27 fix feature separate composite score grid search from aqs benchmark and add instanexus optimize cli#28
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…_combination Replace AQS weights (0.35/0.25/0.25/0.15) with the Composite Score formula as defined in Reverenna et al., bioRxiv 2025: 0.5 * coverage + 0.3 * N50 + 0.1 * (1 - scaffolds_count) + 0.1 * max_length Additional fixes: - add max_length to evaluate_combination return dict - fix FileNotFoundError when output_folder='' via tempfile.TemporaryDirectory - fix numpy int64 JSON serialization with .item() - add _build_instanexus_command for ready-to-run CLI output
Add optimize.py as a thin entry point delegating to grid_search.main(). Register instanexus-optimize in [project.scripts] and add scikit-learn>=1.3 as a core dependency (required by MinMaxScaler in the grid search).
…utilities Integrate two genuinely new functions from utils.py into analyze_optimization.py: - combine_json_to_csv: walks output dirs, merges JSON stats into a single CSV - plot_coverages_from_runs: barplots of contig/scaffold coverage across runs
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marcoreverenna
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27-fix-feature-separate-composite-score-grid-search-from-aqs-benchmark-and-add-instanexus-optimize-cli
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