Refactor/Cleanup#5
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Cleaned up llmize entire codebase for shipping, removes tooluniverse and enrichment stack, consolidate JSON-reduction modules, and fixes stalls with smaller models.
What changed
Removals / decoupling
Deleted enrich.py and all ToolUniverse/enrichment wiring (--enrich, deps, Docker/Nextflow flags); moved extract_entities into verify.py (its only consumer).
Removed dead code: call_ollama, json_reduction/main.py, json_reduction/json_topKeys.py, plus unused imports/params. Dropped tooluniverse/PyYAML from requirements and the Docker build.
Simplification
Unified whole-report and section-by-section into a single interpret_report() (whole report = one chunk; synthesis only when >1).
interpret.py is now a pure library; pipeline.py is the single CLI entry point.
Consolidated json_reduction/ (json_load/clean/write/merger → one reduction.py).
Reduction + annotation now run in memory; --save-intermediates writes the intermediate JSON only when requested.
Fixes
Fixed a small-model stall on numeric sections (e.g. deconvolved_probs): _round_floats() strips spurious 17-digit float precision from prompts, which was triggering repetition loops.
Reconciled with main: preserved the gene-split (verify.py), prompt-injection escaping (main.nf), prompt tweaks, and the data-grounding review feature; repaired the review path's extract_entities import after enrich removal.
Verification
Deterministic outputs (annotated report, entities, prompts) byte-identical to the pre-refactor baseline, except the intended prompt-float rounding.
compileall and pipeline.py --check pass; no reintroduced enrich/ToolUniverse references.
Full offline Docker and Nextflow runs complete end-to-end with a small model.
Summary generated by Claude Code