Fix add_hmmer_domains crashes on DigitalSequenceBlock and query=True (2.1.5)

[YalanBi]

Summary

Closes #53: add_hmmer_domains crashed on any call, in two independent ways.

• get_hmmer_sequences returned a plain Python list, but Pipeline.search_hmm has required a DigitalSequenceBlock since pyhmmer 0.7.0 (pinned version: 0.12.1) -- reproduced directly: TypeError: Function call with ambiguous argument types.
• query/ref_query (default query=True, ref_query=False, documented as "True/False to include/exclude all transcripts") were passed straight through as filter expressions into iter_transcripts/iter_ref_transcripts. True crashed with AssertionError: expression should be a string, since _filter_function asserts its input is a string. Verified query=None returns all transcripts unfiltered (same as omitting the argument), so the fix preserves the documented "True = include all" contract.

Bumps version to 2.1.5.

Test plan

• Full pytest suite passes (26 passed, 1 pre-existing unrelated failure deselected -- test_anno_domains fails on master too, from a local pandas/pickle version mismatch unrelated to this change)
• New regression tests reproduce both original crashes against the pre-fix code and pass after the fix, including a real end-to-end pipeline.search_hmm() call
• flake8/black clean
• python -m build + twine check dist/* pass at 2.1.5

[github-actions]

Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

Scanned Files

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