Strengthen supplement matched protein sequence ID test

[wwood]

Motivation

• Ensure matched protein sequence IDs produced by the supplement flow contain the originating SingleM/GraftM package basename for clearer provenance.
• Validate that the code which replaces raw HMM names in output IDs with package basenames is working as expected.

Description

• Updated the supplement worker to map HMM NAME entries to graftm_package_basename and to use that package basename when constructing matched protein sequence IDs.
• Added validation when concatenating HMMs to fail on missing or duplicate HMM NAME entries and pass a hmm_name_to_package mapping into the per-genome worker.
• Strengthened test_output_matched_protein_sequences in test/test_supplement.py to acquire the metapackage, collect package basenames via graftm_package_basename(), and assert the matched protein record IDs include one of those basenames.

Testing

• Ran the focused test file with pixi run -e dev pytest test/test_supplement.py.
• Test results: 7 passed, 2 skipped, 1 warning and the test run completed successfully.

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[chatgpt-codex-connector]

Allow metapackages with shared HMM NAMEs

The new duplicate check raises an exception whenever two packages share the same HMM NAME. Metapackages can legitimately include multiple SingleM packages that reuse the same GraftM alignment HMM (e.g., different window sizes or taxonomy variants backed by the same align_hmm), which means their NAME fields collide; in that case supplement will now abort before running hmmsearch even though it previously worked. If you need the package basename in matched protein IDs, consider disambiguating by rewriting HMM NAME entries to include the package basename (or falling back to the original HMM name when duplicates exist) instead of failing on duplicates.

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