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Complete Python 3 rewrite with native prediction workflow and regression parity - #2
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…rediction batches
Alexander-Mitrofanov
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Alexander-Mitrofanov
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October 21, 2026 17:25
# Conflicts: # AGENTS.md
…ssed genome reuse
Fix formatting and punctuation in README.md regarding DAVID service requirements and report generation.
Updated email account for DAVID requests and clarified CSV import handling.
…ntext Fix genomic target accessibility boundaries
Prepare the Python-only CopraRNA 3.0.0 release
Address review: CopraRNA2, IntaRNAsTar, compressed genomes and vector reports
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Implements phases 0–5 of #1: an installable Python 3 counterpart for all 41 legacy scripts, including complete comparative prediction, exact statistical ports, conservation/Jalview exports, plotting, NCBI/DAVID adapters, maintenance and isolated parallel prediction batches. Every original tracked file remains byte unchanged.
Validation includes captured small-script oracles, 120-cluster statistical fixtures, all 17 bundled genomes in three region modes, and full synthetic CopraRNA1/CopraRNA2 runs. Prediction tables and all 203 Jalview files match the original programs byte for byte; R-data objects, plot geometry and heatmap data/order match semantically. A fresh pinned environment and installed wheel are validated. CI includes Python 3.11–3.13 and a complete scientific/browser integration job.
Matplotlib and Chromium replace the old rendering engines, so graphic bytes and typography differ. Historical R 3.2.2/IntaRNA 2.2.0 numerical equivalence and live external service availability are not certified. Known legacy defects remain documented and preserved here; the separate stacked PR implements phase 6 with individual regression tests. See README.2.md, AGENTS.md and the adjacent per-script mapping documents.