fix(protpardelle): pipe sampling options through guidance CLI

[xraymemory]

Summary

• add Protpardelle-specific CLI flags for config path and sampling controls
• forward config path into ProtpardelleWrapper construction
• forward sampling options into annotate_structure_for_protpardelle
• keep guidance --help lightweight by lazy-loading runtime dependencies

Fixes #258

Validation

• uvx ty check src/sampleworks/utils/guidance_script_arguments.py src/sampleworks/utils/guidance_script_utils.py src/sampleworks/cli/guidance.py tests/cli/test_guidance_cli.py tests/models/protpardelle/test_protpardelle_wrapper.py
• uvx ruff check src/sampleworks/utils/guidance_script_arguments.py src/sampleworks/utils/guidance_script_utils.py src/sampleworks/cli/guidance.py tests/cli/test_guidance_cli.py tests/models/protpardelle/test_protpardelle_wrapper.py
• PYTHONPATH=src uvx --python 3.12 --with pytest pytest --noconftest tests/cli/test_guidance_cli.py -q
• PYTHONPATH=src uvx --python 3.12 --with pytest pytest --noconftest tests/models/protpardelle/test_protpardelle_wrapper.py -q (skipped locally: Protpardelle not installed)

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✨ Finishing Touches

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• Create PR with unit tests
• Commit unit tests in branch michaelanzuoni/issue-258-protpardelle-options

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[manzuoni-astera]

ACTL validation update:

• Started a fresh sampleworks-258 ACTL workspace in diffuse using the sampleworks image.
• Found and fixed an ACTL sync issue from the Protpardelle base branch: .actlignore was excluding src/sampleworks/data/, so the bundled Protpardelle config did not sync. Added fix(actl): sync packaged data files (fb88333).
• ACTL tests passed on the synced workspace:
  • RUNTIME_PIXI=1 pixi run -e protpardelle-dev pytest tests/cli/test_guidance_cli.py tests/models/protpardelle/test_protpardelle_wrapper.py::TestAnnotateStructure::test_adds_sampling_options -q → 56 passed
• A full standalone smoke for this PR now reaches model setup/config loading, then hits the known Protpardelle runtime/device issue fixed in sibling PR fix(protpardelle): complete denoising step wiring #267.
• To validate the intended stacked state, I locally applied fix(protpardelle): complete denoising step wiring #267 on top of this branch (not pushed) and reran the reduced Protpardelle smoke with the new Pipe protpardelle options through to the model #258 options (--protpardelle-config-path, --protpardelle-s-churn, --protpardelle-step-scale, --protpardelle-temperature, --protpardelle-top-p). That completed with Guidance run successfully!.

So: parser/annotation behavior is directly validated on ACTL for #270, and the end-to-end Protpardelle smoke passes on ACTL once #267 is included/merged first.