Bump webPORPID to 0.3.16 after the functional alignment fix

cli-src/porpid-cli.mjs

@@ -6,6 +6,7 @@ import { basename, dirname, isAbsolute, join, resolve } from "node:path";
 import { createInterface } from "node:readline";
 import { createGunzip } from "node:zlib";
 import { Worker as NodeWorker } from "node:worker_threads";
+import packageInformation from "../package.json" with { type: "json" };
 
 import { bytesToHex } from "@noble/hashes/utils.js";
 import { classifyContamination } from "../src/contamination.ts";
@@ -22,7 +23,7 @@ import { createMafftRunner } from "./direct-mafft.mjs";
 import { createMsaRunner } from "./direct-msa.mjs";
 import { createIndependentPanelFilterRunner } from "./direct-panel-filter.mjs";
 
-const VERSION = "0.3.15";
+const VERSION = packageInformation.version;
 const UPSTREAM_COMMIT = "201af7942029cfb7974880e41674be9f0ddfaf3b";
 const CLI_DIRECTORY = dirname(new URL(import.meta.url).pathname);
 

cli/porpid-cli.mjs

@@ -12,6 +12,9 @@ import { basename, dirname, isAbsolute, join, resolve } from "node:path";
 import { createInterface } from "node:readline";
 import { createGunzip } from "node:zlib";
 import { Worker as Worker$1 } from "node:worker_threads";
+//#region package.json
+var version = "0.3.16";
+//#endregion
 //#region src/contamination.ts
 /** Samples without donor metadata remain separate biological self groups. */
 function selfGroupsBySample(config) {
@@ -4753,7 +4756,7 @@ function createIndependentPanelFilterRunner(workerPath = new URL("../porpid-pane
 }
 //#endregion
 //#region cli-src/porpid-cli.mjs
-const VERSION = "0.3.15";
+const VERSION = version;
 const UPSTREAM_COMMIT = "201af7942029cfb7974880e41674be9f0ddfaf3b";
 const CLI_DIRECTORY = dirname(new URL(import.meta.url).pathname);
 function defaultCliAssets() {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "webporpid",
-  "version": "0.3.15",
+  "version": "0.3.16",
   "private": true,
   "type": "module",
   "scripts": {

src/components/results-explorer.tsx

@@ -1,4 +1,5 @@
 import { useEffect, useMemo, useRef, useState } from "react";
+import packageInformation from "../../package.json";
 import {
   ALIVIBE_BRIDGE_VERSION, ALIVIBE_SOURCE_REVISION, assertAlivibeInitialLoad, assertAlivibeRoundTripTarget,
   getAlivibeBridge, loadAlivibeNucleotideFasta, readAlivibeNucleotideFasta, type AlivibeEditorWindow, type AlivibeMsaJob,
@@ -598,7 +599,7 @@ export function ResultsExplorer({ bundle, onSaveResults, onBundleChange }: { bun
     const targetSample = sampleRef.current, current = effectiveAlignment(bundleRef.current, targetSample, variant); if (!current.fasta) return;
     setAlignmentError(""); setAlignmentStatus("Opening the bundled Alivibe editor…");
     const applicationBase = new URL(import.meta.env.BASE_URL, document.baseURI), editorUrl = new URL("tools/alivibe.html", applicationBase);
-    editorUrl.searchParams.set("swigBridge", String(ALIVIBE_BRIDGE_VERSION)); editorUrl.searchParams.set("source", ALIVIBE_SOURCE_REVISION.slice(0, 12)); editorUrl.searchParams.set("release", "0.3.15");
+    editorUrl.searchParams.set("swigBridge", String(ALIVIBE_BRIDGE_VERSION)); editorUrl.searchParams.set("source", ALIVIBE_SOURCE_REVISION.slice(0, 12)); editorUrl.searchParams.set("release", packageInformation.version);
     const token = globalThis.crypto?.randomUUID?.() ?? `${Date.now()}-${Math.random().toString(36).slice(2)}`;
     const popup = window.open(editorUrl.href, `webporpid-alivibe-${token}`, "popup,width=1500,height=920") as AlivibeEditorWindow | null;
     if (!popup) { setAlignmentError("The browser blocked the Alivibe window. Allow pop-ups for this site and try again."); return; }

src/pipeline-worker.ts

@@ -1,6 +1,7 @@
 /// <reference lib="webworker" />
 
 import { bytesToHex } from "@noble/hashes/utils.js";
+import packageInformation from "../package.json";
 import coreWasmUrl from "/webporpid.wasm?url";
 import { classifyContaminationAsync } from "./contamination";
 import { runAlivibeMsa } from "./alivibe-msa-runtime";
@@ -114,7 +115,7 @@ async function run(request: RunRequest, signal: AbortSignal): Promise<ResultBund
   const storageLabel = store.mode === "external-directory" ? "user-selected external scratch directory"
     : store.mode === "opfs" ? "browser OPFS" : "bounded memory fallback";
 	  activeBackgroundMode = Boolean(request.runWhenNotInFocus);
-	  const inputHash = createStreamingHash(), log = [`${now()} webPORPID 0.3.15 started`,
+	  const inputHash = createStreamingHash(), log = [`${now()} webPORPID ${packageInformation.version} started`,
     `${now()} execution: ${workers} WASM workers; ${storageLabel} ${request.config.parameters.maxReadsPerSample > 0 ? "adaptive selected-read" : "all-read"} partition spool`,
     `${now()} background execution aid: ${activeBackgroundMode ? "requested; quiet audible processing hum controlled by the browser UI" : "disabled"}`,
     `${now()} parameters: error_rate=${request.config.parameters.errorRate}, lengths=(${request.config.parameters.minLength},${request.config.parameters.maxLength}), lda=${request.config.parameters.ldaThreshold}, panel_filter=${request.config.parameters.panelFilterMode ?? "mafft-batch"}`];
@@ -451,7 +452,7 @@ async function run(request: RunRequest, signal: AbortSignal): Promise<ResultBund
     progress({ stage: "complete", fraction: 1, detail: "Results ready" });
     return {
       schema: "webporpid-results/1",
-      provenance: { webporpidVersion: "0.3.15", createdUtc: now(), engine: "C++20 WASM/WASI SIMD",
+      provenance: { webporpidVersion: packageInformation.version, createdUtc: now(), engine: "C++20 WASM/WASI SIMD",
         workers, inputName: request.file.name, inputSha256: finishStreamingHash(inputHash),
         configSha256: bytesToHex(new Uint8Array(configHashBytes)), deterministicSeed: request.config.parameters.deterministicSeed.toString(),
         upstreamBranch: "nanopore", upstreamCommit: "201af7942029cfb7974880e41674be9f0ddfaf3b" },