Fix pandas 3 collection, empty-source validation and genotype filtering #437

Fresh CI environments install pandas 3. PR #436 exposed three compatibility failures:

• tests/test_args_outputs.py imports the removed pandas.errors.SettingWithCopyWarning.
• Mapping is_stated over an empty string Series retains string dtype rather than creating a boolean mask.
• Genotype-aware filtering modifies a read-only array returned from pandas (peptide_level |= ...), failing two existing allele-set tests.

Initial collection failure: https://github.com/openvax/topiary/actions/runs/36606156748/job/109535583824
Full pandas 3 run: https://github.com/openvax/topiary/actions/runs/36614230290/job/109563027323

Use the existing boolean stated_values API, check whichever assignment warning class exists while preserving the original-frame assertion, and combine genotype masks without mutating pandas-backed arrays. Verify both pandas generations and the complete CI suite. Fixes are in #436.