From 07efb8452a559cff69e70d8f545d2155cd250da4 Mon Sep 17 00:00:00 2001 From: Luc Patiny Date: Sat, 18 Apr 2026 07:44:46 +0200 Subject: [PATCH 1/3] chore: align with current standards and upgrade dependencies - Upgrade dependencies to latest (keep ESLint 9.x, TypeScript 5.x) - Add snapshotFormat.maxOutputLength to vitest config - Add .claude to .gitignore - Apply eslint auto-fix (toThrowError -> toThrow) from cheminfo-typescript v22 --- .gitignore | 2 ++ vitest.config.ts | 3 +++ 2 files changed, 5 insertions(+) diff --git a/.gitignore b/.gitignore index 741cc55..c03d94e 100644 --- a/.gitignore +++ b/.gitignore @@ -119,5 +119,7 @@ dist .DS_Store +.claude + lib lib-esm diff --git a/vitest.config.ts b/vitest.config.ts index 63fe258..3adf9f4 100644 --- a/vitest.config.ts +++ b/vitest.config.ts @@ -6,5 +6,8 @@ export default defineConfig({ include: ['src/**'], }, setupFiles: ['vitest.setup.ts'], + snapshotFormat: { + maxOutputLength: Number.MAX_SAFE_INTEGER, + }, }, }); From 6c763313297cf2d4539f627d0fd7acf8e8538dbc Mon Sep 17 00:00:00 2001 From: Luc Patiny Date: Tue, 23 Jun 2026 18:38:45 +0200 Subject: [PATCH 2/3] chore: align scripts with generator and upgrade dependencies - Restore generator-form eslint scripts (drop --cache / node --run) - Order dependencies before devDependencies; add @types/node - Add types: [node] to tsconfig; clean removes coverage too - Add ignore-scripts to .npmrc - Use istanbul coverage provider (numeric package) - Upgrade dependencies (ESLint kept on 9.x) --- .npmrc | 1 + package.json | 33 ++++++++++++++++---------------- src/filters/x/ensureGrowing.ts | 2 +- src/filters/x/reverseIfNeeded.ts | 2 +- tsconfig.json | 3 ++- vitest.config.ts | 1 + 6 files changed, 23 insertions(+), 19 deletions(-) diff --git a/.npmrc b/.npmrc index 43c97e7..9951b11 100644 --- a/.npmrc +++ b/.npmrc @@ -1 +1,2 @@ package-lock=false +ignore-scripts=true diff --git a/package.json b/package.json index ad7e8c2..2c94ba4 100644 --- a/package.json +++ b/package.json @@ -17,14 +17,14 @@ ], "scripts": { "check-types": "tsc --noEmit", - "clean": "rimraf lib", + "clean": "rimraf coverage lib", "createSchema": "typescript-json-schema --refs false ./tsconfig.json FilterXYType > FilterXYSchema.json", - "eslint": "eslint . --cache", - "eslint-fix": "node --run eslint -- --fix", + "eslint": "eslint .", + "eslint-fix": "eslint . --fix", "prepack": "npm run createSchema && npm run tsc", "prettier": "prettier --check .", "prettier-write": "prettier --write .", - "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types", + "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier", "test-only": "vitest run --coverage", "tsc": "npm run clean && npm run tsc-build", "tsc-build": "tsc --project tsconfig.build.json" @@ -37,23 +37,24 @@ "url": "https://github.com/mljs/signal-processing/issues" }, "homepage": "https://github.com/mljs/signal-processing#readme", + "dependencies": { + "baselines": "^1.1.10", + "cheminfo-types": "^1.15.0", + "ml-gsd": "^13.1.1", + "ml-savitzky-golay-generalized": "^5.0.0", + "ml-spectra-processing": "^14.29.1" + }, "devDependencies": { - "@vitest/coverage-v8": "^4.1.5", + "@types/node": "^25.6.0", + "@vitest/coverage-istanbul": "^4.1.9", "@zakodium/tsconfig": "^1.0.5", "eslint": "^9.39.2", - "eslint-config-cheminfo-typescript": "^22.0.0", + "eslint-config-cheminfo-typescript": "^22.1.0", "jest-matcher-deep-close-to": "^3.0.2", - "prettier": "^3.8.3", + "prettier": "^3.8.4", "rimraf": "^6.1.3", "typescript": "^6.0.3", - "typescript-json-schema": "^0.67.1", - "vitest": "^4.1.5" - }, - "dependencies": { - "baselines": "^1.1.10", - "cheminfo-types": "^1.15.0", - "ml-gsd": "^13.1.1", - "ml-savitzky-golay-generalized": "^5.0.0", - "ml-spectra-processing": "^14.28.1" + "typescript-json-schema": "^0.67.4", + "vitest": "^4.1.9" } } diff --git a/src/filters/x/ensureGrowing.ts b/src/filters/x/ensureGrowing.ts index 8e6e388..5874323 100644 --- a/src/filters/x/ensureGrowing.ts +++ b/src/filters/x/ensureGrowing.ts @@ -7,7 +7,7 @@ export interface EnsureGrowingFilter { /** * Ensure X values are strictly monotonic increasing - * http://www-groups.mcs.st-andrews.ac.uk/~john/analysis/Lectures/L8.html + * https://www-groups.mcs.st-andrews.ac.uk/~john/analysis/Lectures/L8.html * @param data */ export function ensureGrowing(data: DataXY): { diff --git a/src/filters/x/reverseIfNeeded.ts b/src/filters/x/reverseIfNeeded.ts index 6c24e5a..ef9a323 100644 --- a/src/filters/x/reverseIfNeeded.ts +++ b/src/filters/x/reverseIfNeeded.ts @@ -7,7 +7,7 @@ export interface ReverseIfNeededFilter { /** * Ensure X values are strictly monotonic increasing - * http://www-groups.mcs.st-andrews.ac.uk/~john/analysis/Lectures/L8.html + * https://www-groups.mcs.st-andrews.ac.uk/~john/analysis/Lectures/L8.html * @param data */ export function reverseIfNeeded(data: DataXY): { diff --git a/tsconfig.json b/tsconfig.json index e4f3895..a68fc7e 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,8 +1,9 @@ { "extends": "@zakodium/tsconfig", "compilerOptions": { + "noUncheckedIndexedAccess": false, "outDir": "lib", - "noUncheckedIndexedAccess": false + "types": ["node"] }, "include": ["src", "vite*.ts"] } diff --git a/vitest.config.ts b/vitest.config.ts index 3adf9f4..3ac1194 100644 --- a/vitest.config.ts +++ b/vitest.config.ts @@ -4,6 +4,7 @@ export default defineConfig({ test: { coverage: { include: ['src/**'], + provider: 'istanbul', }, setupFiles: ['vitest.setup.ts'], snapshotFormat: { From 99f34cbd759473fb874001c61b491083c9a7dea3 Mon Sep 17 00:00:00 2001 From: Luc Patiny Date: Tue, 23 Jun 2026 18:39:09 +0200 Subject: [PATCH 3/3] feat: update ml-gsd to v14 Exposes ml-gsd v14's new gsd options (shape-optimization parameters and maxAbsoluteRatio peak filter) through calibrateX. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 2c94ba4..f11a5bc 100644 --- a/package.json +++ b/package.json @@ -40,7 +40,7 @@ "dependencies": { "baselines": "^1.1.10", "cheminfo-types": "^1.15.0", - "ml-gsd": "^13.1.1", + "ml-gsd": "^14.2.0", "ml-savitzky-golay-generalized": "^5.0.0", "ml-spectra-processing": "^14.29.1" },