renkin 1.0.0 → 1.0.2

package/README.md

@@ -171,9 +171,16 @@ Use `--format mermaid` for GitHub/Notion-compatible flowcharts.
 
 ## Current Limitations
 
-⚠️ Benchmark numbers are under active re-measurement after a validator-accuracy
-fix — historical 78.0%/95.9%/81.8%(ChEMBL) figures elsewhere in this repo predate
-that fix and are invalidated. RENKIN does not predict yields, calibrated
+Current release: **v1.0.2**.
+
+⚠️ The corrected 4,903-target v1.0.1 shared-stock comparison is complete. RENKIN
+recorded 591/4,903 primary successes (12.05%) versus AiZynthFinder 4.4.1's
+200/4,903 (4.08%); the paired difference was +7.975 percentage points with 95%
+CI [+7.098, +8.852]. The full v1.0.1 arm passed integrity verification, so both
+the statistical and formal publication gates pass. This is a result for the
+declared shared-stock endpoint, not universal CASP superiority. Historical
+78.0%/95.9%/81.8%(ChEMBL) figures
+elsewhere in this repo predate validator fixes and are invalidated. RENKIN does not predict yields, calibrated
 experimental success probabilities, or side reactions, and does not search
 the literature automatically (`success_probability` is a template-frequency
 search-ranking score, not a calibrated prediction — see
@@ -410,16 +417,17 @@ for the full acceptance criteria and licensing split.
 | **Ring-context safety guard** | `--ring-context-policy conservative --ring-context-sidecar <path>` — opt-in match-level filter that rejects an extracted template's ring-opening/closing disconnection when its historical training data never observed that bond as ring-forming/-breaking; default `disabled` (unchanged legacy behavior) — see [Issue #72](https://github.com/kent-tokyo/renkin/issues/72) |
 | **LightGBM candidate reranker** | `--reranker-model`/`--reranker-freq-table` (CLI) or `reranker_model_path`/`reranker_freq_table_path` (Python) — opt-in, ordering-only re-ranking via a frozen LightGBM model; never changes which candidates are generated, only their order, and reproduces legacy ordering byte-for-byte when off. Paired 100-target route-search gate: `route_to_configured_stock` 16→20 (+4/-0). `python3 scripts/fetch_reranker_model.py` fetches the frozen model (SHA-256-verified, not bundled in any package — see [Roadmap](#roadmap)) |
 | **Coverage mode** (opt-in) | `--search-mode coverage --coverage-templates <path>` (CLI) or `search_mode="coverage"`, `coverage_templates_path=...` (Python) — if the default template set finds no route, automatically escalates to a larger, separately loaded template set, cooperatively cancellable via `--coverage-timeout-secs`. Standard-mode output is byte-for-byte unchanged when not used. `python3 scripts/fetch_coverage_templates.py` fetches the frozen 2,000-template Stage-2 set (SHA-256-verified, not bundled in any package, same reasoning as the reranker model — see [Roadmap](#roadmap)) |
+| **Staged recovery** (opt-in, native) | `--search-mode recovery --beam-diversity-slots N` preserves a successful baseline and conditionally escalates element gating, diversity, depth, and caller-supplied narrow-to-broad coverage tiers. Every attempt is audit-visible; standard mode and its defaults are unchanged. See [staged recovery mode](docs/guides/staged-recovery.md) |
 | **RENKIN Bridge / `audit-route`** | `renkin audit-route route.json [--format auto\|renkin\|aizynthfinder\|syntheseus\|synplanner] [--stock stock.smi] [--output human\|json]` — tool-neutral route audit: structural integrity, stock, and declared-reaction forward-replay validation, each reported independently as `pass`/`fail`/`not_evaluable`, rolled up into a route-level `pass`/`fail`/`partial` verdict. Reads RENKIN-native route JSON (v0.25.0), real AiZynthFinder route JSON — single-target and gzip-compressed batch output, verified against AiZynthFinder 4.3.2, 4.4.0, and 4.4.1 specifically, not claimed for every version (v0.26.0, version matrix widened v0.32.0) — Syntheseus routes via the optional `renkin.syntheseus_exporter`'s `syntheseus-route-v1` interchange schema, since Syntheseus itself has no native route export (v0.30.0) — and real SynPlanner 1.6.0 `write_routes_json` exports directly, no exporter package needed (v0.34.0); `--format auto` detects the input shape and hard-errors rather than guessing on anything ambiguous. [AiZynthFinder walkthrough →](https://kent-tokyo.github.io/renkin/guides/aizynthfinder-audit-demo/) · [Syntheseus walkthrough →](https://kent-tokyo.github.io/renkin/guides/syntheseus-audit-demo/) · [SynPlanner walkthrough →](https://kent-tokyo.github.io/renkin/guides/synplanner-audit-demo/) |
-| **Route scoring** | `confidence`, `step_confidence`, `success_probability` (Retro-prob style), `convergency`, `atom_economy`, `route_cost` (`Σ BB cost + steps×0.5`, or actual prices via `--bb-prices`/`--stock`) per step/route — see caveat below the table |
+| **Route scoring & diagnostics** | Separate `confidence`, `success_probability`, cost, feasibility findings, building-block diversity, and template-proxy chemical-idea diversity; no aggregate laboratory-feasibility score is fabricated — see the caveat below and the [diagnostics](docs/guides/route-feasibility-diagnostics.md) / [diversity](docs/guides/route-set-diversity.md) guides |
 | **Step metadata provenance** | Each step reports `metadata_source`/`metadata_scope` so it's machine-readable whether `conditions`/`reaction_family` came from a rule-author default vs. something more grounded; absent (not fabricated) for extracted templates |
 | **Pareto multi-objective search** | `--format pareto` returns a Pareto front across `route_cost`/`success_probability`/`steps`; objectives configurable via `--objectives` |
 | **Constraint DSL** | `--constraints constraints.json` — element/building-block filters, step/cost limits, confidence thresholds, required/avoided/preferred reaction families; enables LLM → RENKIN pipelines |
 | **Output formats & diagnostics** | `--format json\|tree\|mermaid\|explain\|compare\|compare-json\|pareto`; zero-route JSON includes a `diagnostics` block with `likely_causes`/`suggestions` |
 | **`renkin-forward` toolkit** | `predict` (rank forward products), `enumerate` (bounded products from one reactant + partner library), `hints` (partner-free retrieval hints, no concrete product), `validate` (forward-verify each retro step) — see the [Forward guides](docs/guides/forward-retrieval-hints.md#predict--enumerate--hints-at-a-glance) |
 | **`renkin-bench`** | USPTO-50k/PaRoutes evaluation with `--plausibility` (forward-validated composite score), `--failure-taxonomy`, atom-balance checks (`target_MW > Σ precursor_MW`), and multi-stage `cascade` re-runs on unsolved targets — see [Benchmark](#benchmark) |
-| **Stock management** | `renkin stock stats\|validate\|coverage` for legacy CSV plus the `vendor_stock` library API for v0.38 CSV/TSV vendor records (SMILES, ID, vendor, price, lead time, availability), explicit exact/parent/stereo/tautomer match modes, and an InChIKey candidate index |
-| **MCP server** | `renkin-mcp` exposes 6 tools: `find_routes`, `validate_route`, `explain_route`, `find_pareto_routes`, `plan_with_constraints`, `estimate_diversity` |
+| **Stock management** | `renkin stock stats\|validate\|coverage\|compile`; integrity-checked `.rstock` snapshots avoid reparsing large stocks, while the `vendor_stock` API supports source, price, lead-time, availability, and exact/parent/stereo/tautomer policy |
+| **MCP server** | `renkin-mcp` exposes 7 tools over stdio (`find_routes`, `validate_route`, `explain_route`, `find_pareto_routes`, `plan_with_constraints`, `estimate_diversity`, `diagnose_failure`) and supports the legacy `2024-11-05` and modern `2026-07-28` protocol revisions; see the [MCP guide](docs/guides/mcp.md) |
 | **`renkin-doctor`** | Environment diagnostic binary — templates, building blocks, Python import, tool versions, data integrity |
 | **`renkin-kg`** | Reaction knowledge graph builder — bipartite mol↔reaction graphs from routes, GraphML/Cypher export |
 | **Multi-target** | `pip install renkin` (pre-built wheels, Linux/macOS/Windows) · `npm install renkin` (~500 KB WASM, near-native browser speed) |
@@ -469,6 +477,23 @@ USPTO-50k test set (4,907 molecules, full evaluation):
 
 > **Evaluation definition**: A molecule is *solved* if `find_routes` returns at least one route whose leaf precursors are all in the building block set, within depth=5 and beam=100. Ground-truth reactants from USPTO-50k are **not** checked — any commercially accessible route counts.
 
+### Formal v1.0.1 shared-stock comparison (4,903 paired targets)
+
+| Arm | Primary route-to-shared-stock successes | Rate |
+|---|---:|---:|
+| RENKIN v1.0.1 | 591 / 4,903 | 12.05% |
+| AiZynthFinder 4.4.1 | 200 / 4,903 | 4.08% |
+
+The paired RENKIN-minus-AiZynthFinder difference is **+7.975 percentage
+points**, with paired-bootstrap 95% CI **[+7.098, +8.852]**. The statistical
+and formal publication gates both **PASS**. The complete v1.0.1 arm passed
+target-set, manifest, schema, and route-hash integrity verification; all 591
+reported routes had parseable normalized trees terminating in the configured
+shared stock. The frozen v1.0.0 HOLD artifact remains preserved separately.
+This is a shared-stock route endpoint, not experimental yield or universal CASP
+superiority. [Protocol and status](docs/benchmark/formal-v1.0-competitor-comparison.md)
+· [corrected report](data/comparison/formal_v1.0.1/formal_report.md)
+
 ### Corrected baseline (commit `e20dc8c`, 2026-07-22)
 
 | Public label | Internal metric | Value |
@@ -557,7 +582,7 @@ The JSON output includes `avg_nodes_expanded`, `avg_confidence`, `avg_convergenc
 }
 ```
 
-**Tools** (6):
+**Tools** (7):
 
 | Tool | Description |
 |---|---|
@@ -567,13 +592,18 @@ The JSON output includes `avg_nodes_expanded`, `avg_confidence`, `avg_convergenc
 | `find_pareto_routes` | Pareto-front multi-objective route search |
 | `plan_with_constraints` | Constraint-DSL planning (element/building-block filters, step/cost limits, confidence thresholds, required/avoided/preferred reaction families) |
 | `estimate_diversity` | Route diversity and coverage metrics |
+| `diagnose_failure` | Structured explanation of why a search found no route |
 
 `find_routes` also accepts `search_mode: "coverage"` with a required
 `coverage_templates` path. It runs the standard Stage 1 first and escalates
 to Stage 2 only when Stage 1 finds no route; the response reports the selected
 stage, timeout status, and per-stage elapsed time.
 
-The server auto-detects `data/building_blocks.smi` and `data/templates_extracted_5000.smi` in the working directory. Falls back to the embedded `DEFAULT_BUILDING_BLOCKS` / `default_rules()` defaults if not found (152 unique building blocks per `ChemEnv::bb_count()`, 22 handcrafted rules, including the new graph-based `carbamate_cleavage` rule).
+The server auto-detects `data/building_blocks.smi` and the optional, locally
+generated `data/templates_extracted_5000.smi` in the working directory. It
+falls back to the embedded `DEFAULT_BUILDING_BLOCKS` / `default_rules()`
+defaults if they are not found (152 unique building blocks per
+`ChemEnv::bb_count()`, 23 handcrafted rules).
 
 ```bash
 cargo build --release
@@ -612,7 +642,7 @@ Target SMILES
 ┌─────────────────────────┐
 │     chem_env.rs         │  ← chematic wrapper
 │  - SMILES parse         │     canonical-SMILES FxHashSet BB lookup (O(1))
-│  - 21 built-in + up to 50k via --templates  │     fragment sanitization + ring-leak filter
+│  - 23 built-in + up to 50k via --templates  │     fragment sanitization + ring-leak filter
 │  - Building block check │     apply_retro memoization cache
 └────────────┬────────────┘
              │  par_iter (rayon / sequential on WASM)
@@ -655,7 +685,8 @@ renkin/                          ← Cargo workspace root
 │   ├── bin/benchmark.rs         # renkin-bench binary (--plausibility flag)
 │   ├── bin/doctor.rs            # renkin-doctor diagnostic binary
 │   ├── bin/fp.rs                # renkin-fp ECFP4 fingerprint (nn-scoring feature)
-│   ├── bin/mcp.rs               # renkin-mcp MCP server (6 tools)
+│   ├── bin/mcp.rs               # renkin-mcp stdio launcher
+│   ├── mcp/                     # Dual-era protocol + 7 tool handlers
 │   ├── chem_env.rs              # retro rules + BB lookup + template loader
 │   ├── score.rs                 # SA Score heuristic + step cost
 │   ├── search.rs                # A* / AND-OR tree engine + beam pruning
@@ -669,7 +700,7 @@ renkin/                          ← Cargo workspace root
 │   └── renkin-kg/               # reaction knowledge graph builder (GraphML / Cypher export)
 ├── data/
 │   ├── building_blocks.smi              # 402 curated commercial starting materials (loaded/deduplicated count)
-│   ├── templates_extracted_5000.smi     # 5,000 auto-extracted SMIRKS templates
+│   ├── templates_extracted_500.smi      # 500 checked-in auto-extracted SMIRKS templates
 │   ├── benchmark_targets.smi            # internal benchmark set
 │   └── bench_chunks/                    # USPTO-50k per-chunk results
 ├── scripts/
@@ -706,7 +737,7 @@ see "Earlier milestones" below for older shipped work.
 
 ### In progress
 
-- [ ] Candidate-generation coverage gap — 33.0% (1,618/4,903) of the formal TEST corpus has zero positive candidates in-pool, a ceiling reranking cannot fix by construction; template-diversity-scaling confirmed as a strong mechanism (Phase A.5/B.2, see coverage mode above), higher-level-template research direction not yet started
+- [ ] Candidate-generation coverage gap — 33.0% (1,618/4,903) of the formal TEST corpus has zero positive candidates in-pool, a ceiling reranking cannot fix by construction. Template-diversity scaling remains a strong mechanism; a first provenance-bounded radius-zero abstraction track is now implemented and disjoint-VAL gated ([#240](https://github.com/kent-tokyo/renkin/issues/240)), but its 4/22 targeted residual recovery is not a full-corpus remeasurement or a shipped default
 - [ ] Template retrieval index (element bitmask + bond-center prefilter) for the 50k template set
 - [ ] Calibrated route confidence (map `success_probability` to empirical solve rate)
 
@@ -752,12 +783,12 @@ see [Benchmark](#benchmark) for the corrected historical baseline.
 - [x] `renkin-doctor` — environment diagnostic binary (templates, BBs, Python, binaries)
 - [x] Failure diagnostics — zero-route output includes `likely_causes` + `suggestions` JSON block
 - [x] `--format explain|compare|compare-json` — human-readable and tabular route output
-- [x] `renkin stock stats|validate|coverage` — stock CSV management subcommand
+- [x] `renkin stock stats|validate|coverage|compile` — stock inspection plus integrity-checked compiled `.rstock` snapshots
 - [x] Pareto multi-objective search — `--format pareto`, `--objectives`, `find_pareto_routes` MCP
 - [x] Constraint DSL — `--constraints JSON`, `plan_with_constraints` MCP tool
 - [x] `renkin template stats|validate|dedup|explain|coverage` — template quality tools
 - [x] `renkin-kg` — reaction knowledge graph (bipartite mol↔reaction, GraphML/Cypher export)
-- [x] MCP server (`renkin-mcp`) — expanded to 6 tools (`explain_route`, `find_pareto_routes`, `plan_with_constraints`, ...)
+- [x] MCP server (`renkin-mcp`) — 7 tools with legacy `2024-11-05` and modern `2026-07-28` stdio protocol support
 - [x] Core search engine foundation — SMIRKS retro-reaction rules + fragment sanitization, A\*/AND-OR tree search with closed list + degenerate-route filter, SA Score heuristic + beam search, `rayon` parallel rule application (sequential fallback on WASM), FxHashMap/SmallVec beam frontier/SA-Score-memoization/`Arc<PathNode>` path-sharing perf work
 - [x] Multi-target packaging — Python bindings (PyO3 + maturin, `pip install renkin`), WASM build (`npm install renkin`), published to crates.io/PyPI/npm with GitHub Actions CI/CD, WASM browser playground + i18n (EN/JA/ZH)
 - [x] Benchmark CLI (`renkin-bench`) + USPTO-50k evaluation, `--format tree|mermaid` visualization, MkDocs documentation site + GitHub Pages playground

package/package.json

@@ -5,7 +5,7 @@
     "kent-tokyo <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "Ultra-fast retrosynthesis engine for computer-aided synthesis planning (CASP) — pure Rust, WASM-ready, Python bindings via PyO3",
-  "version": "1.0.0",
+  "version": "1.0.2",
   "license": "MIT",
   "repository": {
     "type": "git",