apcamargo/genomad: geNomad v1.12.0

Changed

• Refactor extend_provirus_edges in the find-proviruses module to simplify the provirus boundary-extension logic while preserving the behavior.

Fixed

• Restore temperature scaling in utils.softmax. A regression introduced in version 1.11.1 caused the function to ignore the temperature parameter.
• Fix FASTA parsing when the final line lacks a trailing newline by removing only "\n" with removesuffix("\n") instead of always dropping the last character.
• Fix left-boundary provirus extension across chromosome markers in the find-proviruses module. A sign error caused the marker-range check to inspect the wrong interval during leftward extensions, so blocking host markers could be missed.
• Fix summary fallback to nn-classification with provirus results. The plain nn path incorrectly selected calibrated provirus neural network scores instead of uncalibrated ones.
• Fix FDR threshold handling so --max-fdr 0 does not disable FDR filtering, and scores with FDR exactly equal to the configured maximum are retained.
• Fix detection of calibrated marker-classification outputs in summary. It now checks the NPZ file that the module actually consumes, instead of the TSV file.