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chore: clean up redundant scripts and consolidate thresholds
- Archive 16 redundant/one-off scripts to scripts/archive/ - Archive 3 duplicate Python files from notebooks/pfam/ - Remove "simple" CSV files, add full threshold tables to GETTING_STARTED.md - Keep 4 clean SLURM scripts: build, embed, fdr, fnr - Update .gitignore for archive directories Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>dd5ecfc
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fix: FDR computation bug, clean up CLEAN/DALI notebooks
- Fix argument order bug in compute_fdr_table.py: get_thresh_FDR expects (labels, sims, alpha) not (sims, labels, alpha) All previous FDR results were invalid (threshold=0.0) - Clean up CLEAN notebook (analyze_clean_hierarchical_loss_protein_vec.ipynb): - Add proper documentation and paper references - Use relative paths from repo root - Remove debug imports (pdb, ipdb) - Streamline to focus on conformal calibration demo - Clean up DALI notebook (scope_dali_prefilter_foldseek.ipynb): - Add documentation explaining data requirements - Use pre-computed results from dali_thresholds.csv - Add verification against paper claims - Archive original notebooks to notebooks/archive/ - Fix verify_clean.py and verify_dali.py paths - Add slurm_compute_fdr_all.sh for unified FDR computation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>e33fa0e -
chore: clean up stale results, add partial FNR script
- Remove old demo output files from results/ - Archive CLEAN and DALI notebook originals - Add slurm_compute_fnr_partial.sh for partial-match FNR computation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>43965f0 -
refactor: consolidate CLI to single 'cpr search' command
- Remove 'cpr find' command - Make 'cpr search' accept both FASTA and embeddings (auto-detect) - Clean up genes_unknown.ipynb (use relative paths, clear outputs) - Archive original notebook to notebooks/archive/ - Update GETTING_STARTED.md to reflect new CLI - Add merge_fdr_results.py and submit_fdr_parallel.sh scripts The search command now handles the complete workflow: - FASTA input: embed -> search -> filter -> output - Embeddings input: search -> filter -> output Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>aae26ca
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Merge gradio-ron branch: add Gradio UI, reorganize notebooks
- Add Gradio interface with backend (collaborative, visualization) - Add Dockerfile and environment.yml - Reorganize notebooks into notebooks/ directory - Add FDR/FNR threshold scripts - Add requirements.txt Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>3553828
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bunch of renaming and refactoring
30c3022