@zakodium/nmrium-core 0.1.0 → 0.1.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
package/README.md CHANGED
@@ -19,6 +19,7 @@ Provide state and migrate it for different version of NMRium.
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  Delegate loading and processing state to plugins.
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  It contains the following features:
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+
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  - **read**: read a file and return a data structure with the spectra and molecules for `.nmrium` files
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  - **plugin system**: allow to register plugins to handle different file formats
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  - **serialize**: Serialize the state
@@ -48,7 +49,7 @@ console.log(result);
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  // molecules: [],
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  // }
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- // readSource function accept a partial FileCollectionItems and a baseURL to generate a
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+ // readSource function accept a partial FileCollectionItems and a baseURL to generate a
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  // data structure with a source object inside with { files, filter, baseURL }
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  const nmriumObject = await core.readFromWebSource(
@@ -63,7 +64,6 @@ const nmriumObject = await core.readFromWebSource(
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  },
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  {},
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  );
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-
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  ```
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  ## License
@@ -77,5 +77,7 @@ This package is based on MIT-licensed code that can be found here: https://doi.o
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  [download-image]: https://img.shields.io/npm/dm/@zakodium/nmrium-core.svg
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  [download-url]: https://www.npmjs.com/package/@zakodium/nmrium-core
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  [doi-image]: https://zenodo.org/badge/DOI/10.5281/zenodo.7101438.svg
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+
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  <!-- TODO: fix doi-url for nmrium-core package -->
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- [doi-url]: https://doi.org/10.5281/zenodo.7101438
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+
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+ [doi-url]: https://doi.org/10.5281/zenodo.7101438
@@ -16,7 +16,6 @@ import type { NmrData2D } from 'cheminfo-types';
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  import type { Peaks } from 'nmr-processing';
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  import type { Ranges } from 'nmr-processing';
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  import { SerializedNmriumState } from './core_serialize.js';
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- import { UUID } from 'crypto';
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  import type { WebSource } from 'filelist-utils';
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  import type { Zones } from 'nmr-processing';
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@@ -295,7 +294,7 @@ declare interface GeneralPreferences {
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  invertScroll: boolean;
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  }
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- export declare const generateID: () => UUID;
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+ export declare const generateID: () => `${string}-${string}-${string}-${string}-${string}`;
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  /**
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  * It returns an element if the input is an array otherwise it returns the input.
package/package.json CHANGED
@@ -1,68 +1,46 @@
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  {
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  "name": "@zakodium/nmrium-core",
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- "version": "0.1.0",
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+ "version": "0.1.2",
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  "description": "The core of NMRium: types, state, state migration and plugin system.",
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+ "author": "Zakodium Sàrl",
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+ "license": "CC-BY-NC-SA-4.0",
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  "type": "module",
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  "exports": {
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  ".": {
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- "types": "./dist/nmrium-core.d.ts",
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- "require": "./dist/nmrium-core.cjs",
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- "default": "./dist/nmrium-core.mjs"
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+ "nmrium-internal": "./src/index.ts",
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+ "default": "./dist/nmrium-core.js"
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  }
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  },
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  "files": [
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- "dist/nmrium-core.d.ts",
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- "dist/nmrium-core.cjs",
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- "dist/nmrium-core.mjs"
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+ "dist"
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  ],
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  "scripts": {
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- "api-extractor": "api-extractor run --local",
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- "bundle": "npm run bundle-cjs && npm run bundle-esm && npm run bundle-types",
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- "bundle-common": "esbuild src/index.ts --bundle --packages=external --minify",
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- "bundle-cjs": "npm run bundle-common -- --format=cjs --outfile=./dist/nmrium-core.cjs",
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- "bundle-esm": "npm run bundle-common -- --format=esm --outfile=./dist/nmrium-core.mjs",
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- "bundle-types": "npm run tsc && npm run api-extractor",
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- "check-types": "tsc --noEmit",
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- "clean": "rimraf types",
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- "eslint": "eslint src --cache",
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- "eslint-fix": "npm run eslint -- --fix",
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+ "bundle": "node scripts/esbuild.js && npm run bundle-types",
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+ "bundle-types": "npm run tsc && yarn g:api-extractor",
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+ "clean": "rimraf types dist coverage",
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  "dev:eslint-fix": "eslint --cache --fix $(git diff --name-only --relative) --quiet",
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- "prepack": "npm run bundle",
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- "prettier": "prettier --check src",
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- "prettier-write": "prettier --write src",
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+ "prepack": "npm run clean && npm run bundle",
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  "dev:prettier-write": "prettier --write $(git diff --name-only --relative)",
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- "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
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- "test-only": "vitest run --coverage",
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+ "test": "yarn g:test-only && yarn g:check-types && yarn g:eslint && yarn g:prettier",
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  "tsc": "tsc --project tsconfig.types.json"
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  },
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- "bugs": {
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- "url": "https://github.com/cheminfo/nmrium/issues/new?title=%5Bnmrium-core%5D"
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- },
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- "author": "",
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- "license": "CC-BY-NC-SA-4.0",
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  "devDependencies": {
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- "@microsoft/api-extractor": "^7.52.1",
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  "@types/lodash.merge": "^4.6.9",
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- "@types/node": "^22.13.11",
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- "@vitest/coverage-istanbul": "^3.0.9",
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- "esbuild": "^0.25.1",
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- "eslint": "^9.22.0",
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- "eslint-config-cheminfo-typescript": "^18.0.0",
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+ "@types/node": "^22.15.29",
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+ "esbuild": "^0.25.5",
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  "jest-matcher-deep-close-to": "^3.0.2",
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- "prettier": "^3.5.3",
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  "rimraf": "^6.0.1",
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- "typescript": "^5.8.2",
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- "vitest": "^3.0.9"
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+ "vitest": "^3.1.4"
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  },
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  "dependencies": {
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- "brukerconverter": "^8.0.3",
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+ "cheminfo-types": "^1.8.1",
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  "fifo-logger": "^1.0.0",
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  "filelist-utils": "^1.11.3",
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  "is-any-array": "^2.0.1",
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  "lodash.merge": "^4.6.2",
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- "ml-spectra-processing": "^14.11.0",
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+ "ml-spectra-processing": "^14.12.0",
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  "nmr-correlation": "^2.3.5",
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- "nmr-processing": "^18.0.1"
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+ "nmr-processing": "^18.1.0"
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  },
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  "volta": {
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  "extends": "../../../package.json"
@@ -1,4 +0,0 @@
1
- "use strict";var Re=Object.create;var R=Object.defineProperty;var ve=Object.getOwnPropertyDescriptor;var Ce=Object.getOwnPropertyNames;var we=Object.getPrototypeOf,Fe=Object.prototype.hasOwnProperty;var Ae=(e,t)=>{for(var n in t)R(e,n,{get:t[n],enumerable:!0})},H=(e,t,n,r)=>{if(t&&typeof t=="object"||typeof t=="function")for(let o of Ce(t))!Fe.call(e,o)&&o!==n&&R(e,o,{get:()=>t[o],enumerable:!(r=ve(t,o))||r.enumerable});return e};var Me=(e,t,n)=>(n=e!=null?Re(we(e)):{},H(t||!e||!e.__esModule?R(n,"default",{value:e,enumerable:!0}):n,e)),Te=e=>H(R({},"__esModule",{value:!0}),e);var pt={};Ae(pt,{ANALYSIS_COLUMN_TYPES:()=>Q,ANALYSIS_COLUMN_VALUES_KEYS:()=>ee,CURRENT_EXPORT_VERSION:()=>P,EXTERNAL_API_KEYS:()=>re,NMRiumCore:()=>z,formatSpectra:()=>ae,generateID:()=>b,getOneIfArray:()=>w,migrateSettings:()=>he,units:()=>te});module.exports=Te(pt);var Q={NORMAL:"NORMAL",FORMULA:"FORMULA"};var ee={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var 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t&&(s.nuclei=Ye(t)),n&&(s.panels=n),s}function Ye(e){let t=[],n={name:"nucleus",ppm:"ppmFormat",hz:"hzFormat"};for(let r in e)t.push(x(e[r],n));return t}function G(e){if(e?.version===7)return e;let t={...e,version:7};return t?.settings&&(t.settings=F(t.settings,"nmrium")),t}function A(e,t="localStorage"){if(e?.version===8)return e;if(t==="nmrium")return ce(e);let n={...e,version:8};for(let r in e.workspaces)n.workspaces[r]=ce(n.workspaces[r]);return n}function ce(e){let{version:t,...n}=e,r={...n};return r.display.panels=Ge(e),r}function Ge(e){let t={},n=e.display.panels;for(let r of Object.keys(n)){let{display:o,open:s}=n[r];t[r]={display:o,visible:o,open:s}}return t}function Z(e){if(e?.version===8)return e;let t={...e,version:8};t?.settings&&(t.settings=A(t.settings,"nmrium"));for(let n of t?.data?.spectra||[]){let{filters:r=[]}=n;for(let i=0;i<r.length;i++){let{flag:a,isDeleteAllow:c,label:f,...l}=r[i];r[i]={...l,enabled:a}}let o=r.findIndex(i=>i.name==="apodization");if(o!==-1){let i=r[o],{lineBroadening:a,gaussBroadening:c,lineBroadeningCenter:f}=i.value;i.value={exponential:{apply:!0,options:{lineBroadening:c>0?-a:a}}},c>0&&(i.value.gaussian={apply:!0,options:{lineBroadening:.6*c,lineBroadeningCenter:f}}),r[o]=i}let s=r.findIndex(i=>i.name==="apodizationDimension1"),u=r.findIndex(i=>i.name==="apodizationDimension2");if(s!==-1){let i=r[s],{shapes:a}=i.value.compose;i.value=ue(a)}if(u!==-1){let i=r[u],{shapes:a}=i.value.compose;i.value=ue(a)}}return t}function ue(e){let t={};for(let{shape:n}of e){let{kind:r,options:o}=n;if(r==="sineBell"){let{exponent:s,offset:u}=o,i=s===2?"sineSquare":"sineBell";t[i]={apply:!0,options:{offset:u}}}}return t}function $(e){let{version:t,plugins:n,...r}=e;return t===9?e:{version:9,plugins:{},...r}}var Ze=[_,U,K,W,X,Y,G,Z,$];function pe(e,t,n){let r=structuredClone(e),o=Object.entries(e?.plugins??{});for(let[i,{version:a}]of o){let c=n.get(i);if(!(c&&c.version>=a)){if(c){console.warn(`Plugin "${c.id}" is loaded with a version older (${c.version}) than the one used to save the state (${a}).
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- NMRium may fail to load the state.
3
- Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${i}@${a}" is not registered. NMRium may fail to load the state.
4
- Please consider open this file with the plugin installed.`)}}let s=new Set,u=()=>{let i=r.version;for(let a of n.values())for(let c of a.migrations){if(s.has(c)||i<c.minCore||c.maxCore&&i>c.maxCore)continue;if((r.plugins?.[a.id]?.version||0)===a.version)break;r=c.up(r),s.add(c)}};for(let i=e?.version||0;i<t;i++){let a=Ze[i];r=a(r),u()}u(),r.plugins||(r.plugins={});for(let i of n.values())r.plugins?.[i.id]||(r.plugins[i.id]={id:i.id,version:i.version}),r.plugins[i.id].id=i.id,r.plugins[i.id].version=i.version;return r}var Se=require("filelist-utils");var me={SDF:"sdf",MOL:"mol",NMRIUM:"nmrium",JSON:"json",JCAMP:"jcamp",DX:"dx",JDX:"jdx",JDF:"jdf",NMREDATA:"nmredata",SMILES:"smiles",SMI:"smi"};function M(e){return e.includes(".")?e.replace(/^.*\./,"").toLowerCase():""}function E(e,t={},n){let{data:r,...o}=e;if(!r)return e;let{spectra:s=[]}=r,{keep1D:u=!0,keep2D:i=!0,onlyReal:a}=t,c=a?"ft":t.dataSelection||"both",f=[];for(let l of s){if(!l.info){f.push(l);continue}let{isFid:d,dimension:m,name:p}=l.info;if(!T(m===1&&!u,p,n)&&!T(m===2&&!i,p,n)&&!T(d&&c==="ft",p,n)&&!T(!d&&c==="fid",p,n))if(a&&!d)if(l.info.isComplex=!1,$e(l)){let{rr:g}=l.data;f.push({...l,data:{rr:g}})}else{let{re:g,x:y}=l.data;f.push({...l,data:{re:g,x:y}})}else f.push(l)}return{data:{...r,spectra:f},...o}}function T(e,t,n){return e?(n?.warn(`Skipping ${t} because it didn't match the import filters.`),!0):!1}function $e(e){let{info:t}=e;return t?.dimension===2}function I(e){let{nmriumState:t,plugins:n,options:r}=e;for(let o of n.values()){let s=o.onReadProcess?.onProcessing;s&&s(t,r)}}async function k(e,t,n={}){let{sourceSelector:r,converter:o,keepSource:s,logger:u}=n,i=[],a=[];for(let m of t.values()){let{onReadProcess:p}=m;p&&(p?.onFiles&&i.push(m),p?.supportedExtensions?.length&&p?.onFile&&a.push(m))}let c=await Promise.allSettled(i.map(m=>m.onReadProcess.onFiles(e,n))),f=[],l=await Promise.allSettled(e.files.flatMap(m=>{let p=M(m.name).toLowerCase();return a.flatMap(g=>{let{supportedExtensions:y,onFile:S}=g.onReadProcess;return y.includes(p)?(f.push({file:m,plugin:g}),S(m,{logger:u,sourceSelector:r,converter:o,keepSource:s})):[]})})),d={spectra:[],molecules:[]};for(let m=0;m<c.length;m++){let p=c[m];switch(p.status){case"fulfilled":{let{spectra:g=[],molecules:y=[]}=p.value||{};d.spectra.push(...g),d.molecules.push(...y);break}case"rejected":{let g=p.reason,y=i[m];n.logger?.error(`Load file collection with plugin ${y.id}@${y.version} fails with: ${g}`);break}}}for(let m=0;m<l.length;m++){let p=l[m];switch(p.status){case"fulfilled":{let{spectra:g=[],molecules:y=[]}=p.value||{};d.spectra.push(...g),d.molecules.push(...y);break}case"rejected":{let g=p.reason,{file:y,plugin:S}=f[m];n.logger?.error(`Load file ${y.relativePath} with plugin ${S.id}@${S.version} fails with: ${g}`);break}}}return d}var de=require("filelist-utils");var fe=require("filelist-utils"),q=Me(require("lodash.merge"),1),ge=require("ml-spectra-processing");async function j(e){let{nmriumObjectInput:t,options:n={},migrator:r,plugins:o}=e,s=r(t),{data:u,...i}=s;if(!u)return{...i};let a={data:{...u,spectra:[]},...i},c=a.data,{source:f,spectra:l,molecules:d}=c,m;f&&(m=await(0,fe.fileCollectionFromWebSource)(f,{unzip:{zipExtensions:["zip","nmredata"]}}));let p=[];for(let g of u.spectra)if(m){let{sourceSelector:y}=g,S=L({input:m,migrator:r,plugins:o,options:{...n,sourceSelector:y}}).then(D=>{let{nmriumState:{data:O}}=D,{spectra:De=[],molecules:J=[]}=O||{};J.length>0&&d.length===0&&d.push(...J);for(let Oe of De)l.push(qe(g,Je(Oe)))});p.push(S)}else{let{dimension:y}=g.info;if(y===1){if(!(0,ge.xIsEquallySpaced)(g.data)){n.logger?.error('The ".nmrium" file is corrupted; 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File without changes