diff-grok 1.3.0 → 1.4.0

package/README.MD

@@ -1,12 +1,14 @@
 # Diff Grok
 
+[![LNNS](https://img.shields.io/badge/LNNS-paper-red.svg)](https://link.springer.com/chapter/10.1007/978-3-032-22236-7_31)
+[![JOSS](https://joss.theoj.org/papers/10.21105/joss.09090/status.svg)](https://doi.org/10.21105/joss.09090)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.19219694.svg)](https://doi.org/10.5281/zenodo.19219694)
 [![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://datagrok-ai.github.io/diff-grok/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://github.com/datagrok-ai/diff-grok/blob/main/LICENSE)
 [![Build Status](https://github.com/datagrok-ai/diff-grok/actions/workflows/libraries.yaml/badge.svg)](https://github.com/datagrok-ai/diff-grok/actions/workflows/libraries.yaml)
 [![Run tests](https://github.com/datagrok-ai/diff-grok/actions/workflows/test.yaml/badge.svg)](https://github.com/datagrok-ai/diff-grok/actions/workflows/test.yaml)
 
-A lightweight TypeScript library for solving initial value problem ([IVP](https://en.wikipedia.org/wiki/Initial_value_problem)) for ordinary differential equations ([ODEs](https://en.wikipedia.org/wiki/Ordinary_differential_equation)) using numerical methods. The primary solvers are [LSODA](https://doi.org/10.1137/0904010) — a variable-order method that automatically detects stiffness and switches between Adams (non-stiff) and BDF (stiff) formulations — and [CVODE](https://sundials.readthedocs.io/en/latest/cvode/index.html) — a variable-order, variable-step solver from the SUNDIALS suite supporting both Adams and BDF methods.
+A lightweight TypeScript library for solving initial value problem ([IVP](https://en.wikipedia.org/wiki/Initial_value_problem)) for ordinary differential equations ([ODEs](https://en.wikipedia.org/wiki/Ordinary_differential_equation)) using numerical methods. The primary solvers are [LSODA](https://doi.org/10.1137/0904010) - a variable-order method that automatically detects stiffness and switches between Adams (non-stiff) and BDF (stiff) formulations - and [CVODE](https://sundials.readthedocs.io/en/latest/cvode/index.html) - a variable-order, variable-step solver from the SUNDIALS suite supporting both Adams and BDF methods.
 
 ## Features
 
@@ -423,7 +425,7 @@ Find this example in [scripting.ts](./src/examples/scripting.ts).
 
 ### Pipelines
 
-Diff Grok **pipeline** is a powerful feature for complex process simulation and model analysis in webworkers. It wraps the main solver with a set of actions that perform pre- and post-processing of a model inputs & outputs. In addition, they provide an output customization.
+Diff Grok **pipeline** is a powerful feature for complex process simulation and model analysis in webworkers (see our [paper](https://link.springer.com/chapter/10.1007/978-3-032-22236-7_31) in Lecture Notes in Networks and Systems). It wraps the main solver with a set of actions that perform pre- and post-processing of a model inputs & outputs. In addition, they provide an output customization.
 
 1. Start with imports:
 
@@ -673,6 +675,40 @@ node src/examples/basic-use.js
 
 </details>
 
+## Citation
+
+If you use this library for research purposes, please cite the following papers:
+
+* [Diff Studio: Ecosystem for Interactive Modeling by Ordinary Differential Equations](https://joss.theoj.org/papers/10.21105/joss.09090) in Journal of Open Source Software (2026).
+
+```
+@article{diffstudio2026joss,
+  title = {Diff Studio: Ecosystem for Interactive Modeling by Ordinary Differential Equations},
+  author = {Viktor Makarichev, Larisa Bankurova, Gennadii Zakharov, Leonid Stolbov, Steven Mehrman, Dan Skatov, Jeffrey Cohen, Paul Sass, Davit Rizhinashvili, Andrew Skalkin},
+  journal = {Journal of Open Source Software},
+  year = {2026},
+  volume = {11},
+  number = {120},
+  doi = {10.21105/joss.09090}
+}
+```
+
+* [Diff Studio: Web-Based Environment for Interactive Modeling with Ordinary Differential Equations](https://link.springer.com/chapter/10.1007/978-3-032-22236-7_31) in Springer, CoMeSySo 2025 Proceedings (Lecture Notes in Networks and Systems, vol. 1901) - foundational paper.
+
+```
+@InProceedings{diffstudio2026lnns,
+title = {Diff Studio: Web-Based Environment for Interactive Modeling with Ordinary Differential Equations},
+author = {Viktor Makarichev, Larisa Bankurova, Gennadii Zakharov, Leonid Stolbov, Steven Mehrman, Dan Skatov, Jeffrey Cohen, Paul Sass, Davit Rizhinashvili, Andrew Skalkin},
+editor = {Radek Silhavy, Petr Silhavy},
+booktitle = {Focus on Artificial Intelligence in Intelligent Systems Design},
+year = {2026},
+publisher = {Springer Nature Switzerland},
+address = {Cham},
+pages = {390--401},
+doi = {10.1007/978-3-032-22236-7_31}
+}
+```
+
 ## References
 
 * L. Petzold, "Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations," *SIAM J. Sci. Stat. Comput.*, 4(1), 136–148, 1983. [doi:10.1137/0904010](https://doi.org/10.1137/0904010)

package/dist/src/latex-export/generator/document-builder.js

@@ -30,28 +30,28 @@ export function buildLatexDocument(model, options) {
     }
     if (model.equations.length > 0) {
         parts.push(`\\subsection{${plural('Equation', model.equations.length)}}`);
-        parts.push(buildLatexAlign(model.equations));
+        parts.push(buildLatexAlign(model.equations, opts));
         if (model.argument.entries.length >= 3)
             parts.push(buildLatexArgRange(model));
     }
     if (model.expressions.length > 0) {
         parts.push(`\\subsection{${plural('Expression', model.expressions.length)}}`);
-        parts.push(buildLatexAlign(model.expressions));
+        parts.push(buildLatexAlign(model.expressions, opts));
     }
     const loopInfo = extractLoopInfo(model);
     if (loopInfo && loopInfo.updates.length > 0) {
         parts.push('\\subsection{Cyclic Update}');
-        const lines = loopInfo.updates.map((u) => `  ${renderLoopUpdateLine(u)}`);
+        const lines = loopInfo.updates.map((u) => `  ${renderLoopUpdateLine(u, opts)}`);
         parts.push(`Before each cycle:\n\\begin{align}\n${lines.join(' \\\\\n')}\n\\end{align}`);
     }
     const stages = extractStageInfos(model);
     if (stages.length > 0) {
         parts.push('\\subsection{Stage Transitions}');
         for (const stage of stages) {
-            const dur = stage.duration ? ` (duration: $${expressionToLatex(stage.duration)}$)` : '';
+            const dur = stage.duration ? ` (duration: $${expressionToLatex(stage.duration, opts)}$)` : '';
             parts.push(`\\textbf{${stage.stageName}}${dur}`);
             if (stage.transitions.length > 0) {
-                const lines = stage.transitions.map((t) => `  ${renderTransitionLine(t)}`);
+                const lines = stage.transitions.map((t) => `  ${renderTransitionLine(t, opts)}`);
                 parts.push(`Before this stage:\n\\begin{align}\n${lines.join(' \\\\\n')}\n\\end{align}`);
             }
         }
@@ -90,28 +90,28 @@ export function buildMarkdownDocument(model, options) {
     }
     if (model.equations.length > 0) {
         parts.push(`### ${plural('Equation', model.equations.length)}`);
-        parts.push(buildMarkdownAlign(model.equations));
+        parts.push(buildMarkdownAlign(model.equations, opts));
         if (model.argument.entries.length >= 3)
             parts.push(buildMarkdownArgRange(model));
     }
     if (model.expressions.length > 0) {
         parts.push(`### ${plural('Expression', model.expressions.length)}`);
-        parts.push(buildMarkdownAlign(model.expressions));
+        parts.push(buildMarkdownAlign(model.expressions, opts));
     }
     const loopInfo = extractLoopInfo(model);
     if (loopInfo && loopInfo.updates.length > 0) {
         parts.push('### Cyclic Update');
-        const lines = loopInfo.updates.map((u) => `  ${renderLoopUpdateLine(u)}`);
+        const lines = loopInfo.updates.map((u) => `  ${renderLoopUpdateLine(u, opts)}`);
         parts.push(`Before each cycle:\n\n$$\n\\begin{aligned}\n${lines.join(' \\\\\n')}\n\\end{aligned}\n$$`);
     }
     const stages = extractStageInfos(model);
     if (stages.length > 0) {
         parts.push('### Stage Transitions');
         for (const stage of stages) {
-            const dur = stage.duration ? ` (duration: $${expressionToLatex(stage.duration)}$)` : '';
+            const dur = stage.duration ? ` (duration: $${expressionToLatex(stage.duration, opts)}$)` : '';
             parts.push(`**${stage.stageName}**${dur}`);
             if (stage.transitions.length > 0) {
-                const lines = stage.transitions.map((t) => `  ${renderTransitionLine(t)}`);
+                const lines = stage.transitions.map((t) => `  ${renderTransitionLine(t, opts)}`);
                 parts.push(`Before this stage:\n\n$$\n\\begin{aligned}\n${lines.join(' \\\\\n')}\n\\end{aligned}\n$$`);
             }
         }
@@ -193,18 +193,18 @@ function renderFormulaLhs(f) {
         return `${lhs}(${f.arrowParams.join(', ')})`;
     return lhs;
 }
-function buildLatexAlign(formulas) {
+function buildLatexAlign(formulas, opts) {
     const lines = formulas.map((f) => {
         const lhs = renderFormulaLhs(f);
-        const rhs = expressionToLatex(f.rhs);
+        const rhs = expressionToLatex(f.rhs, opts);
         return `  ${lhs} &= ${rhs}`;
     });
     return `\\begin{align}\n${lines.join(' \\\\\n')}\n\\end{align}`;
 }
-function buildMarkdownAlign(formulas) {
+function buildMarkdownAlign(formulas, opts) {
     const lines = formulas.map((f) => {
         const lhs = renderFormulaLhs(f);
-        const rhs = expressionToLatex(f.rhs);
+        const rhs = expressionToLatex(f.rhs, opts);
         return `  ${lhs} &= ${rhs}`;
     });
     return `$$\n\\begin{aligned}\n${lines.join(' \\\\\n')}\n\\end{aligned}\n$$`;
@@ -225,10 +225,10 @@ function compactInlineItems(model) {
         return `${name}(${t0}) = ${e.value}`;
     });
 }
-function compactExprItems(model) {
+function compactExprItems(model, opts) {
     return model.expressions.map((f) => {
         const lhs = renderFormulaLhs(f);
-        const rhs = expressionToLatex(f.rhs);
+        const rhs = expressionToLatex(f.rhs, opts);
         return `${lhs} = ${rhs}`;
     });
 }
@@ -248,9 +248,9 @@ function extractLoopInfo(model) {
     }
     return count ? { count, updates } : undefined;
 }
-function renderLoopUpdateLine(u) {
+function renderLoopUpdateLine(u, opts) {
     const varLatex = identifierToLatex(u.variable);
-    const valLatex = expressionToLatex(u.value);
+    const valLatex = expressionToLatex(u.value, opts);
     return `${varLatex} \\leftarrow ${varLatex} + ${valLatex}`;
 }
 /** Replace internal argument refs (_t0, _t1, _h) with actual values from #argument. */
@@ -296,9 +296,9 @@ function extractStageInfos(model) {
         return { stageName: block.stageName, duration, transitions };
     });
 }
-function renderTransitionLine(t) {
+function renderTransitionLine(t, opts) {
     const varLatex = identifierToLatex(t.variable);
-    const valLatex = expressionToLatex(t.value);
+    const valLatex = expressionToLatex(t.value, opts);
     if (t.isIncrement)
         return `${varLatex} \\leftarrow ${varLatex} + ${valLatex}`;
     return `${varLatex} \\leftarrow ${valLatex}`;
@@ -309,7 +309,7 @@ function buildLatexCompact(model, opts) {
         parts.push(`\\textbf{${model.name}}`);
     if (model.equations.length > 0) {
         parts.push(`${plural('Equation', model.equations.length)}:`);
-        parts.push(buildLatexAlign(model.equations));
+        parts.push(buildLatexAlign(model.equations, opts));
         if (model.argument.entries.length >= 3)
             parts.push(buildLatexArgRange(model));
     }
@@ -318,19 +318,19 @@ function buildLatexCompact(model, opts) {
         parts.push(`${compactInitsLabel(model)}:\n${lines.join('\n')}`);
     }
     if (model.expressions.length > 0) {
-        const lines = compactExprItems(model).map((item) => `\\[ ${item} \\]`);
+        const lines = compactExprItems(model, opts).map((item) => `\\[ ${item} \\]`);
         parts.push(`where\n${lines.join('\n')}`);
     }
     const loopInfo = extractLoopInfo(model);
     if (loopInfo && loopInfo.updates.length > 0) {
-        const lines = loopInfo.updates.map((u) => `\\[ ${renderLoopUpdateLine(u)} \\]`);
+        const lines = loopInfo.updates.map((u) => `\\[ ${renderLoopUpdateLine(u, opts)} \\]`);
         parts.push(`before each cycle:\n${lines.join('\n')}`);
     }
     const stages = extractStageInfos(model);
     for (const stage of stages) {
         if (stage.transitions.length > 0) {
-            const dur = stage.duration ? ` ($${expressionToLatex(stage.duration)}$)` : '';
-            const lines = stage.transitions.map((t) => `\\[ ${renderTransitionLine(t)} \\]`);
+            const dur = stage.duration ? ` ($${expressionToLatex(stage.duration, opts)}$)` : '';
+            const lines = stage.transitions.map((t) => `\\[ ${renderTransitionLine(t, opts)} \\]`);
             parts.push(`before ${stage.stageName}${dur}:\n${lines.join('\n')}`);
         }
     }
@@ -346,7 +346,7 @@ function buildMarkdownCompact(model, opts) {
         parts.push(`**${model.name}**`);
     if (model.equations.length > 0) {
         parts.push(`${plural('Equation', model.equations.length)}:`);
-        parts.push(buildMarkdownAlign(model.equations));
+        parts.push(buildMarkdownAlign(model.equations, opts));
         if (model.argument.entries.length >= 3)
             parts.push(buildMarkdownArgRange(model));
     }
@@ -355,19 +355,19 @@ function buildMarkdownCompact(model, opts) {
         parts.push(`${compactInitsLabel(model)}:\n${lines.join('\n')}`);
     }
     if (model.expressions.length > 0) {
-        const lines = compactExprItems(model).map((item) => `$$${item}$$`);
+        const lines = compactExprItems(model, opts).map((item) => `$$${item}$$`);
         parts.push(`where\n${lines.join('\n')}`);
     }
     const loopInfo = extractLoopInfo(model);
     if (loopInfo && loopInfo.updates.length > 0) {
-        const lines = loopInfo.updates.map((u) => `$$${renderLoopUpdateLine(u)}$$`);
+        const lines = loopInfo.updates.map((u) => `$$${renderLoopUpdateLine(u, opts)}$$`);
         parts.push(`before each cycle:\n${lines.join('\n')}`);
     }
     const stages = extractStageInfos(model);
     for (const stage of stages) {
         if (stage.transitions.length > 0) {
-            const dur = stage.duration ? ` ($${expressionToLatex(stage.duration)}$)` : '';
-            const lines = stage.transitions.map((t) => `$$${renderTransitionLine(t)}$$`);
+            const dur = stage.duration ? ` ($${expressionToLatex(stage.duration, opts)}$)` : '';
+            const lines = stage.transitions.map((t) => `$$${renderTransitionLine(t, opts)}$$`);
             parts.push(`before ${stage.stageName}${dur}:\n${lines.join('\n')}`);
         }
     }

package/dist/src/latex-export/generator/document-builder.js.map

@@ -1 +1 @@
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package/dist/src/latex-export/generator/latex-generator.d.ts

@@ -1,16 +1,19 @@
 import { ASTNode } from '../types';
+export interface RenderOptions {
+    useCdot: boolean;
+}
 /** Convert an expression string to LaTeX by parsing and rendering the AST.
  *  @param expr  expression string (RHS of a formula)
+ *  @param opts  render options (useCdot flag)
  *  @returns     LaTeX string
  */
-export declare function expressionToLatex(expr: string): string;
+export declare function expressionToLatex(expr: string, opts?: RenderOptions): string;
 /** Render an AST node to LaTeX.
- *  @param node       AST node to render
- *  @param _parentOp  parent operator (unused, reserved for context)
- *  @param _position  child position (unused, reserved for context)
- *  @returns          LaTeX string
+ *  @param node  AST node to render
+ *  @param opts  render options (useCdot flag)
+ *  @returns     LaTeX string
  */
-export declare function nodeToLatex(node: ASTNode, _parentOp?: string, _position?: 'left' | 'right'): string;
+export declare function nodeToLatex(node: ASTNode, opts?: RenderOptions): string;
 /** Convert a derivative LHS to LaTeX (e.g. "dy/dt" → "\frac{dy}{dt}").
  *  @param lhs  derivative string, e.g. "d(X)/dt" or "dX/dt"
  *  @returns    LaTeX string

package/dist/src/latex-export/generator/latex-generator.js

@@ -4,62 +4,66 @@ import { identifierToLatex } from '../transformer/identifier';
 import { functionToLatex } from '../transformer/functions';
 import { operatorToLatex } from '../transformer/operators';
 import { needsParentheses, wrapParens } from './bracket-manager';
+const DEFAULT_RENDER_OPTS = { useCdot: true };
+function mulSeparator(opts) {
+    return opts.useCdot ? ' \\cdot ' : ' \\, ';
+}
 /** Convert an expression string to LaTeX by parsing and rendering the AST.
  *  @param expr  expression string (RHS of a formula)
+ *  @param opts  render options (useCdot flag)
  *  @returns     LaTeX string
  */
-export function expressionToLatex(expr) {
+export function expressionToLatex(expr, opts = DEFAULT_RENDER_OPTS) {
     const ast = parseExpression(expr);
-    return nodeToLatex(ast);
+    return nodeToLatex(ast, opts);
 }
 /** Render an AST node to LaTeX.
- *  @param node       AST node to render
- *  @param _parentOp  parent operator (unused, reserved for context)
- *  @param _position  child position (unused, reserved for context)
- *  @returns          LaTeX string
+ *  @param node  AST node to render
+ *  @param opts  render options (useCdot flag)
+ *  @returns     LaTeX string
  */
-export function nodeToLatex(node, _parentOp, _position) {
+export function nodeToLatex(node, opts = DEFAULT_RENDER_OPTS) {
     switch (node.type) {
         case 'number':
             return numberToLatex(node.value);
         case 'identifier':
             return identifierToLatex(node.name);
         case 'unary': {
-            const operand = nodeToLatex(node.operand);
+            const operand = nodeToLatex(node.operand, opts);
             const needsWrap = node.operand.type === 'binary' || node.operand.type === 'ternary';
             return `${node.op}${needsWrap ? `\\left(${operand}\\right)` : operand}`;
         }
         case 'binary':
-            return renderBinary(node);
+            return renderBinary(node, opts);
         case 'call': {
-            const args = node.args.map((a) => nodeToLatex(a));
+            const args = node.args.map((a) => nodeToLatex(a, opts));
             return functionToLatex(node.name, args);
         }
         case 'ternary': {
-            const cond = nodeToLatex(node.condition);
-            const cons = nodeToLatex(node.consequent);
-            const alt = nodeToLatex(node.alternate);
+            const cond = nodeToLatex(node.condition, opts);
+            const cons = nodeToLatex(node.consequent, opts);
+            const alt = nodeToLatex(node.alternate, opts);
             return `\\begin{cases} ${cons}, & \\text{if } ${cond} \\\\ ${alt}, & \\text{otherwise} \\end{cases}`;
         }
     }
 }
-function renderBinary(node) {
+function renderBinary(node, opts) {
     const { op, left, right } = node;
     // Division → \frac; flatten into product of fractions when chain has multiple divisions
     if (op === '/') {
         const factors = flattenMulDivChain(node);
         const divisorCount = factors.filter((f) => f.isDivisor).length;
         if (divisorCount > 1)
-            return renderProductOfFractions(factors);
-        const l = nodeToLatex(left);
-        const r = nodeToLatex(right);
+            return renderProductOfFractions(factors, opts);
+        const l = nodeToLatex(left, opts);
+        const r = nodeToLatex(right, opts);
         return operatorToLatex('/', l, r);
     }
     // Exponentiation → base^{exp}
     if (op === '**') {
         const isCompound = left.type === 'binary' || left.type === 'unary' || left.type === 'ternary';
-        const l = nodeToLatex(left);
-        const r = nodeToLatex(right);
+        const l = nodeToLatex(left, opts);
+        const r = nodeToLatex(right, opts);
         return operatorToLatex('**', l, r, { baseIsCompound: isCompound });
     }
     // For *, +, -, comparisons: use precedence-based bracketing
@@ -67,10 +71,10 @@ function renderBinary(node) {
     const rightOp = getNodeOp(right);
     const leftNeedsParen = needsParentheses(leftOp, op, 'left');
     const rightNeedsParen = needsParentheses(rightOp, op, 'right');
-    const l = wrapParens(nodeToLatex(left), leftNeedsParen);
-    const r = wrapParens(nodeToLatex(right), rightNeedsParen);
+    const l = wrapParens(nodeToLatex(left, opts), leftNeedsParen);
+    const r = wrapParens(nodeToLatex(right, opts), rightNeedsParen);
     if (op === '*')
-        return operatorToLatex('*', l, r, { useCdot: true });
+        return operatorToLatex('*', l, r, { useCdot: opts.useCdot });
     return operatorToLatex(op, l, r);
 }
 function getNodeOp(node) {
@@ -96,23 +100,23 @@ function flattenMulDivChain(node) {
     collect(node);
     return factors;
 }
-/** Render a list of factors joined with \cdot, adding parens where needed. */
-function renderProductTerm(nodes) {
+/** Render a list of factors joined with the configured multiplication separator. */
+function renderProductTerm(nodes, opts) {
     if (nodes.length === 0)
         return '1';
     if (nodes.length === 1)
-        return nodeToLatex(nodes[0]);
+        return nodeToLatex(nodes[0], opts);
     return nodes.map((n) => {
-        const latex = nodeToLatex(n);
+        const latex = nodeToLatex(n, opts);
         if (n.type === 'binary' && (n.op === '+' || n.op === '-'))
             return `\\left(${latex}\\right)`;
         if (n.type === 'ternary')
             return `\\left(${latex}\\right)`;
         return latex;
-    }).join(' \\cdot ');
+    }).join(mulSeparator(opts));
 }
 /** Render factors as a product of fractions. */
-function renderProductOfFractions(factors) {
+function renderProductOfFractions(factors, opts) {
     const groups = [];
     let cur = { nums: [], dens: [] };
     for (const f of factors) {
@@ -129,13 +133,13 @@ function renderProductOfFractions(factors) {
     }
     groups.push(cur);
     const parts = groups.map((g) => {
-        const num = renderProductTerm(g.nums);
+        const num = renderProductTerm(g.nums, opts);
         if (g.dens.length === 0)
             return num;
-        const den = renderProductTerm(g.dens);
+        const den = renderProductTerm(g.dens, opts);
         return `\\frac{${num}}{${den}}`;
     });
-    return parts.join(' \\cdot ');
+    return parts.join(mulSeparator(opts));
 }
 /** Convert a derivative LHS to LaTeX (e.g. "dy/dt" → "\frac{dy}{dt}").
  *  @param lhs  derivative string, e.g. "d(X)/dt" or "dX/dt"

package/dist/src/latex-export/generator/latex-generator.js.map

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package/dist/src/pipeline/loops-pipeline-creator.js

@@ -1,5 +1,5 @@
 import { MATH_CONSTS, MATH_FUNCS, POW_IDX } from '../scripting-tools/scripting-tools';
-import { getOutputCode } from './output';
+import { getOutputCode, getStageOutputCode } from './output';
 import { PipelineCreator } from './pipeline-creator';
 import { argName2IdxMap, ARG, ARG_COL_IDX, CORRECTION_FACTOR, DEFAULT_CORRECTION, LOOP_MIN_COUNT } from './constants';
 /** Pipeline creator for cyclic model
@@ -191,10 +191,11 @@ export class CyclicModelPipelineCreator extends PipelineCreator {
         const preCode = preProcLines.join('\n');
         const postCode = postProcLines.join('\n');
         const wrappers = new Array(repetitions);
+        const stageOut = getStageOutputCode(this.ivp);
         for (let i = 0; i < repetitions; ++i) {
             wrappers[i] = {
                 preproc: preCode,
-                out: null,
+                out: stageOut,
                 postproc: postCode,
             };
         }

package/dist/src/pipeline/loops-pipeline-creator.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/output.d.ts

@@ -1,4 +1,8 @@
 import { IVP } from '../scripting-tools/scripting-tools';
+/** Return per-stage output code for cyclic/multistage models: recompute the output expressions
+    for this stage (using this stage's parameters), then APPEND them as columns to the stage
+    solution. Returns null when the model has no expressions in its outputs. */
+export declare function getStageOutputCode(ivp: IVP): string | null;
 /** Return a code for output extraction
  * @internal
  */

package/dist/src/pipeline/output.js

@@ -22,16 +22,28 @@ function getOutputNoExprs(ivp) {
     lines.push('return solution;');
     return lines.join('\n');
 } // getOutputNoExprs
-/** Return output for the model WITH expressions */
-function getOutputWithExprs(ivp) {
+/** Output-expression names, in #expressions order — the columns a stage appends. */
+function outputExprNames(ivp) {
+    const outputs = ivp.outputs;
+    const exprs = ivp.exprs;
+    if (outputs === null || exprs === null)
+        return [];
+    const names = [];
+    exprs.forEach((_, name) => {
+        if (outputs.has(name))
+            names.push(name);
+    });
+    return names;
+} // outputExprNames
+/** Lines that recompute the expressions row-by-row from the argument & solution columns of
+    arguments[0], reading parameters from the input vector arguments[1], and fill a Float64Array
+    <name>Raw for each output expression. Shared by the basic recompute and the per-stage code. */
+function getExprComputeLines(ivp) {
     const outputs = ivp.outputs;
-    if (outputs === null)
-        throw new Error('Grok Lib issue: no outputs in the initial value problem');
     const exprs = ivp.exprs;
-    if (!exprsInOutputs(ivp) || (exprs === null))
-        throw new Error('Grok Lib issue: expressions must be given');
     const argName = ivp.arg.name;
-    const lines = ['const solution = [];'];
+    const funcNames = ivp.deqs.solutionNames;
+    const lines = [];
     // Used math funcs
     ivp.usedMathFuncs.forEach((idx) => {
         if (idx !== POW_IDX)
@@ -44,37 +56,50 @@ function getOutputWithExprs(ivp) {
     // Model constants
     if (ivp.consts !== null)
         ivp.consts.forEach((input, name) => lines.push(`const ${name} = ${input.value};`));
-    // Model parameters
+    // Model parameters (per-stage input vector)
     if (ivp.params !== null) {
-        let idx = ARG_INP_COUNT + ivp.deqs.solutionNames.length;
+        let idx = ARG_INP_COUNT + funcNames.length;
         ivp.params.forEach((_, name) => {
             lines.push(`const ${name} = arguments[1][${idx}];`);
             ++idx;
         });
     }
     lines.push('');
-    lines.push('const length = arguments[0][0].length;');
-    const funcNames = ivp.deqs.solutionNames;
+    // __len / __i are underscore-prefixed so they cannot collide with a model constant or parameter
+    // (e.g. a model with a constant named `k` would otherwise be shadowed by the loop counter).
+    lines.push('const __len = arguments[0][0].length;');
     lines.push(`let ${argName} = 0;`);
     funcNames.forEach((name) => lines.push(`let ${name} = 0;`));
     lines.push('');
     exprs.forEach((_, name) => {
         lines.push(`let ${name} = 0;`);
         if (outputs.has(name))
-            lines.push(`let ${name}Raw = new Float64Array(length);`);
+            lines.push(`let ${name}Raw = new Float64Array(__len);`);
     });
     lines.push('');
-    lines.push('for (let k = 0; k < length; ++k) {');
-    lines.push(`  ${argName} = arguments[0][0][k];`);
-    funcNames.forEach((name, idx) => lines.push(`  ${name} = arguments[0][${SHIFT + idx}][k];`));
+    lines.push('for (let __i = 0; __i < __len; ++__i) {');
+    lines.push(`  ${argName} = arguments[0][0][__i];`);
+    funcNames.forEach((name, idx) => lines.push(`  ${name} = arguments[0][${SHIFT + idx}][__i];`));
     lines.push('');
     exprs.forEach((expr, name) => {
         lines.push(`  ${name} = ${expr};`);
         if (outputs.has(name))
-            lines.push(`  ${name}Raw[k] = ${name};`);
+            lines.push(`  ${name}Raw[__i] = ${name};`);
     });
     lines.push('}');
     lines.push('');
+    return lines;
+} // getExprComputeLines
+/** Return output for a basic (non-cyclic, non-multistage) model WITH expressions.
+    Recomputes the output expressions once, at top level, over the full solution. */
+function getOutputWithExprs(ivp) {
+    const outputs = ivp.outputs;
+    const exprs = ivp.exprs;
+    if (outputs === null || exprs === null || !exprsInOutputs(ivp))
+        throw new Error('Grok Lib issue: expressions must be given');
+    const argName = ivp.arg.name;
+    const lines = getExprComputeLines(ivp);
+    lines.push('const solution = [];');
     outputs.forEach((_, name) => {
         if (name === argName)
             lines.push('solution.push(arguments[0][0]);');
@@ -89,6 +114,44 @@ function getOutputWithExprs(ivp) {
     lines.push('return solution;');
     return lines.join('\n');
 } // getOutputWithExprs
+/** Return per-stage output code for cyclic/multistage models: recompute the output expressions
+    for this stage (using this stage's parameters), then APPEND them as columns to the stage
+    solution. Returns null when the model has no expressions in its outputs. */
+export function getStageOutputCode(ivp) {
+    if (!exprsInOutputs(ivp))
+        return null;
+    const lines = getExprComputeLines(ivp);
+    // Keep [arg, f0..fN] intact and append the output-expression columns after them.
+    lines.push('const solution = arguments[0];');
+    outputExprNames(ivp).forEach((name) => lines.push(`solution.push(${name}Raw);`));
+    lines.push('return solution;');
+    return lines.join('\n');
+} // getStageOutputCode
+/** Return top-level output code for cyclic/multistage models with output expressions: the stages
+    already appended the expression columns, so this only selects columns into #output order. */
+function getOutputSelectWithExprCols(ivp) {
+    const outputs = ivp.outputs;
+    const argName = ivp.arg.name;
+    const funcNames = ivp.deqs.solutionNames;
+    const exprNames = outputExprNames(ivp);
+    const lines = ['const solution = [];'];
+    outputs.forEach((_, name) => {
+        if (name === argName) {
+            lines.push('solution.push(arguments[0][0]);');
+            return;
+        }
+        const funcIdx = funcNames.indexOf(name);
+        if (funcIdx > -1) {
+            lines.push(`solution.push(arguments[0][${funcIdx + 1}]);`);
+            return;
+        }
+        const exprIdx = exprNames.indexOf(name);
+        if (exprIdx > -1)
+            lines.push(`solution.push(arguments[0][${1 + funcNames.length + exprIdx}]);`);
+    });
+    lines.push('return solution;');
+    return lines.join('\n');
+} // getOutputSelectWithExprCols
 /** Return a code for output extraction
  * @internal
  */
@@ -96,11 +159,13 @@ export function getOutputCode(ivp) {
     const outputs = ivp.outputs;
     if (outputs === null)
         return null;
-    checkApplicability(ivp);
-    if (exprsInOutputs(ivp))
-        return getOutputWithExprs(ivp);
-    else
+    if (!exprsInOutputs(ivp))
         return getOutputNoExprs(ivp);
+    // Cyclic (#loop) & multistage (#update) models compute expression columns per stage; the
+    // top level only selects them. Basic models recompute the expressions here.
+    if (ivp.loop !== null || ivp.updates !== null)
+        return getOutputSelectWithExprCols(ivp);
+    return getOutputWithExprs(ivp);
 } // getOutputCode
 /** Check whether outputs have items from expressions */
 function exprsInOutputs(ivp) {
@@ -114,24 +179,6 @@ function exprsInOutputs(ivp) {
     exprs.forEach((_, name) => flag ||= outputs.has(name));
     return flag;
 }
-/** Check applicability of model outputs */
-function checkApplicability(ivp) {
-    const outputs = ivp.outputs;
-    if (outputs === null)
-        throw new Error('Model has no outputs');
-    const exprs = ivp.exprs;
-    if (exprs === null)
-        return;
-    if (ivp.loop !== null) {
-        if (exprsInOutputs(ivp))
-            throw new Error('Non-supported model: expressions in output & loops');
-        return;
-    }
-    if (ivp.updates !== null) {
-        if (exprsInOutputs(ivp))
-            throw new Error('Non-supported model: expressions in output and updates');
-    }
-} // checkApplicability
 /** Return names of the model outputs
  * @param ivp - initial value problem
  * @returns an array of names of the model outputs

package/dist/src/pipeline/output.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/updates-pipeline-creator.js

@@ -1,6 +1,6 @@
 /* eslint-disable max-len */
 import { MATH_CONSTS, MATH_FUNCS, POW_IDX } from '../scripting-tools/scripting-tools';
-import { getOutputCode } from './output';
+import { getOutputCode, getStageOutputCode } from './output';
 import { PipelineCreator } from './pipeline-creator';
 import { argName2IdxMap, ARG, ARG_COL_IDX, CORRECTION_FACTOR, DEFAULT_CORRECTION } from './constants';
 /** Pipeline creator for model with updates
@@ -141,9 +141,10 @@ export class UpdatesModelPipelineCreator extends PipelineCreator {
     getPipeline(inputs) {
         if (this.ivp.updates === null)
             throw new Error('Incorrect use of UpdatesModelPipelineCreator: model has no updates');
+        const stageOut = getStageOutputCode(this.ivp);
         const wrappers = [{
                 preproc: null,
-                out: null,
+                out: stageOut,
                 postproc: null,
             }];
         this.ivp.updates.forEach((update) => {
@@ -200,7 +201,7 @@ export class UpdatesModelPipelineCreator extends PipelineCreator {
             lines.push('return inputs;');
             wrappers.push({
                 preproc: lines.join('\n'),
-                out: null,
+                out: stageOut,
                 postproc: null,
             });
         });

package/dist/src/pipeline/updates-pipeline-creator.js.map

@@ -1 +1 @@
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package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "license": "MIT",
-  "version": "1.3.0",
+  "version": "1.4.0",
   "description": "Tools for solving initial value problem for ordinary differential equations",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -45,7 +45,6 @@
   },
   "repository": {
     "type": "git",
-    "url": "git@github.com:datagrok-ai/DiffGrok.git",
-    "directory": ""
+    "url": "git+https://github.com/datagrok-ai/diff-grok.git"
   }
 }