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Commits on May 15, 2026

• bump Diamond dependency to v2.2.0

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Commits on Feb 9, 2026

• bump Diamond dependency to v2.1.22

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Commits on Feb 2, 2026

• Update Diamond link in README.md [skip ci]

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Commits on Jan 29, 2026

• polish readme [skip ci]

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• bump version to v1.12.0

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• catch rare product None cases #415

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• set Diamond load threads parameter

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Commits on Jan 28, 2026

• discard wrong user protein CI tests #407

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• relax handling of incorrectly formatted user proteins from errors to warnings #407

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• update readme

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• bump tRNAscan-SE dependency to v2.0.12

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• bump Infernal dependency to v1.1.5

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• bump Pyrodigal dependency test to v3.7.0

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• bump PyHMMER dependency test to v0.12.0

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• bump Diamond dependency to v2.1.21

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• bump BLAST dependency to v2.17.0

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• bump AMRFinderPlus dependency to v4.2.7

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• fixed wrong reverse stranded tmRNA tag_peptide positions #420

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• fix unsupported complement operator in tmRNA tag_peptide qualifier #420

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• fix gapped CRISPR repeat stop positions #410

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• catch PILER-CR errors and provide warning instead of Bakta failure #411 #416

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• Update PyHMMER to `v0.12.0` (#421)

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• fix bug in CRISPR spacer detection due to not fully supported IUPAC code in regex #416

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Commits on Jan 27, 2026

• Improve diamond sorf search (#379)

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• Bump Python to v3.13 (#422)

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• update bio.tools patch [skip ci]

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  b4e0cb3

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• bump pyrodigal to v3.7.0

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Commits on Jan 26, 2026

• tmp pin PyHMMER to >=0.10.15,<0.12.0

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• remove Python v3.12 from CI lists

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• bump GH PyPI + CI workflow Python to 3.11

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• bump GH linting + packaging workflows to Python 3.10 to 3.12

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• bump Pyrodigal to v3.7.0

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Commits on Jan 21, 2026

• add User-Agent header to db download http requests #417 #419

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Commits on Jan 9, 2026

• relax import of user-provided CDS regions #389

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• refactor deprecated log warn msg

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