renkin 0.28.0 → 0.30.0

package/README.md

@@ -36,7 +36,7 @@ Use RENKIN as an independent audit layer for retrosynthesis routes generated by
 ```bash
 pip install renkin          # Python
 cargo add renkin            # Rust
-npm install renkin          # JavaScript / Node.js
+npm install renkin          # JavaScript (browser / bundler -- see docs/api/wasm.md)
 ```
 
 ---
@@ -346,7 +346,7 @@ 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)) |
-| **RENKIN Bridge / `audit-route`** | `renkin audit-route route.json [--format auto\|renkin\|aizynthfinder] [--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) and real AiZynthFinder route JSON — single-target and gzip-compressed batch output, verified against AiZynthFinder v4.4.1 specifically, not claimed for every version (v0.26.0); `--format auto` detects the input shape and hard-errors rather than guessing on anything ambiguous. [5-minute walkthrough with real output →](https://kent-tokyo.github.io/renkin/guides/aizynthfinder-audit-demo/) |
+| **RENKIN Bridge / `audit-route`** | `renkin audit-route route.json [--format auto\|renkin\|aizynthfinder\|syntheseus] [--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 v4.4.1 specifically, not claimed for every version (v0.26.0) — and 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); `--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/) |
 | **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 |
 | **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` |
@@ -622,6 +622,8 @@ see "Earlier milestones" below for older shipped work.
 
 ### Recently shipped
 
+- [x] **Syntheseus Bridge** (`--format syntheseus`, shipped v0.30.0) — *Syntheseus has no route export. RENKIN built one — and audits it exactly like every other adapter.* A third route adapter alongside RENKIN-native and AiZynthFinder: the optional `renkin.syntheseus_exporter` (`pip install renkin[syntheseus]`) turns a real Syntheseus `SynthesisGraph` into the `syntheseus-route-v1` interchange schema, which `renkin audit-route --format syntheseus` (also auto-detected) consumes through the identical audit pipeline every adapter shares. Forward validation honestly reports `not_evaluable` for every real Syntheseus route today — `reaction_smiles` carries no atom mapping, never faked into a pass. The [browser playground](https://kent-tokyo.github.io/renkin/playground/)'s Audit tab gained Syntheseus as a third format option. [5-minute walkthrough with real output →](https://kent-tokyo.github.io/renkin/guides/syntheseus-audit-demo/)
+- [x] **Audit Policy Profiles** (`--policy informational|standard|strict`, shipped v0.29.0) — *One set of findings. Three ways to derive the verdict.* Audit the same route under `informational`, `standard`, or `strict` policy without ever hiding or changing the underlying findings — policy only changes how the overall pass/fail/partial verdict is derived from findings already collected, recorded in `audit_manifest.policy`. Consistent across every surface: `renkin audit-route --policy`, the Rust API, the first Python binding for route auditing (`renkin.audit_route()`), and a new WASM `audit_route_v2()` (the existing `audit_route()` stays as a `standard`-policy wrapper). The [browser playground](https://kent-tokyo.github.io/renkin/playground/)'s Audit tab gained a policy selector.
 - [x] **Audit Playground** (`[ Audit a Route ]` tab, shipped v0.28.0) — *Audit a route in your browser — the same pipeline, the same verdict, zero network calls.* The [browser playground](https://kent-tokyo.github.io/renkin/playground/) now audits a RENKIN or AiZynthFinder route export (single-route or Pandas batch) and an optional stock list entirely client-side, via a new `audit_route` WASM export that calls the identical report-building pipeline `renkin audit-route` uses — the same pass/fail/partial verdict either way, not a separately-maintained copy. Paste or upload, run off the main thread, download the JSON report.
 - [x] **Reproducible Route Audit** (`audit_manifest` on `renkin audit-route --output json`, shipped v0.27.0) — *Reproduce what was audited, from which input, with which stock and policy.* Every audit report now records RENKIN version, report schema version, source format/version, input/stock content SHA-256 hashes, and audit policy — tested for byte-identical determinism (auditing the same input twice), not just claimed. Adds a shared adapter conformance suite across RENKIN-native and AiZynthFinder route inputs, plus a written [reproducibility/compatibility contract](https://kent-tokyo.github.io/renkin/guides/audit-reproducibility-contract/) (verified-vs-supported versions, unknown-field tolerance, report-schema rules, adapter-fixture runbook). The [browser playground](https://kent-tokyo.github.io/renkin/playground/) also got a safety/UX pass this release: search runs off the main thread with cancel/time-budget support, structure rendering stays local by default (no third-party SMILES transmission), and search settings round-trip exactly through Copy CLI/Python.
 - [x] **RENKIN Bridge — Cross-Tool Route Audit** (`renkin audit-route`, RENKIN-native adapter shipped v0.25.0, AiZynthFinder adapter shipped v0.26.0) — *Keep AiZynthFinder. Audit its routes with RENKIN.* A tool-neutral route audit model: 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 — never a silently force-passed boolean. v0.26.0 adds a real AiZynthFinder adapter (single-target and gzip batch JSON, verified against captured v4.4.1 output — see [`PROVENANCE.md`](tests/fixtures/aizynthfinder/v4.4.1/PROVENANCE.md)) plus `--format auto` detection, so both tools' routes run through the exact same audit pipeline; auditing the real fixtures also surfaced and fixed a shared forward-replay bug where precursor ordering, not just chemistry, affected the verdict. `renkin audit-route route.json --stock stock.smi --output json` audits every route in a file and aggregates the results into one machine-readable report, regardless of which tool produced it.

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": "0.28.0",
+  "version": "0.30.0",
   "license": "MIT",
   "repository": {
     "type": "git",

package/renkin.d.ts

@@ -25,6 +25,19 @@
  */
 export function audit_route(content: string, format: string, stock_text: string): string;
 
+/**
+ * Same as [`audit_route`], plus `policy` (v0.29.0 Audit Policy Profiles):
+ * `"informational" | "standard" | "strict"`, same vocabulary as the CLI's
+ * `--policy` flag -- controls only how each route's `status` is derived
+ * from findings already collected, never which findings are detected or
+ * reported. A distinct function name rather than a 4th parameter on
+ * `audit_route`, so a caller on a pre-v0.29.0 build gets a real "no such
+ * export" `TypeError` instead of a silently-ignored argument -- the same
+ * reasoning `find_routes_v2` already established in this codebase.
+ * `audit_route` itself is now a thin `"standard"` wrapper around this.
+ */
+export function audit_route_v2(content: string, format: string, stock_text: string, policy: string): string;
+
 /**
  * Static capabilities of this WASM build (browser edition), as a JSON
  * string -- real counts read from the same compiled-in data `find_routes`
@@ -81,6 +94,7 @@ export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembl
 export interface InitOutput {
     readonly memory: WebAssembly.Memory;
     readonly audit_route: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number];
+    readonly audit_route_v2: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number];
     readonly capabilities: () => [number, number];
     readonly find_routes: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly find_routes_v2: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number) => [number, number];

package/renkin.js

@@ -45,6 +45,43 @@ export function audit_route(content, format, stock_text) {
     }
 }
 
+/**
+ * Same as [`audit_route`], plus `policy` (v0.29.0 Audit Policy Profiles):
+ * `"informational" | "standard" | "strict"`, same vocabulary as the CLI's
+ * `--policy` flag -- controls only how each route's `status` is derived
+ * from findings already collected, never which findings are detected or
+ * reported. A distinct function name rather than a 4th parameter on
+ * `audit_route`, so a caller on a pre-v0.29.0 build gets a real "no such
+ * export" `TypeError` instead of a silently-ignored argument -- the same
+ * reasoning `find_routes_v2` already established in this codebase.
+ * `audit_route` itself is now a thin `"standard"` wrapper around this.
+ * @param {string} content
+ * @param {string} format
+ * @param {string} stock_text
+ * @param {string} policy
+ * @returns {string}
+ */
+export function audit_route_v2(content, format, stock_text, policy) {
+    let deferred5_0;
+    let deferred5_1;
+    try {
+        const ptr0 = passStringToWasm0(content, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(format, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passStringToWasm0(stock_text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len2 = WASM_VECTOR_LEN;
+        const ptr3 = passStringToWasm0(policy, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len3 = WASM_VECTOR_LEN;
+        const ret = wasm.audit_route_v2(ptr0, len0, ptr1, len1, ptr2, len2, ptr3, len3);
+        deferred5_0 = ret[0];
+        deferred5_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred5_0, deferred5_1, 1);
+    }
+}
+
 /**
  * Static capabilities of this WASM build (browser edition), as a JSON
  * string -- real counts read from the same compiled-in data `find_routes`