Repository navigation
Complete Python 3 rewrite with native prediction workflow and regression parity - #2
Open
Alexander-Mitrofanov wants to merge 17 commits into
Open
Alexander-Mitrofanov wants to merge 17 commits into
Alexander-Mitrofanov wants to merge 17 commits into
Conversation
…rediction batches
Alexander-Mitrofanov
changed the title
Alexander-Mitrofanov
marked this pull request as ready for review
October 21, 2026 17:25
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.