BenKuhnhaeuser/GPID: GeneParliamentID manuscript re-submitted

GPID v1.2.0 GPID v1.2.0 is a substantial update released alongside the resubmission of the GPID manuscript following peer review. This release incorporates changes made in response to reviewer feedback, with a particular focus on improving usability, reliability, reproducibility, and packaging. Key changes The confidence workflow has been renamed: gpid validate is now gpid confidence gpid validate confidence is now gpid confidence estimate Calibration, confidence, and identification outputs have been streamlined, with more consistent file names and output locations thresholds_filtering.csv now uses a long-format parameter,value structure, while legacy threshold files remain supported Calibration and confidence workflows now include improved plotting, clearer threshold visualisation and updated confidence calculations Input validation and error handling have been strengthened across reference preparation, calibration, confidence estimation and identification A bug has been fixed that caused a silent exit of gpid identify at step 5/6 in some computational environments. BLAST processing and pipeline failure reporting have been improved to reduce the risk of incomplete or misleading outputs Help messages, output announcements, and script documentation have been made more consistent throughout GPID Packaging and reproducibility The Conda packaging has been updated to reflect the current GPID implementation and development environment. This includes revised dependency requirements, updated installation checks, and expanded tests covering BLAST, R packages, plotting, and file installation. Compatibility This release includes changes to command names, output paths, and some output-file formats. Existing scripts written for earlier versions of GPID may therefore require minor updates. In particular, users should update workflows that rely on the previous validation commands or previous calibration and confidence output locations. Previously generated files are not automatically converted when upgrading to v1.2.0.