@datagrok/peptides 0.8.13 → 0.8.14

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@datagrok/peptides",
-  "version": "0.8.13",
+  "version": "0.8.14",
   "description": "",
   "repository": {
     "type": "git",
@@ -10,7 +10,7 @@
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
     "@datagrok-libraries/bio": "^0.0.5",
-    "@datagrok-libraries/ml": ">=0.0.16 <0.1.21",
+    "@datagrok-libraries/ml": "^1.0.0",
     "@datagrok-libraries/statistics": "^0.1.6",
     "@datagrok-libraries/utils": "^0.1.2",
     "cash-dom": "latest",
@@ -35,11 +35,11 @@
     "typescript": "latest",
     "webpack": "latest",
     "webpack-cli": "latest",
-    "@types/jest": "latest",
-    "jest": "latest",
-    "jest-html-reporter": "latest",
-    "puppeteer": "^13.1.2",
-    "ts-jest": "^27.1.2"
+    "jest-html-reporter": "^3.5.0",
+    "jest": "^27.0.0",
+    "@types/jest": "^27.0.0",
+    "ts-jest": "^27.0.0",
+    "puppeteer": "latest"
   },
   "sources": [
     "common/ngl_viewer/ngl.js"
@@ -74,4 +74,4 @@
   "canView": [
     "All users"
   ]
-}
+}

package/src/tests/utils.ts

@@ -49,7 +49,7 @@ export async function _testDimensionalityReducer(columnData: Array<string>, meth
 
   try {
     embcols = await createDimensinalityReducingWorker(
-      {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+      {data: columnData, metric: measure as StringMetrics}, method, {cycles: cyclesCount});
   } catch (error) {
     noException = false;
   }

package/src/utils/peptide-similarity-space.ts

@@ -47,7 +47,7 @@ export async function createPeptideSimilaritySpaceViewer(
     .map((v) => AlignedSequenceEncoder.clean(v));
 
   const embcols = await createDimensinalityReducingWorker(
-    {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+    {data: columnData, metric: measure as StringMetrics}, method, {cycles: cyclesCount});
 
   const columns = Array.from(
     embcols as Coordinates, (v: Float32Array, k) => DG.Column.fromFloat32Array(axesNames[k], v));

package/src/viewers/peptide-space-viewer.ts

@@ -80,7 +80,7 @@ export async function computeWeights(
       .map((v) => AlignedSequenceEncoder.clean(v));
 
     const embcols = await createDimensinalityReducingWorker(
-      {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+      {data: columnData, metric: measure as StringMetrics}, method, {cycles: cyclesCount});
 
     const columns = Array.from(
       embcols as Coordinates, (v: Float32Array, k) => DG.Column.fromFloat32Array(axesNames[k], v));

package/src/workers/dimensionality-reducer.ts

@@ -1,6 +1,5 @@
 import {DimensionalityReducer, KnownMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {KnownMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
 /**
  * Worker thread receiving data function.
@@ -8,23 +7,24 @@ import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
  * @param {any[]} columnData Samples to process.
  * @param {string} method Embedding method.
  * @param {string} measure Distance metric.
- * @param {number} cyclesCount Number of cycles to repeat.
- * @return {Coordinates} Embedding.
+ * @param {any} options Options to pass to algorithm.
+ * @return {any} Embedding (and distance matrix where applicable).
  */
-function onMessage(columnData: any[], method: KnownMethods, measure: KnownMetrics, cyclesCount: number): Coordinates {
+function onMessage(columnData: any[], method: KnownMethods, measure: KnownMetrics, options: any): any {
   const reducer = new DimensionalityReducer(
     columnData,
     method,
     measure,
-    {cycles: cyclesCount},
+    options,
   );
   return reducer.transform(true);
 }
 
-self.onmessage = ({data: {columnData, method, measure, cyclesCount}}) => {
-  const embedding = onMessage(columnData, method, measure, cyclesCount);
+self.onmessage = ({data: {columnData, method, measure, options}}) => {
+  const embedding = onMessage(columnData, method, measure, options);
   self.postMessage({
-    embedding: embedding,
+    distance: embedding.distance,
+    embedding: embedding.embedding,
   });
 };
 

package/{test-Peptides-f8114def7953-4bf59d70.html → test-Peptides-2f94f62b59a8-c6d7c434.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=f8114def7953. Commit 4bf59d70.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=2f94f62b59a8. Commit c6d7c434.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=f8114def7953. Commit 4bf59d70.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-05-08 20:15:31</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">117.567s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=2f94f62b59a8. Commit c6d7c434.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-05-09 13:23:40</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">117.439s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.002s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
 Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:22:1)
     at Runtime._execModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1646:24)