diff-grok 1.2.0 → 1.3.1

package/dist/src/latex-export/transformer/identifier.js

@@ -0,0 +1,194 @@
+/* Identifier-to-LaTeX transformer: converts identifier names to their LaTeX representations. */
+const SPECIAL = {
+    'PI': '\\pi',
+    'Inf': '\\infty',
+    'inf': '\\infty',
+};
+const GREEK_LOWER = [
+    ['varepsilon', '\\varepsilon'],
+    ['varsigma', '\\varsigma'],
+    ['vartheta', '\\vartheta'],
+    ['epsilon', '\\epsilon'],
+    ['omicron', 'o'],
+    ['upsilon', '\\upsilon'],
+    ['lambda', '\\lambda'],
+    ['varphi', '\\varphi'],
+    ['varrho', '\\varrho'],
+    ['alpha', '\\alpha'],
+    ['delta', '\\delta'],
+    ['gamma', '\\gamma'],
+    ['kappa', '\\kappa'],
+    ['omega', '\\omega'],
+    ['sigma', '\\sigma'],
+    ['theta', '\\theta'],
+    ['beta', '\\beta'],
+    ['iota', '\\iota'],
+    ['zeta', '\\zeta'],
+    ['chi', '\\chi'],
+    ['eta', '\\eta'],
+    ['phi', '\\phi'],
+    ['psi', '\\psi'],
+    ['rho', '\\rho'],
+    ['tau', '\\tau'],
+    ['mu', '\\mu'],
+    ['nu', '\\nu'],
+    ['pi', '\\pi'],
+    ['xi', '\\xi'],
+];
+const GREEK_UPPER = [
+    ['Epsilon', '\\mathrm{E}'],
+    ['Omicron', '\\mathrm{O}'],
+    ['Upsilon', '\\Upsilon'],
+    ['Lambda', '\\Lambda'],
+    ['Kappa', '\\mathrm{K}'],
+    ['Sigma', '\\Sigma'],
+    ['Theta', '\\Theta'],
+    ['Omega', '\\Omega'],
+    ['Alpha', '\\mathrm{A}'],
+    ['Delta', '\\Delta'],
+    ['Gamma', '\\Gamma'],
+    ['Beta', '\\mathrm{B}'],
+    ['Zeta', '\\mathrm{Z}'],
+    ['Iota', '\\mathrm{I}'],
+    ['Eta', '\\mathrm{H}'],
+    ['Chi', '\\mathrm{X}'],
+    ['Mu', '\\mathrm{M}'],
+    ['Nu', '\\mathrm{N}'],
+    ['Phi', '\\Phi'],
+    ['Psi', '\\Psi'],
+    ['Rho', '\\mathrm{P}'],
+    ['Tau', '\\mathrm{T}'],
+    ['Pi', '\\Pi'],
+    ['Xi', '\\Xi'],
+];
+// Combined, sorted by key length descending
+const ALL_GREEK = [...GREEK_LOWER, ...GREEK_UPPER]
+    .sort((a, b) => b[0].length - a[0].length);
+// Quick lookup for exact matches
+const GREEK_MAP = new Map(ALL_GREEK);
+/** Convert an identifier to its LaTeX representation.
+ *  @param name  identifier name (e.g. "alpha1", "CO2", "x")
+ *  @returns     LaTeX string
+ */
+export function identifierToLatex(name) {
+    // 1. Special constants
+    if (name in SPECIAL)
+        return SPECIAL[name];
+    // 2. Greek exact match
+    const greek = matchGreekExact(name);
+    if (greek !== undefined)
+        return greek;
+    // 3. Greek prefix + digit suffix
+    const greekPrefix = matchGreekPrefix(name);
+    if (greekPrefix !== undefined)
+        return `${greekPrefix.latex}_{${greekPrefix.suffix}}`;
+    // 4. Single letter (no digits)
+    if (name.length === 1)
+        return name;
+    // 5. Single letter + digits
+    if (name.length > 1 && isLetter(name[0]) && isAllDigits(name, 1))
+        return `${name[0]}_{${name.slice(1)}}`;
+    // 6. Chemical formula (all uppercase letters + digits, at least one digit)
+    const chem = matchChemicalFormula(name);
+    if (chem !== undefined)
+        return chem;
+    // 7. Multi-letter → \mathrm{name}
+    return `\\mathrm{${name}}`;
+}
+/** Check if an identifier is a known Greek letter (exact match).
+ *  @param name  identifier name
+ *  @returns     LaTeX command or undefined
+ */
+export function matchGreekExact(name) {
+    return GREEK_MAP.get(name);
+}
+/** Check if an identifier starts with a Greek letter name followed by digits only.
+ *  @param name  identifier name (e.g. "alpha1")
+ *  @returns     latex command and digit suffix, or undefined
+ */
+export function matchGreekPrefix(name) {
+    for (const [key, latex] of ALL_GREEK) {
+        if (name.length > key.length && name.startsWith(key)) {
+            const suffix = name.slice(key.length);
+            // Only match if suffix is all digits (not starting with a letter)
+            if (isAllDigits(suffix, 0))
+                return { latex, suffix };
+            // Suffix starts with a letter → not Greek
+            return undefined;
+        }
+    }
+    return undefined;
+}
+/** Detect and format chemical formula patterns like CO2, N2O5, SO4.
+ *  @param name  identifier name
+ *  @returns     LaTeX string or undefined if not a chemical formula
+ */
+export function matchChemicalFormula(name) {
+    // Chemical formula: all letters are uppercase, contains at least one digit
+    let hasDigit = false;
+    let hasMultipleLetters = false;
+    let letterCount = 0;
+    for (let i = 0; i < name.length; i++) {
+        const ch = name[i];
+        if (isDigit(ch))
+            hasDigit = true;
+        else if (isUpperCase(ch))
+            letterCount++;
+        else {
+            // lowercase letter or other char → not a chemical formula
+            return undefined;
+        }
+    }
+    hasMultipleLetters = letterCount >= 2;
+    if (!hasDigit || !hasMultipleLetters)
+        return undefined;
+    // Parse into segments: alternating letter groups and digit groups
+    const segments = [];
+    let i = 0;
+    while (i < name.length) {
+        let letters = '';
+        while (i < name.length && isUpperCase(name[i]))
+            letters += name[i++];
+        let digits = '';
+        while (i < name.length && isDigit(name[i]))
+            digits += name[i++];
+        if (letters || digits)
+            segments.push({ letters, digits });
+    }
+    // Count how many segments have digits
+    const segmentsWithDigits = segments.filter((s) => s.digits).length;
+    if (segmentsWithDigits <= 1) {
+        // Simple case: trailing digits only (CO2, HO2, MEO2, SO4)
+        const allLetters = segments.map((s) => s.letters).join('');
+        const trailingDigits = segments[segments.length - 1].digits;
+        if (trailingDigits)
+            return `\\mathrm{${allLetters}}_{${trailingDigits}}`;
+        return `\\mathrm{${allLetters}}`;
+    }
+    // Interleaved case: N2O5, C2O3
+    let inner = '';
+    for (const seg of segments) {
+        inner += seg.letters;
+        if (seg.digits)
+            inner += `_{${seg.digits}}`;
+    }
+    return `\\mathrm{${inner}}`;
+}
+function isLetter(ch) {
+    return (ch >= 'a' && ch <= 'z') || (ch >= 'A' && ch <= 'Z');
+}
+function isUpperCase(ch) {
+    return ch >= 'A' && ch <= 'Z';
+}
+function isDigit(ch) {
+    return ch >= '0' && ch <= '9';
+}
+function isAllDigits(str, from) {
+    if (from >= str.length)
+        return false;
+    for (let i = from; i < str.length; i++)
+        if (!isDigit(str[i]))
+            return false;
+    return true;
+}
+//# sourceMappingURL=identifier.js.map

package/dist/src/latex-export/transformer/identifier.js.map

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package/dist/src/latex-export/transformer/operators.d.ts

@@ -0,0 +1,9 @@
+import { OperatorContext } from '../types';
+/** Render a binary operator with its operands as LaTeX.
+ *  @param op       operator string (+, -, *, /, **, <, >, <=, >=, ==, !=)
+ *  @param left     already-rendered LaTeX for the left operand
+ *  @param right    already-rendered LaTeX for the right operand
+ *  @param context  optional context flags
+ *  @returns        LaTeX string
+ */
+export declare function operatorToLatex(op: string, left: string, right: string, context?: OperatorContext): string;

package/dist/src/latex-export/transformer/operators.js

@@ -0,0 +1,41 @@
+/* Operator-to-LaTeX transformer: renders binary and comparison operators as LaTeX. */
+/** Render a binary operator with its operands as LaTeX.
+ *  @param op       operator string (+, -, *, /, **, <, >, <=, >=, ==, !=)
+ *  @param left     already-rendered LaTeX for the left operand
+ *  @param right    already-rendered LaTeX for the right operand
+ *  @param context  optional context flags
+ *  @returns        LaTeX string
+ */
+export function operatorToLatex(op, left, right, context) {
+    switch (op) {
+        case '+':
+        case '-':
+            return `${left} ${op} ${right}`;
+        case '*':
+            if (context?.useCdot === false)
+                return `${left} \\, ${right}`;
+            return `${left} \\cdot ${right}`;
+        case '/':
+            if (context?.insideExponent)
+                return `${left} / ${right}`;
+            return `\\frac{${left}}{${right}}`;
+        case '**': {
+            const base = context?.baseIsCompound ? `\\left(${left}\\right)` : left;
+            return `${base}^{${right}}`;
+        }
+        case '>=':
+            return `${left} \\geq ${right}`;
+        case '<=':
+            return `${left} \\leq ${right}`;
+        case '!=':
+            return `${left} \\neq ${right}`;
+        case '==':
+            return `${left} = ${right}`;
+        case '<':
+        case '>':
+            return `${left} ${op} ${right}`;
+        default:
+            return `${left} ${op} ${right}`;
+    }
+}
+//# sourceMappingURL=operators.js.map

package/dist/src/latex-export/transformer/operators.js.map

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package/dist/src/latex-export/types.d.ts

@@ -0,0 +1,122 @@
+export type TokenType = 'NUMBER' | 'IDENTIFIER' | 'OPERATOR' | 'LPAREN' | 'RPAREN' | 'COMPARISON' | 'QUESTION' | 'COLON' | 'COMMA' | 'ARROW' | 'ASSIGN' | 'SEMICOLON';
+export interface Token {
+    type: TokenType;
+    value: string;
+    position: number;
+}
+export interface NumberNode {
+    type: 'number';
+    value: string;
+}
+export interface IdentifierNode {
+    type: 'identifier';
+    name: string;
+}
+export interface BinaryNode {
+    type: 'binary';
+    op: string;
+    left: ASTNode;
+    right: ASTNode;
+}
+export interface UnaryNode {
+    type: 'unary';
+    op: string;
+    operand: ASTNode;
+}
+export interface CallNode {
+    type: 'call';
+    name: string;
+    args: ASTNode[];
+}
+export interface TernaryNode {
+    type: 'ternary';
+    condition: ASTNode;
+    consequent: ASTNode;
+    alternate: ASTNode;
+}
+export type ASTNode = NumberNode | IdentifierNode | BinaryNode | UnaryNode | CallNode | TernaryNode;
+export interface FormulaLine {
+    /** Left-hand side: e.g. "dx/dt", "E1", "func1" */
+    lhs: string;
+    /** Right-hand side expression */
+    rhs: string;
+    /** True if LHS is a derivative: d(...)/dt or dX/dt */
+    isDerivative: boolean;
+    /** True if RHS contains => (arrow function) */
+    isArrowFunction: boolean;
+    /** Parameter names for arrow functions, e.g. ["p", "t"] */
+    arrowParams?: string[];
+}
+export interface AnnotatedLine {
+    name: string;
+    value: string;
+    units?: string;
+    caption?: string;
+    category?: string;
+    tooltip?: string;
+    min?: string;
+    max?: string;
+    step?: string;
+}
+export interface OutputLine {
+    name: string;
+    caption?: string;
+}
+export interface LoopBlock {
+    entries: AnnotatedLine[];
+}
+export interface UpdateBlock {
+    stageName: string;
+    entries: AnnotatedLine[];
+}
+export interface ParsedModel {
+    name?: string;
+    description?: string;
+    comment?: string;
+    equations: FormulaLine[];
+    expressions: FormulaLine[];
+    inits: AnnotatedLine[];
+    parameters: AnnotatedLine[];
+    constants: AnnotatedLine[];
+    argument: {
+        name: string;
+        stageName?: string;
+        entries: AnnotatedLine[];
+    };
+    loops: LoopBlock[];
+    updates: UpdateBlock[];
+    output: OutputLine[];
+    tolerance?: string;
+    solverMeta?: string;
+}
+export interface ConvertOptions {
+    /** Output format: 'latex' or 'markdown'. Default: 'latex' */
+    format: 'latex' | 'markdown';
+    /** Include metadata sections (name, description, comment). Default: true */
+    includeMetadata: boolean;
+    /** Include initial conditions table. Default: true */
+    includeInits: boolean;
+    /** Include parameters table. Default: true */
+    includeParameters: boolean;
+    /** Include constants table. Default: true */
+    includeConstants: boolean;
+    /** Use \cdot for multiplication. Default: true. If false, use juxtaposition. */
+    useCdot: boolean;
+    /** Compact mode: no section headings, inline initial conditions, text labels. Default: false */
+    compact: boolean;
+}
+export interface OperatorContext {
+    useCdot?: boolean;
+    baseIsCompound?: boolean;
+    insideExponent?: boolean;
+}
+export declare const ERROR_MSG: {
+    expectedToken: (type: string, value: string | undefined, tok?: {
+        type: string;
+        value: string;
+    }) => string;
+    unexpectedToken: (tok?: {
+        type: string;
+        value: string;
+    }) => string;
+};

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

@@ -0,0 +1,10 @@
+/* IVP-to-LaTeX converter — type definitions. */
+// Centralized error messages (cf. solver-defs.ts ERROR_MSG)
+function tokenStr(tok) {
+    return tok ? `${tok.type} '${tok.value}'` : 'EOF';
+}
+export const ERROR_MSG = {
+    expectedToken: (type, value, tok) => `Expected ${type}${value ? ` '${value}'` : ''}, got ${tokenStr(tok)}`,
+    unexpectedToken: (tok) => `Unexpected token: ${tokenStr(tok)}`,
+};
+//# sourceMappingURL=types.js.map

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

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package/{src/pipeline/basic-pipeline-creator.ts → dist/src/pipeline/basic-pipeline-creator.d.ts}

@@ -1,9 +1,6 @@
-/* eslint-disable max-len */
-import {IVP} from '../scripting-tools';
-import {getOutputCode} from './output';
-import {Pipeline} from './pipeline';
-import {PipelineCreator} from './pipeline-creator';
-
+import { IVP } from '../scripting-tools';
+import { Pipeline } from './pipeline';
+import { PipelineCreator } from './pipeline-creator';
 /** Pipeline creator for a model
  * @example
  *  // Here, we consider modeling queues: https://en.wikipedia.org/wiki/M/M/c_queue
@@ -96,25 +93,11 @@ import {PipelineCreator} from './pipeline-creator';
  * } catch (err) {
  *   console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
  * } */
-export class BasicModelPipelineCreator extends PipelineCreator {
-  /** @param ivp - initial value problem to be solved */
-  constructor(ivp: IVP) {
-    super(ivp);
-  }
-
-  /** Return a pipeline corresponding to the specified input vector
-   * @param inputs - a vector of the model inputs
-  */
-  public getPipeline(inputs: Float64Array): Pipeline {
-    return {
-      wrappers: [
-        {
-          preproc: null,
-          out: null,
-          postproc: null,
-        },
-      ],
-      out: getOutputCode(this.ivp),
-    };
-  }
-} // BasicModelPipelineCreator
+export declare class BasicModelPipelineCreator extends PipelineCreator {
+    /** @param ivp - initial value problem to be solved */
+    constructor(ivp: IVP);
+    /** Return a pipeline corresponding to the specified input vector
+     * @param inputs - a vector of the model inputs
+    */
+    getPipeline(inputs: Float64Array): Pipeline;
+}

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

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package/dist/src/pipeline/constants.d.ts

@@ -0,0 +1,14 @@
+export declare const ARG_INP_COUNT = 3;
+export declare const ARG_COL_IDX = 0;
+export declare const CORRECTION_FACTOR = 0.5;
+export declare const DEFAULT_CORRECTION = 1e-7;
+export declare const LOOP_PARAMS_CONT = 1;
+export declare const LOOP_MIN_COUNT = 1;
+/** Default argument names*/
+export declare enum ARG {
+    START = "_t0",
+    FINISH = "_t1",
+    STEP = "_h"
+}
+export declare const LOOP_COUNT_NAME = "_count";
+export declare const argName2IdxMap: Map<string, number>;

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

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package/dist/src/pipeline/index.d.ts

@@ -0,0 +1,7 @@
+export { Pipeline, Wrapper, applyPipeline, getPipelineCreator } from './pipeline';
+export { getOutputCode, getOutputNames } from './output';
+export { PipelineCreator } from './pipeline-creator';
+export { BasicModelPipelineCreator } from './basic-pipeline-creator';
+export { CyclicModelPipelineCreator } from './loops-pipeline-creator';
+export { UpdatesModelPipelineCreator } from './updates-pipeline-creator';
+export { getInputVector } from './input';

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

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package/dist/src/pipeline/input.d.ts

@@ -0,0 +1,3 @@
+import { IVP } from '../scripting-tools';
+/** Return inputs in a form of a vector */
+export declare function getInputVector(inputs: Record<string, number>, ivp: IVP): Float64Array;

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

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package/dist/src/pipeline/loops-pipeline-creator.d.ts

@@ -0,0 +1,124 @@
+import { IVP } from '../scripting-tools';
+import { Pipeline } from './pipeline';
+import { PipelineCreator } from './pipeline-creator';
+/** Pipeline creator for cyclic model
+ * @example
+ * // This example shows how to apply pipelines and cyclic models.
+ * // This approach can be used for in-webworkers analysis of models.
+ * // Here, we consider pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model.
+ * import * as DGL from 'diff-grok';
+ *
+ * // 1. Model specification
+ * const model = `#name: PK-PD
+ * #tags: model
+ * #description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
+ * #equations:
+ *   d(depot)/dt = -KA * depot
+ *   d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
+ *   d(peri)/dt  = Q * C2 - Q * C3
+ *   d(eff)/dt  = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
+ *
+ * #expressions:
+ *   C2 = centr / V2
+ *   C3 = peri / V3
+ *
+ * #loop:
+ *   _count = 10 {caption: count; category: Dosing; min: 1; max: 20} [Number of doses]
+ *   depot += dose
+ *
+ * #argument: t
+ *   _t0 = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1} [Begin of dosing interval]
+ *   _t1 = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15} [End of dosing interval]
+ *   _h = 1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1} [Time step of simulation]
+ *
+ * #inits:
+ *   depot = 0 {category: Initial values}
+ *   centr = 0 {category: Initial values} [Central]
+ *   peri = 0 {category: Initial values} [Peripheral]
+ *   eff = 0.2 {category: Initial values} [Effective compartment rate]
+ *
+ * #parameters:
+ *   dose = 1e4 {category: Dosing; min: 1e3; max: 2e4; step: 1e3} [Dosage]
+ *   KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
+ *   CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
+ *   V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10} [Central compartment volume]
+ *   Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1} [Intercompartmental rate]
+ *   V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40} [Peripheral compartment volume]
+ *   EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
+ *   Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5} [The first-order production constant]
+ *   Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5} [The first-order dissipation rate constant]
+ *
+ * #tolerance: 1e-9`;
+ *
+ * // 2. Generate IVP-objects: for the main thread & for computations in webworkers
+ * const ivp = DGL.getIVP(model);
+ * const ivpWW = DGL.getIvp2WebWorker(ivp);
+ *
+ * // 3. Perform computations
+ * try {
+ *   // 3.1) Extract names of outputs
+ *   const outputNames = DGL.getOutputNames(ivp);
+ *   const outSize = outputNames.length;
+ *
+ *   // 3.2) Set model inputs
+ *   const inputs = {
+ *     _count: 10,
+ *     _t0: 0,
+ *     _t1: 16,
+ *     _h: 1,
+ *     depot: 0,
+ *     centr: 0,
+ *     peri: 0,
+ *     eff: 0.2,
+ *     dose: 10000,
+ *     KA: 0.63,
+ *     CL: 3.2,
+ *     V2: 6.58,
+ *     Q: 0.622,
+ *     V3: 35.6,
+ *     EC50: 5.41,
+ *     Kin: 0.272,
+ *     Kout: 0.276,
+ *   };
+ *
+ *   const inputVector = DGL.getInputVector(inputs, ivp);
+ *
+ *   // 3.3) Create a pipeline
+ *   const creator = DGL.getPipelineCreator(ivp);
+ *   const pipeline = creator.getPipeline(inputVector);
+ *
+ *   // 3.4) Apply pipeline to perform computations
+ *   const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+ *
+ *   // 3.5) Print results
+ *
+ *   // 3.5.1) Table header
+ *   let line = '         ';
+ *   outputNames.forEach((name) => line += name + '           ');
+ *   console.log(line);
+ *
+ *   // 3.5.2) Table with solution
+ *   const length = solution[0].length;
+ *   for (let i = 0; i < length; ++i) {
+ *     line = '';
+ *
+ *     for (let j = 0; j < outSize; ++j)
+ *       line += solution[j][i].toFixed(8) + '     ';
+ *
+ *     console.log(line);
+ *   }
+ * } catch (err) {
+ *   console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+ * } */
+export declare class CyclicModelPipelineCreator extends PipelineCreator {
+    /**
+     * @param ivp - initial value problem to be solved
+     */
+    constructor(ivp: IVP);
+    /** Return computations pipeline corresponding to the given input vector
+     * @param inputs - input vector of the model
+     */
+    getPipeline(inputs: Float64Array): Pipeline;
+    /** Return code for correction of an argument */
+    private getArgumentCorrectionCode;
+}

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

@@ -0,0 +1 @@
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package/dist/src/pipeline/output.d.ts

@@ -0,0 +1,10 @@
+import { IVP } from '../scripting-tools/scripting-tools';
+/** Return a code for output extraction
+ * @internal
+ */
+export declare function getOutputCode(ivp: IVP): string | null;
+/** Return names of the model outputs
+ * @param ivp - initial value problem
+ * @returns an array of names of the model outputs
+ */
+export declare function getOutputNames(ivp: IVP): string[];

package/{src → dist/src}/pipeline/output.js

@@ -111,7 +111,7 @@ function exprsInOutputs(ivp) {
     if (exprs === null)
         return false;
     let flag = false;
-    exprs.forEach((_, name) => flag || (flag = outputs.has(name)));
+    exprs.forEach((_, name) => flag ||= outputs.has(name));
     return flag;
 }
 /** Check applicability of model outputs */