@nice2dev/ui-science 1.0.10

package/README.md

@@ -0,0 +1,50 @@
+# @nice2dev/ui-science
+
+Scientific visualization components for React.
+
+## Features
+
+- **NiceScientificChart** — Advanced scientific charting with error bars, annotations
+- **Nice3DPlot** — 3D surface plots, scatter plots, and vector fields
+- **NiceMolecularViewer** — Molecular structure visualization (PDB, MOL2)
+- **NicePhylogeneticTree** — Evolutionary tree visualization
+- **NiceGeographicMap** — GeoJSON-based mapping with projections
+
+## Installation
+
+```bash
+npm install @nice2dev/ui-science
+```
+
+## Usage
+
+```tsx
+import { NiceScientificChart, Nice3DPlot, NiceMolecularViewer } from '@nice2dev/ui-science';
+
+function App() {
+  return (
+    <div>
+      <NiceScientificChart
+        data={[
+          { x: 1, y: 2.5, error: 0.3 },
+          { x: 2, y: 4.1, error: 0.2 },
+        ]}
+        showErrorBars
+      />
+
+      <Nice3DPlot
+        type="surface"
+        data={(x, y) => Math.sin(x) * Math.cos(y)}
+        xRange={[-Math.PI, Math.PI]}
+        yRange={[-Math.PI, Math.PI]}
+      />
+
+      <NiceMolecularViewer format="pdb" data={pdbContent} style="ball-and-stick" />
+    </div>
+  );
+}
+```
+
+## License
+
+MIT

package/dist/index.cjs

@@ -0,0 +1,69 @@
+"use strict";var nt=Object.defineProperty;var st=(e,t,s)=>t in e?nt(e,t,{enumerable:!0,configurable:!0,writable:!0,value:s}):e[t]=s;var ye=(e,t,s)=>st(e,typeof t!="symbol"?t+"":t,s);Object.defineProperty(exports,Symbol.toStringTag,{value:"Module"});const n=require("react/jsx-runtime"),u=require("react");class Ye{constructor(t){ye(this,"config");ye(this,"notebooks",new Map);this.config=t}async createNotebook(t){const s={id:this.generateId(),name:t.name||"Untitled Notebook",description:t.description,project:t.project,owner:t.owner||"current-user",collaborators:t.collaborators||[],entries:[],createdAt:new Date().toISOString(),updatedAt:new Date().toISOString(),isArchived:!1,settings:t.settings||{requireSignatures:!0,requireWitness:!1,autoLockAfterSign:!0,defaultEntryType:"experiment",customFields:[],templates:[]}};return this.notebooks.set(s.id,s),s}async getNotebook(t){return this.notebooks.get(t)||null}async listNotebooks(){return Array.from(this.notebooks.values())}async createEntry(t,s){const i=this.notebooks.get(t);if(!i)throw new Error(`Notebook not found: ${t}`);const r={id:this.generateId(),notebookId:t,type:s.type||i.settings.defaultEntryType,status:"draft",title:s.title||"Untitled Entry",objective:s.objective,hypothesis:s.hypothesis,methods:s.methods,results:s.results,conclusions:s.conclusions,sections:s.sections||[],attachments:[],tags:s.tags||[],linkedEntries:s.linkedEntries||[],createdAt:new Date().toISOString(),updatedAt:new Date().toISOString(),createdBy:"current-user",lastModifiedBy:"current-user",version:1,signatures:[],comments:[]};return i.entries.push(r),i.updatedAt=new Date().toISOString(),r}async updateEntry(t,s,i){const r=this.notebooks.get(t);if(!r)throw new Error(`Notebook not found: ${t}`);const o=r.entries.findIndex(c=>c.id===s);if(o===-1)throw new Error(`Entry not found: ${s}`);const a=r.entries[o];if(a.status==="locked")throw new Error("Cannot modify locked entry");const l={...a,...i,id:a.id,notebookId:t,updatedAt:new Date().toISOString(),lastModifiedBy:"current-user",version:a.version+1};return r.entries[o]=l,r.updatedAt=new Date().toISOString(),l}async signEntry(t,s,i){const r=this.notebooks.get(t);if(!r)throw new Error(`Notebook not found: ${t}`);const o=r.entries.find(l=>l.id===s);if(!o)throw new Error(`Entry not found: ${s}`);const a={...i,signedAt:new Date().toISOString(),signatureHash:this.generateSignatureHash(o,i.userId)};return o.signatures.push(a),r.settings.autoLockAfterSign&&i.role==="author"&&(o.status="signed"),o.updatedAt=new Date().toISOString(),o}async addAttachment(t,s,i){const r=this.notebooks.get(t);if(!r)throw new Error(`Notebook not found: ${t}`);const o=r.entries.find(l=>l.id===s);if(!o)throw new Error(`Entry not found: ${s}`);const a={id:this.generateId(),name:i.name,type:i.type,size:i.size,url:URL.createObjectURL(i),uploadedAt:new Date().toISOString(),uploadedBy:"current-user"};return o.attachments.push(a),o.updatedAt=new Date().toISOString(),a}async searchEntries(t,s){var o,a,l,c,h,p;const i=[],r=t.toLowerCase();for(const f of this.notebooks.values())if(!(s!=null&&s.notebookId&&f.id!==s.notebookId))for(const m of f.entries)s!=null&&s.type&&m.type!==s.type||s!=null&&s.status&&m.status!==s.status||(o=s==null?void 0:s.tags)!=null&&o.length&&!s.tags.some(v=>m.tags.includes(v))||s!=null&&s.dateFrom&&m.createdAt<s.dateFrom||s!=null&&s.dateTo&&m.createdAt>s.dateTo||(m.title.toLowerCase().includes(r)||(a=m.objective)!=null&&a.toLowerCase().includes(r)||(l=m.hypothesis)!=null&&l.toLowerCase().includes(r)||(c=m.methods)!=null&&c.toLowerCase().includes(r)||(h=m.results)!=null&&h.toLowerCase().includes(r)||(p=m.conclusions)!=null&&p.toLowerCase().includes(r))&&i.push(m);return i}async exportEntry(t,s,i){const r=this.notebooks.get(t);if(!r)throw new Error(`Notebook not found: ${t}`);const o=r.entries.find(l=>l.id===s);if(!o)throw new Error(`Entry not found: ${s}`);const a=this.generateEntryHTML(o,r);return i==="html"?new Blob([a],{type:"text/html"}):new Blob([a],{type:"text/html"})}generateEntryHTML(t,s){return`
+      <!DOCTYPE html>
+      <html>
+      <head>
+        <meta charset="utf-8">
+        <title>${t.title}</title>
+        <style>
+          body { font-family: 'Times New Roman', serif; max-width: 800px; margin: 0 auto; padding: 20px; }
+          h1 { border-bottom: 2px solid #333; }
+          .meta { color: #666; font-size: 0.9em; }
+          .section { margin: 20px 0; }
+          .signatures { border-top: 1px solid #ccc; margin-top: 40px; padding-top: 20px; }
+        </style>
+      </head>
+      <body>
+        <h1>${t.title}</h1>
+        <div class="meta">
+          <p>Notebook: ${s.name}</p>
+          <p>Entry ID: ${t.id}</p>
+          <p>Type: ${t.type}</p>
+          <p>Created: ${new Date(t.createdAt).toLocaleString()}</p>
+          <p>Version: ${t.version}</p>
+        </div>
+        ${t.objective?`<div class="section"><h2>Objective</h2><p>${t.objective}</p></div>`:""}
+        ${t.hypothesis?`<div class="section"><h2>Hypothesis</h2><p>${t.hypothesis}</p></div>`:""}
+        ${t.methods?`<div class="section"><h2>Methods</h2><p>${t.methods}</p></div>`:""}
+        ${t.results?`<div class="section"><h2>Results</h2><p>${t.results}</p></div>`:""}
+        ${t.conclusions?`<div class="section"><h2>Conclusions</h2><p>${t.conclusions}</p></div>`:""}
+        ${t.signatures.length>0?`
+          <div class="signatures">
+            <h2>Signatures</h2>
+            ${t.signatures.map(i=>`
+              <p><strong>${i.userName}</strong> (${i.role}) - ${new Date(i.signedAt).toLocaleString()}</p>
+            `).join("")}
+          </div>
+        `:""}
+      </body>
+      </html>
+    `}generateId(){return Date.now().toString(36)+Math.random().toString(36).substring(2)}generateSignatureHash(t,s){const i=JSON.stringify({entry:t,userId:s,timestamp:Date.now()});return Buffer.from(i).toString("base64").substring(0,32)}}function it(e){return new Ye(e)}const _e=u.createContext(null);function Ne(){const e=u.useContext(_e);if(!e)throw new Error("useLabNotebook must be used within LabNotebookProvider");return e}function Pe({service:e,children:t}){const[s,i]=u.useState([]),[r,o]=u.useState(null),[a,l]=u.useState(null),c=u.useCallback(async()=>{const v=await e.listNotebooks();i(v)},[e]),h=u.useMemo(()=>s.find(v=>v.id===r)||null,[s,r]),p=u.useMemo(()=>(h==null?void 0:h.entries.find(v=>v.id===a))||null,[h,a]),f=u.useCallback(v=>{o(v),l(null)},[]),m={service:e,notebooks:s,currentNotebook:h,currentEntry:p,setCurrentNotebook:f,setCurrentEntry:l,refresh:c};return n.jsx(_e.Provider,{value:m,children:t})}const 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lt({entry:e}){const{service:t,currentNotebook:s,refresh:i}=Ne(),[r,o]=u.useState(!1),[a,l]=u.useState(e),c=e.status==="locked"||e.status==="signed",h=async()=>{s&&(await t.updateEntry(s.id,e.id,a),await i(),o(!1))},p=async()=>{s&&(await t.signEntry(s.id,e.id,{userId:"current-user",userName:"Current User",role:"author"}),await i())};return n.jsxs("div",{children:[n.jsxs("div",{style:{display:"flex",justifyContent:"space-between",alignItems:"flex-start",marginBottom:"24px"},children:[n.jsxs("div",{children:[n.jsx("h2",{style:{margin:0},children:e.title}),n.jsxs("div",{style:{display:"flex",gap:"8px",marginTop:"8px"},children:[n.jsx("span",{style:{..._.badge,backgroundColor:`${Fe[e.status]}20`,color:Fe[e.status]},children:e.status}),n.jsxs("span",{style:{fontSize:"12px",color:"#666"},children:["v",e.version]})]})]}),!c&&n.jsx("div",{style:{display:"flex",gap:"8px"},children:r?n.jsxs(n.Fragment,{children:[n.jsx("button",{onClick:h,style:_.button,children:"Save"}),n.jsx("button",{onClick:()=>{o(!1),l(e)},style:{..._.button,backgroundColor:"#9e9e9e"},children:"Cancel"})]}):n.jsxs(n.Fragment,{children:[n.jsx("button",{onClick:()=>o(!0),style:_.button,children:"Edit"}),n.jsx("button",{onClick:p,style:{..._.button,backgroundColor:"#9c27b0"},children:"Sign"})]})})]}),r?n.jsxs("div",{style:{display:"flex",flexDirection:"column",gap:"16px"},children:[n.jsxs("div",{children:[n.jsx("label",{style:{display:"block",marginBottom:"4px",fontWeight:500},children:"Title"}),n.jsx("input",{type:"text",value:a.title,onChange:f=>l({...a,title:f.target.value}),style:_.input})]}),n.jsxs("div",{children:[n.jsx("label",{style:{display:"block",marginBottom:"4px",fontWeight:500},children:"Objective"}),n.jsx("textarea",{value:a.objective||"",onChange:f=>l({...a,objective:f.target.value}),style:_.textarea})]}),n.jsxs("div",{children:[n.jsx("label",{style:{display:"block",marginBottom:"4px",fontWeight:500},children:"Methods"}),n.jsx("textarea",{value:a.methods||"",onChange:f=>l({...a,methods:f.target.value}),style:_.textarea})]}),n.jsxs("div",{children:[n.jsx("label",{style:{display:"block",marginBottom:"4px",fontWeight:500},children:"Results"}),n.jsx("textarea",{value:a.results||"",onChange:f=>l({...a,results:f.target.value}),style:_.textarea})]}),n.jsxs("div",{children:[n.jsx("label",{style:{display:"block",marginBottom:"4px",fontWeight:500},children:"Conclusions"}),n.jsx("textarea",{value:a.conclusions||"",onChange:f=>l({...a,conclusions:f.target.value}),style:_.textarea})]})]}):n.jsxs("div",{style:{display:"flex",flexDirection:"column",gap:"24px"},children:[e.objective&&n.jsxs("section",{children:[n.jsx("h3",{style:{margin:"0 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s=this.mean(e),i=this.std(e),r=e.map(o=>Math.pow((o-s)/i,3));return t/((t-1)*(t-2))*r.reduce((o,a)=>o+a,0)},kurtosis(e){const t=e.length;if(t<4)return NaN;const s=this.mean(e),i=this.std(e),o=e.map(a=>Math.pow((a-s)/i,4)).reduce((a,l)=>a+l,0);return t*(t+1)/((t-1)*(t-2)*(t-3))*o-3*Math.pow(t-1,2)/((t-2)*(t-3))},correlation(e,t){if(e.length!==t.length||e.length<2)return NaN;const s=e.length,i=this.mean(e),r=this.mean(t);let o=0,a=0,l=0;for(let c=0;c<s;c++){const h=e[c]-i,p=t[c]-r;o+=h*p,a+=h*h,l+=p*p}return o/Math.sqrt(a*l)},correlationMatrix(e){const t=Object.keys(e),s={};for(const i of t){s[i]={};for(const r of t)s[i][r]=this.correlation(e[i],e[r])}return s},covariance(e,t,s=!1){if(e.length!==t.length||e.length<2)return NaN;const i=e.length,r=this.mean(e),o=this.mean(t);let a=0;for(let l=0;l<i;l++)a+=(e[l]-r)*(t[l]-o);return a/(s?i:i-1)},linearRegression(e,t){if(e.length!==t.length||e.length<2)throw new Error("Invalid input arrays");const s=e.length,i=this.mean(e),r=this.mean(t);let o=0,a=0;for(let v=0;v<s;v++)o+=(e[v]-i)*(t[v]-r),a+=Math.pow(e[v]-i,2);const l=o/a,c=r-l*i;let h=0,p=0;for(let v=0;v<s;v++){const M=l*e[v]+c;h+=Math.pow(t[v]-r,2),p+=Math.pow(t[v]-M,2)}const f=1-p/h,m=`y = ${l.toFixed(4)}x + ${c.toFixed(4)}`;return{slope:l,intercept:c,r2:f,equation:m}},tTest(e,t){const s=e.length,i=t.length,r=this.mean(e),o=this.mean(t),a=this.variance(e),l=this.variance(t),c=Math.sqrt(a/s+l/i),h=(r-o)/c,p=Math.pow(a/s+l/i,2)/(Math.pow(a/s,2)/(s-1)+Math.pow(l/i,2)/(i-1)),f=2*(1-this.normalCDF(Math.abs(h)));return{tStatistic:h,pValue:f,degreesOfFreedom:p,meanDiff:r-o}},normalCDF(e){const t=.254829592,s=-.284496736,i=1.421413741,r=-1.453152027,o=1.061405429,a=.3275911,l=e<0?-1:1;e=Math.abs(e)/Math.sqrt(2);const c=1/(1+a*e),h=1-((((o*c+r)*c+i)*c+s)*c+t)*c*Math.exp(-e*e);return .5*(1+l*h)},chiSquare(e,t){if(e.length!==t.length)throw new Error("Arrays must have same length");let s=0;for(let o=0;o<e.length;o++)s+=Math.pow(e[o]-t[o],2)/t[o];const i=e.length-1;return{chiSquare:s,pValue:.05,degreesOfFreedom:i}},zScore(e){const t=this.mean(e),s=this.std(e);return e.map(i=>(i-t)/s)},minMaxNormalize(e,t=0,s=1){const i=Math.min(...e),o=Math.max(...e)-i;return e.map(a=>t+(a-i)/o*(s-t))},describe(e){const t=e.filter(i=>i!=null&&!isNaN(i)),s=this.quartiles(t);return{count:t.length,mean:this.mean(t),median:s.q2,std:this.std(t),min:Math.min(...t),max:Math.max(...t),q1:s.q1,q3:s.q3,skewness:this.skewness(t),kurtosis:this.kurtosis(t),mode:this.mode(t),variance:this.variance(t)}}};class Ve{constructor(t={}){ye(this,"config");ye(this,"datasets",new Map);ye(this,"analyses",new Map);this.config={maxRowsInMemory:1e5,...t}}async importCSV(t,s){const i=(s==null?void 0:s.delimiter)||",",r=(s==null?void 0:s.header)!==!1,o=t.split(`
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Date().toISOString(),source:o};return this.datasets.set(l.id,l),l}inferColumns(t){if(t.length===0)return[];const s=new Set;t.forEach(r=>Object.keys(r).forEach(o=>s.add(o)));const i=[];for(const r of s){const o=t.map(p=>p[r]),a=o.filter(p=>p!=null),l=new Set(a);let c="mixed";a.every(p=>typeof p=="number")?c="number":a.every(p=>typeof p=="string")?c=l.size<a.length*.5?"category":"string":a.every(p=>typeof p=="boolean")?c="boolean":a.every(p=>p instanceof Date||!isNaN(Date.parse(p)))&&(c="date");const h={name:r,type:c,nullable:o.some(p=>p==null),unique:l.size,missing:o.length-a.length};if(c==="number"){const p=a.filter(f=>typeof f=="number");h.stats=ge.describe(p)}i.push(h)}return i}runAnalysis(t,s,i={}){const r=this.datasets.get(t);if(!r)throw new Error(`Dataset not found: ${t}`);const o=performance.now();let a;switch(s){case"descriptive":a=this.descriptiveAnalysis(r,i);break;case"correlation":a=this.correlationAnalysis(r,i);break;case"regression":a=this.regressionAnalysis(r,i);break;case"ttest":a=this.tTestAnalysis(r,i);break;case"distribution":a=this.distributionAnalysis(r,i);break;default:throw new Error(`Unsupported analysis type: ${s}`)}const l=performance.now()-o,c={id:this.generateId(),datasetId:t,type:s,parameters:i,result:a,createdAt:new Date().toISOString(),executionTimeMs:l};return this.analyses.set(c.id,c),c}descriptiveAnalysis(t,s){const i=s.columns||t.columns.filter(o=>o.type==="number").map(o=>o.name),r={};for(const o of i){const a=t.data.map(l=>l[o]).filter(l=>typeof l=="number");r[o]=ge.describe(a)}return r}correlationAnalysis(t,s){const i=s.columns||t.columns.filter(o=>o.type==="number").map(o=>o.name),r={};for(const o of i)r[o]=t.data.map(a=>a[o]).filter(a=>typeof 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r=[...i.data];switch(s.type){case"filter":r=this.applyFilter(r,s);break;case"sort":r=this.applySort(r,s);break;case"fillna":r=this.applyFillNA(r,s);break;case"dropna":r=this.applyDropNA(r,s);break;case"normalize":r=this.applyNormalize(r,s);break;case"standardize":r=this.applyStandardize(r,s);break;default:throw new Error(`Unsupported transformation: ${s.type}`)}return this.createDataset({name:`${i.name} (transformed)`,data:r})}applyFilter(t,s){const{column:i,parameters:r}=s,{operator:o,value:a}=r;return t.filter(l=>{const c=l[i];switch(o){case"==":return c===a;case"!=":return c!==a;case">":return c>a;case">=":return c>=a;case"<":return c<a;case"<=":return c<=a;case"contains":return String(c).includes(a);case"startswith":return String(c).startsWith(a);default:return!0}})}applySort(t,s){const{column:i,parameters:r}=s,o=r.ascending!==!1;return[...t].sort((a,l)=>{const c=a[i],h=l[i];return c<h?o?-1:1:c>h?o?1:-1:0})}applyFillNA(t,s){const{column:i,parameters:r}=s,o=r.value;return t.map(a=>({...a,[i]:a[i]??o}))}applyDropNA(t,s){const i=s.columns||[s.column];return t.filter(r=>i.every(o=>r[o]!=null))}applyNormalize(t,s){const{column:i}=s,r=t.map(c=>c[i]).filter(c=>typeof c=="number"),o=Math.min(...r),l=Math.max(...r)-o;return t.map(c=>({...c,[i]:typeof c[i]=="number"?(c[i]-o)/l:c[i]}))}applyStandardize(t,s){const{column:i}=s,r=t.map(l=>l[i]).filter(l=>typeof l=="number"),o=ge.mean(r),a=ge.std(r);return t.map(l=>({...l,[i]:typeof l[i]=="number"?(l[i]-o)/a:l[i]}))}exportCSV(t){const s=this.datasets.get(t);if(!s)throw new Error(`Dataset not found: ${t}`);const i=s.columns.map(o=>o.name),r=s.data.map(o=>i.map(a=>{const l=o[a];return l==null?"":typeof l=="string"&&(l.includes(",")||l.includes('"'))?`"${l.replace(/"/g,'""')}"`:String(l)}).join(","));return[i.join(","),...r].join(`
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0:A.tooltip)&&n.jsx("div",{style:{position:"absolute",top:y(A.position.lat,A.position.lng).y-30,left:y(A.position.lat,A.position.lng).x,transform:"translateX(-50%)",background:"rgba(0,0,0,0.8)",color:"#FFF",padding:"4px 8px",borderRadius:4,fontSize:"0.75rem",pointerEvents:"none",whiteSpace:"nowrap"},children:A.tooltip}),n.jsxs("div",{style:{position:"absolute",bottom:8,right:8,background:"rgba(255,255,255,0.9)",padding:"2px 6px",borderRadius:4,fontSize:"0.7rem",color:"#666"},children:[V.lat.toFixed(2),"°, ",V.lng.toFixed(2),"°"]}),de&&t.length>0&&n.jsxs("div",{style:{position:"absolute",top:8,left:8,background:"rgba(255,255,255,0.95)",padding:8,borderRadius:4,fontSize:"0.75rem"},children:[n.jsx("div",{style:{fontWeight:"bold",marginBottom:4},children:"Layers"}),t.map(x=>n.jsxs("label",{style:{display:"flex",alignItems:"center",gap:4,cursor:"pointer"},children:[n.jsx("input",{type:"checkbox",checked:S.has(x.id),onChange:b=>{const O=new Set(S);b.target.checked?O.add(x.id):O.delete(x.id),N(O)}}),x.name]},x.id))]}),ne&&n.jsxs("div",{style:{position:"absolute",top:8,right:8,display:"flex",flexDirection:"column",gap:4},children:[n.jsxs("select",{value:d,onChange:x=>g(x.target.value),style:{padding:"2px 4px",fontSize:"0.75rem"},children:[n.jsx("option",{value:"equirectangular",children:"Equirectangular"}),n.jsx("option",{value:"mercator",children:"Mercator"}),n.jsx("option",{value:"orthographic",children:"Orthographic"}),n.jsx("option",{value:"robinson",children:"Robinson"})]}),n.jsx("button",{onClick:()=>{w(1),ie({lat:0,lng:0})},style:{padding:"2px 4px",fontSize:"0.75rem",cursor:"pointer"},children:"Reset View"})]})]})}exports.CitationService=Ke;exports.DataAnalysisService=Ve;exports.LabNotebookProvider=Pe;exports.LabNotebookService=Ye;exports.Nice3DPlot=Bt;exports.NiceCitation=Mt;exports.NiceDataAnalysis=ut;exports.NiceGeographicMap=Ut;exports.NiceLabNotebook=rt;exports.NiceMolecularViewer=Ot;exports.NicePhylogeneticTree=Xt;exports.NiceScientificChart=Nt;exports.Stats=ge;exports.createCitationService=$t;exports.createDataAnalysisService=dt;exports.createLabNotebookService=it;exports.useCitation=Le;exports.useLabNotebook=Ne;