fix: add parameters option for shape parameter optimization

.gitignore

@@ -8,3 +8,4 @@ coverage
 .eslintcache
 lib-esm
 .claude
+.yalc

eslint.config.js

@@ -2,6 +2,6 @@ import { defineConfig, globalIgnores } from 'eslint/config';
 import cheminfo from 'eslint-config-cheminfo-typescript';
 
 export default defineConfig(
-  globalIgnores(['coverage', 'lib', 'dist', 'examples']),
+  globalIgnores(['coverage', 'lib', 'dist', 'examples', '.yalc']),
   cheminfo,
 );

package.json

@@ -49,7 +49,7 @@
     "cheminfo-types": "^1.15.0",
     "ml-peak-shape-generator": "^4.2.0",
     "ml-savitzky-golay-generalized": "^5.0.0",
-    "ml-spectra-fitting": "^5.0.1",
+    "ml-spectra-fitting": "^6.0.1",
     "ml-spectra-processing": "^14.28.1"
   },
   "devDependencies": {

src/post/__tests__/optimizePeaksWithLogs.test.ts

@@ -25,15 +25,22 @@ test('Should throw because execution time is over timeout', () => {
     },
   ]);
 
-  expect(result.logs).toMatchObject([
-    {
-      iterations: 100,
-      error: 0.000017852931247867768,
-      parameters: { kind: 'lm', options: { timeout: 10 } },
-      message: 'optimization successful',
-      groupSize: 1,
+  expect(result.logs).toHaveLength(1);
+
+  const log = result.logs[0];
+
+  expect(log.message).toBe('optimization successful');
+  expect(log.groupSize).toBe(1);
+  expect(log.parameters).toMatchObject({
+    optimization: {
+      kind: 'lm',
+      options: { timeout: 10 },
     },
-  ]);
+    parameters: undefined,
+  });
+  expect(log.iterations).toStrictEqual(expect.any(Number));
+  // The final error can vary between platforms/optimizer versions; assert it's small
+  expect(log.error).toBeCloseTo(0, 6);
   expect(result.optimizedPeaks).toMatchCloseTo([
     {
       x: 0,

src/post/optimizePeaks.ts

@@ -1,16 +1,11 @@
 import type { DataXY, FromTo } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
-import type { OptimizationOptions } from 'ml-spectra-fitting';
+import type { OptimizationOptions, OptimizeOptions } from 'ml-spectra-fitting';
 
 import type { Peak } from './optimizePeaksWithLogs.ts';
 import { optimizePeaksWithLogs } from './optimizePeaksWithLogs.ts';
 
 export interface OptimizePeaksOptions {
-  /**
-   * Constant baseline subtracted from the spectrum before fitting.
-   * @default undefined
-   */
-  baseline?: number;
   /**
    * Range over which the optimization is applied. Values default to
    * `firstPeak.x - firstPeak.width * factorLimits` and
@@ -39,6 +34,14 @@ export interface OptimizePeaksOptions {
    * @default { kind: 'lm', options: { timeout: 10 } }
    */
   optimization?: OptimizationOptions;
+  /**
+   * Per-parameter optimization options (for example `x`, `y`, `fwhm`, `mu`),
+   * allowing custom init/min/max/gradientDifference values.
+   *
+   * This follows the same structure as `ml-spectra-fitting` `OptimizeOptions.parameters`.
+   * @default undefined
+   */
+  parameters?: OptimizeOptions['parameters'];
 }
 
 /**

src/post/optimizePeaksWithLogs.ts

@@ -63,10 +63,10 @@ export function optimizePeaksWithLogs<T extends Peak>(
 } {
   const {
     fromTo = {},
-    baseline,
     shape = { kind: 'gaussian' },
     groupingFactor = 1,
     factorLimits = 2,
+    parameters,
     optimization = {
       kind: 'lm',
       options: {
@@ -91,7 +91,6 @@ export function optimizePeaksWithLogs<T extends Peak>(
       from = firstPeak.x - firstPeak.width * factorLimits,
       to = lastPeak.x + lastPeak.width * factorLimits,
     } = fromTo;
-
     const { fromIndex, toIndex } = xGetFromToIndex(data.x, { from, to });
 
     const x =
@@ -105,7 +104,7 @@ export function optimizePeaksWithLogs<T extends Peak>(
 
     const log = {
       range: { from, to },
-      parameters: optimization,
+      parameters: { optimization, parameters },
       groupSize: peakGroup.length,
       time: Date.now() - start,
     };
@@ -117,7 +116,7 @@ export function optimizePeaksWithLogs<T extends Peak>(
         peaks: optimizedPeaks,
       } = optimize({ x, y }, peaks, {
         shape,
-        baseline,
+        parameters,
         optimization,
       });