renkin 0.29.0 → 0.31.0

package/README.md

@@ -21,13 +21,19 @@
 
 ---
 
+**Keep your planner. Audit every route.** Audit retrosynthesis routes from AiZynthFinder, Syntheseus, or RENKIN — locally, reproducibly, and without sending molecular structures anywhere.
+
+[**Audit a route in your browser →**](https://kent-tokyo.github.io/renkin/playground/) · [**Python quick start ↓**](#audit-a-route) · [**Route planning engine ↓**](#quick-start)
+
+---
+
 ## What is RENKIN?
 
-RENKIN is an open-source **retrosynthesis engine** for **computer-aided synthesis planning (CASP)** that automatically discovers optimal chemical reaction routes from a target molecule back to cheap, commercially available starting materials.
+RENKIN Bridge is a tool-neutral **route auditor**: it checks structural integrity, stock coverage, and declared-reaction forward-replay for routes from **AiZynthFinder**, **Syntheseus**, or RENKIN's own planner — the identical `pass`/`fail`/`partial` pipeline regardless of which tool produced the route, entirely local and reproducible (every audit records a verifiable [`audit_manifest`](https://kent-tokyo.github.io/renkin/guides/audit-reproducibility-contract/)), structures never leaving your machine unless you explicitly ask.
 
-Built entirely in Rust with the [`chematic`](https://docs.rs/chematic/) cheminformatics crate — zero C/C++ dependencies, `#![forbid(unsafe_code)]` throughout. One codebase compiles to a native CLI, a Rust library, Python wheels (PyO3), and a WebAssembly module that runs entirely client-side in the browser.
+RENKIN is also, in its own right, an open-source **retrosynthesis engine** for **computer-aided synthesis planning (CASP)** that automatically discovers chemical reaction routes from a target molecule back to cheap, commercially available starting materials.
 
-Use RENKIN as an independent audit layer for retrosynthesis routes generated by RENKIN or AiZynthFinder — see [RENKIN Bridge / `audit-route`](#key-features) below.
+Built entirely in Rust with the [`chematic`](https://docs.rs/chematic/) cheminformatics crate — zero C/C++ dependencies, `#![forbid(unsafe_code)]` throughout. One codebase compiles to a native CLI, a Rust library, Python wheels (PyO3), and a WebAssembly module that runs entirely client-side in the browser.
 
 ---
 
@@ -39,6 +45,10 @@ cargo add renkin            # Rust
 npm install renkin          # JavaScript (browser / bundler -- see docs/api/wasm.md)
 ```
 
+Auditing Syntheseus routes needs one more, optional package:
+`pip install renkin[syntheseus]` (verified against Syntheseus `0.7.2` and
+`0.8.0` — see the [compatibility spike](https://github.com/kent-tokyo/renkin/blob/master/docs/design/syntheseus-0.8-compatibility-spike.md)).
+
 ---
 
 ## Live Playground
@@ -47,8 +57,44 @@ npm install renkin          # JavaScript (browser / bundler -- see docs/api/wasm
 
 ---
 
+## Audit a Route
+
+Bring a route from wherever you already plan them — every path below runs through the identical audit pipeline: the same `pass`/`fail`/`partial` verdict regardless of source tool, or whether you ran it from the CLI, Python, or a browser tab.
+
+**AiZynthFinder**
+
+```python
+import json
+import renkin
+
+report = json.loads(
+    renkin.audit_route(open("trees.json").read(), format="aizynthfinder")
+)
+print(report["summary"])
+```
+
+**Syntheseus** (`pip install renkin[syntheseus]`)
+
+```python
+import json
+import renkin
+from renkin.syntheseus_exporter import dumps_syntheseus_route_v1
+
+route_json = dumps_syntheseus_route_v1(my_synthesis_graph)
+report = json.loads(renkin.audit_route(route_json, format="syntheseus"))
+print(report["summary"])
+```
+
+**In your browser** — no installation, no upload, no server: [**Try the Playground →**](https://kent-tokyo.github.io/renkin/playground/)
+
+Full walkthroughs with real output, end to end: [AiZynthFinder](https://kent-tokyo.github.io/renkin/guides/aizynthfinder-audit-demo/) · [Syntheseus](https://kent-tokyo.github.io/renkin/guides/syntheseus-audit-demo/).
+
+---
+
 ## Quick Start
 
+*Planning a route from scratch, not auditing one you already have — see [Audit a Route](#audit-a-route) above for that.*
+
 ```python
 import json
 import renkin
@@ -346,7 +392,7 @@ 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 +668,7 @@ 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.

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": "0.29.0",
+  "version": "0.31.0",
   "license": "MIT",
   "repository": {
     "type": "git",