qn-chain

---

name: qn-chain description: Modular workflow chain composing the QuantumNovelty skill catalog (deep_research, quantum_reviewer, logical_fallacies, novelty_audit, cross_llm_prediction, pareto_explorer, quantum_paper, process_summary, ...) into named pipelines for quantum-computing research. Per-stage --with-X / --skip-X toggles, structured telemetry (pipeline_summary.json, decision_history.json, _stage_health.json, HEARTBEAT_AUDIT.md, checkpoint.json — AutoResearchClaw's stage-health pattern), strict no-fallback env defaults, and a cross-model falsifiability fork. The QN-specific contributions are: paper-audit as a first-class pipeline, the 11 quantum-CS-specific fallacy taxonomy in the fallacies stage, the cross-LLM amplitude-prediction skill (cross_llm_prediction) as an opt-in stage, and the audit-and-falsify Pareto novelty check.

QN Chain — workflow runner

A single entry point (chain/run.sh, dispatching to chain/pipelines.py) that composes the QuantumNovelty skill catalog into modular pipelines with per-stage toggles, resumable checkpoints, and structured telemetry.

Pipelines

Pipeline	Building blocks (in order)	Use case
paper-audit	deep_research --mode review → quantum_reviewer --mode full → logical_fallacies → process_summary (Stage-6 CQE)	Audit an existing paper (PDF / TeX / text). Default 4 stages; opt-in novelty-audit + cross-llm.
patent-audit	deep_research --mode review (prior-art) → patent_reviewer --mode full (USPTO panel) → logical_fallacies → process_summary	Examine a quantum patent. Input --patent URL|NUMBER|FILE (Google Patents). 6-voice §§101/102/103/112 + quantum-operability panel → an Office Action + _office_action.json.
full	deep_research --mode full → pareto_explorer → novelty_audit → quantum_paper --mode full → cross_llm_prediction → quantum_reviewer → logical_fallacies → process_summary	Full Stage 1→6 pipeline: literature surface → discovery → audit → draft → cross-LLM → review → CQE.
mid-entry-stage-2.5	deep_research --mode full (lit-1.5) → novelty_audit (audit-only mode) → quantum_reviewer → logical_fallacies → process_summary	Paper exists; integrity-first pass without the discovery / draft stages.
mid-entry-stage-4	quantum_paper --mode revision → quantum_reviewer --mode re-review → process_summary	Reviewer comments in hand; revision pass.

Run bash chain/run.sh --list-stages for the live table.

Option surface

The full flag surface:

# Pipeline + I/O
--pipeline NAME             Pick a pipeline (paper-audit | full | mid-entry-stage-2.5 |
                            mid-entry-stage-4 | status | list-stages)
--llm BACKEND               claude (default) | codex | codex-acp | codex-mcp | anthropic-api
--paper PATH                Existing paper file (text / TeX / PDF-extracted text)
--topic STR                 Research question / paper title — grounds deep_research
--journal STR               Venue context for prompts (npj-quantum-information, prx-quantum, …)
--quantum-lib LIB           Library context for code-gen prompts (qiskit, pennylane, qutip, …)
--outdir DIR                Output root. Auto-derived to runs/<ts>/<llm-slug>/<pipeline>/ if unset.

# Stage toggles (default-on stages of paper-audit shown)
--skip-research             Drop deep_research --mode review
--skip-reviewer             Drop quantum_reviewer --mode full
--skip-fallacies            Drop logical_fallacies
--skip-cqe                  Drop process_summary

# Opt-in stages
--with-novelty-audit        Add novelty_audit  (needs --pareto-archive PATH)
--with-cross-llm            Add cross_llm_prediction  (needs --hamiltonian + --geometry-sweep + --llms)
--with-synthesizer          Add editorial synthesis (ARS editorial_synthesizer
                            pattern). Consumes the panel +
                            fallacy + research outputs already in the outdir;
                            produces an Editorial Decision Package with
                            CONSENSUS-N tags, disagreement resolution,
                            3-priority revision roadmap, response-letter
                            template. Runs as stage 03b, before cqe.

# ARC profile bundles + per-stage flags
--with-arc-pipeline         Bundle: arms every QN-applicable ARC stage
--with-arc-novelty-check    Alias for --with-novelty-audit
--with-arc-problem-tree     | --with-arc-literature-pipeline | --with-arc-paper-outline
--with-arc-draft-quality    | --with-arc-iterative-refine    | --with-arc-citation-integrity
--with-arc-compilation-quality | --with-arc-paper-verification | --with-arc-pdf-review
--with-arc-quality-gate     | --with-arc-research-decision   | --with-arc-knowledge-archive

# Cross-vendor falsifiability
--with-cross-model          Fork the chain on claude + codex (claude_branch/ + codex_branch/),
                            write _cross_model_index.json pointing at both.

# Checkpoints
--pause-after STAGE         Write checkpoint.json after STAGE completes, exit cleanly
--hitl-pause-after STAGE    Alias; same behaviour (sets QN_HITL_PAUSE_AFTER env)
--resume-from STAGE         Treat earlier stages as complete; pick up at STAGE
--force                     Re-run completed stages (override idempotent resume)

# Backend policy
--with-codex-fallback       Re-enable the legacy silent claude→codex fallback.
                            Off by default — framework default is strict.

# Process summary tuning
--no-llm-narrative          Disable the LLM-narrative pass in process_summary

Telemetry

Every paper-audit run writes (alongside the per-stage outputs):

File	Schema source	Purpose
<stage>/_stage_health.json	chain/common/stage_telemetry.sh	stage_id, status, duration_sec, artifacts_count, error, started_iso, ended_iso
pipeline_summary.json	chain/common/telemetry.py::pipeline_summary	Aggregate of every _stage_health.json + content_metrics (CQE composite, fallacy count)
decision_history.json	chain/common/stage_telemetry.sh::decision_log	Append-only log: proceed / refine / pivot / pause / block / fail
HEARTBEAT_AUDIT.md	chain/common/heartbeat.sh::audit_heartbeats	Per-stage OK / TIMED_OUT / HUNG_OR_KILLED / RUNNING / UNTRACKED
checkpoint.json	chain/common/stage_telemetry.sh::checkpoint_write	Resumable pause marker; written when --hitl-pause-after STAGE matches
_chain_config.json	chain/pipelines.py::pipeline_paper_audit	Resolved chain configuration: pipeline preset, llm, default-on/opt-in stages, decision-log
_run_summary.json	chain/pipelines.py::_emit_pipeline_summary	Subprocess-RC view: per-stage exit codes, elapsed-s, skip status
02_reviewer_panel/_quality_gate.json	ARC quality_gate shape (deterministic parse)	{score_1_to_10, verdict, votes, threshold, passes_threshold, required_actions} — mean of per-voice panel scores gated at --gate-threshold (default 7.0). No extra LLM call.

chain/common/heartbeat.sh and chain/common/stage_telemetry.sh implement AutoResearchClaw's stage-health / heartbeat / checkpoint pattern in bash. chain/common/telemetry.py is a Python port of the same six helpers so chain/pipelines.py produces the same JSON shapes when it orchestrates from Python instead of bash.

Strict-env defaults

Set at module load (override only when really needed):

Env var	Default	Purpose
CLAUDE_DISABLE_CODEX_FALLBACK	1	No silent claude→codex fallback inside the claude CLI
INVOKE_LLM_NO_FALLBACK	1	No invoke_llm-level fallback
QN_DISABLE_BACKEND_FALLBACK	1	No QN-level fallback
QN_HITL_PAUSE_AFTER	unset	Stage-id substring; when set, the chain checkpoints + exits after match

Examples

# Default audit of one paper:
bash chain/run.sh --pipeline paper-audit \
  --llm codex --paper paper.txt --journal npj-quantum-information \
  --topic "Generative flow-based warm start of the VQE" --outdir runs/flowvqe

# Reviewer-panel-only run:
bash chain/run.sh --pipeline paper-audit --skip-research --skip-fallacies --skip-cqe ...

# Examine a quantum patent (USPTO examiner panel → Office Action):
bash chain/run.sh --pipeline patent-audit \
  --patent "https://patents.google.com/patent/US10614371B2/en" \
  --art-unit "AU 2128 (CPC G06N10/00)" --llm claude --outdir runs/patent_demo
# Output: 02_examiner_panel/office_action.md + _office_action.json
# (disposition, rejected_claims, rejections_by_statute {101/102/103/112}).

# Add cross-LLM falsifiability:
bash chain/run.sh --pipeline paper-audit \
  --with-cross-llm --hamiltonian H2 \
  --geometry-sweep "R_HH=0.7,0.9,1.1,1.3,1.5 A" \
  --llms claude,codex ...

# Cross-model fork:
bash chain/run.sh --pipeline paper-audit --with-cross-model ...

# Checkpoint after reviewer panel, resume from fallacies:
bash chain/run.sh --pipeline paper-audit --hitl-pause-after reviewer ...
# ...inspect outputs...
bash chain/run.sh --pipeline paper-audit --resume-from fallacies ...

# List every pipeline's stages + their toggle flags:
bash chain/run.sh --list-stages

Files

• chain/run.sh — bash dispatcher; argparse + auto-discover skills + dispatch to pipelines.py
• chain/pipelines.py — Python orchestrator with the canonical stage definitions
• chain/common/heartbeat.sh — heartbeat + sentinel wrapper (ARC pattern)
• chain/common/stage_telemetry.sh — stage-health + checkpoint + decision-log helpers
• chain/common/telemetry.py — Python port of the same six helpers
• tests/test_telemetry.py — 30+ tests pinning the telemetry schema contract

What's NOT here yet

A handful of ARC profile flags are surfaced in the option table but currently route to nothing at runtime — they're documented for forward-compatibility and emit a decision_log entry on activation. As QN ports more ARC stages (--with-arc-citation-integrity and --with-arc-quality-gate are the next ones planned), the flags will start exercising real stages.