<!-- LLM-PathwayCurator/examples/demo/README.md -->
# Demo

This demo reproduces the **core LLM-PathwayCurator pipeline** on a tiny input.

## What it does
Running `./run.sh` generates:
**fgsea results → EvidenceTable → distill → modules → claim proposal → mechanical audit → decision-grade report**.

- No R required (this demo does **not** run fgsea itself; it consumes an fgsea results table).
- All acceptance decisions are mechanical (PASS/ABSTAIN/FAIL); the LLM is not needed.


## Run
From the repository root:

```bash
./examples/demo/run.sh
```

## Inputs
- `inputs/fgsea_results.tsv` : tiny fgsea result table (must include `pathway` and `leadingEdge`)
- `sample_card.json` : study context used for context-conditioned proposal

If `evidence_table.tsv` is not present, it will be generated from `inputs/fgsea_results.tsv`.

## Outputs
All outputs are written to:
- `out/demo/`: outputs generated by your local run
- `expected/`: a precomputed snapshot so reviewers can inspect outputs without running the pipeline

### Key files:
- `report.md` / `report.jsonl` : decision-grade records (final)
- `audit_log.tsv` : mechanical decisions with reason codes
- Intermediate TSVs (EvidenceTable / distilled / modules / proposed claims)

## Notes
This demo is intentionally small and deterministic (fixed seed) to make reviewer reproduction easy.
