟢
pyquil/api/_qam.py	91%	🟢
pyquil/api/_qpu.py	67%	🟢
pyquil/api/_quantum_computer.py	82%	🟢
pyquil/api/_qvm.py	86%	🟢
pyquil/api/_wavefunction_simulator.py	81%	🟢
pyquil/control_flow_graph.py	100%	🟢
pyquil/diagnostics.py	100%	🟢
pyquil/experiment/init.py	100%	🟢
pyquil/experiment/_group.py	92%	🟢
pyquil/experiment/_main.py	81%	🟢
pyquil/experiment/_memory.py	90%	🟢
pyquil/experiment/_program.py	100%	🟢
pyquil/experiment/_result.py	87%	🟢
pyquil/experiment/_setting.py	94%	🟢
pyquil/gates.py	87%	🟢
pyquil/latex/init.py	100%	🟢
pyquil/latex/_diagram.py	92%	🟢
pyquil/latex/_ipython.py	29%	🟢
pyquil/latex/_main.py	100%	🟢
pyquil/latex/latex_generation.py	0%	🟢
pyquil/noise.py	93%	🟢
pyquil/noise_gates.py	86%	🟢
pyquil/operator_estimation.py	89%	🟢
pyquil/paulis.py	95%	🟢
pyquil/pyqvm.py	74%	🟢
pyquil/quantum_processor/init.py	100%	🟢
pyquil/quantum_processor/_base.py	100%	🟢
pyquil/quantum_processor/compiler.py	86%	🟢
pyquil/quantum_processor/graph.py	94%	🟢
pyquil/quantum_processor/qcs.py	79%	🟢
pyquil/quantum_processor/transformers/init.py	100%	🟢
pyquil/quantum_processor/transformers/compiler_isa_to_graph.py	75%	🟢
pyquil/quantum_processor/transformers/graph_to_compiler_isa.py	84%	🟢
pyquil/quantum_processor/transformers/qcs_isa_to_compiler_isa.py	76%	🟢
pyquil/quantum_processor/transformers/qcs_isa_to_graph.py	75%	🟢
pyquil/quil.py	84%	🟢
pyquil/quilatom.py	83%	🟢
pyquil/quilbase.py	94%	🟢
pyquil/quiltcalibrations.py	98%	🟢
pyquil/quiltwaveforms.py	100%	🟢
pyquil/simulation/init.py	100%	🟢
pyquil/simulation/_numpy.py	94%	🟢
pyquil/simulation/_reference.py	76%	🟢
pyquil/simulation/matrices.py	95%	🟢
pyquil/simulation/tools.py	93%	🟢
pyquil/wavefunction.py	79%	🟢
TOTAL	87%	🟢

updated for commit: d21a837 by action🐍

[jselig-rigetti]

Almost entirely nitpicks, but some questions. Looks like you did a bunch of clean up and adding documentation as well 🙌

[MarquessV]

recommonmark is no longer maintained, myst_parser is the recommended alternative.

[MarquessV]

Besides updating the snapshots for syrupy, the changes in these test files are pretty much all related to ruff formatting.