Change log

Major changes to orthofisher are summarized here.

1.1.3:

  • Added --seq-type with protein, nucleotide, and auto modes.

  • --seq-type auto now infers HMM alphabet and dispatches hmmsearch or nhmmer.

  • Added --resume checkpoint mode to continue interrupted runs in an existing output directory.

  • Added tests covering nucleotide auto-dispatch and resume/checkpoint behavior.

  • Updated usage/docs for nucleotide-query workflows and resumed execution.

1.1.2:

  • Default output is now slim (scog/, long_summary.txt, short_summary.txt).

  • Added --verbose-output to also write all_sequences/ and retain hmmsearch_output/ files.

  • Added --force to explicitly overwrite an existing output directory.

  • Updated Python support to 3.10-3.13 and dropped 3.9.

  • long_summary.txt now includes per-hit evalue and bitscore columns.

  • Improved CLI validation for --evalue, --bitscore, and --cpu.

  • Improved runtime error handling with clearer typed exceptions and centralized CLI error reporting.

  • Refactored integration and entrypoint tests to reduce duplication and improve environment portability.

1.0.0: introduced -c, --cpu argument and -o, --output_dir argument

0.2.0: compatible with python 3.9 and biopython 1.79

0.0.8: created -b, --bitscore parameter