Typecheck error in protenix-dev

[DorisMai]

See logs from PR #234. Error appears from src/sampleworks/utils/msa.py and there are a few warning in scripts/eval/classify_altloc_regions.py

This is blocking PR from merged.

[DorisMai]

The error in src/sampleworks/utils/msa.py was fixed in PR #234 . Warnings are not addressed yet.

[manzuoni-astera]

Covered by #266. The Protenix MSA typecheck/runtime issues were fixed there, including the Mapping-based MSA input type, deterministic key ordering, and the Protenix msa_search path argument. Validation passed locally and CI typecheck/tests are green; GPU jobs remain queued separately.

[xraymemory]

Covered by #266. The Protenix MSA typecheck/runtime issues were fixed there, including the Mapping-based MSA input type, deterministic key ordering, and the Protenix msa_search path argument. Validation passed locally and CI typecheck/tests are green; GPU jobs remain queued separately.