diff-grok 1.1.0 → 1.3.0

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

@@ -0,0 +1 @@
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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 */

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

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

@@ -0,0 +1,12 @@
+import { IVP } from '../scripting-tools';
+import { Pipeline } from './pipeline';
+/** Creator of a pipeline for in-webworker computations */
+export declare abstract class PipelineCreator {
+    protected ivp: IVP;
+    protected outputNames: string[];
+    constructor(ivp: IVP);
+    /** Return computational pipeline corresponding to the given model input
+     * @param inputs - a vector of model inputs
+     */
+    abstract getPipeline(inputs: Float64Array): Pipeline;
+}

package/{src → dist/src}/pipeline/pipeline-creator.js

@@ -1,6 +1,8 @@
 import { getOutputNames } from './output';
 /** Creator of a pipeline for in-webworker computations */
 export class PipelineCreator {
+    ivp;
+    outputNames;
     constructor(ivp) {
         this.ivp = ivp;
         this.outputNames = getOutputNames(ivp);

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

@@ -0,0 +1 @@
+{"version":3,"file":"pipeline-creator.js","sourceRoot":"","sources":["../../../src/pipeline/pipeline-creator.ts"],"names":[],"mappings":"AAEA,OAAO,EAAC,cAAc,EAAC,MAAM,UAAU,CAAC;AAGxC,0DAA0D;AAC1D,MAAM,OAAgB,eAAe;IACzB,GAAG,CAAM;IACT,WAAW,CAAW;IAEhC,YAAY,GAAQ;QAClB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC;QACf,IAAI,CAAC,WAAW,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC;IACzC,CAAC;IAAA,CAAC;CAMH"}

package/{src/pipeline/pipeline.ts → dist/src/pipeline/pipeline.d.ts}

@@ -1,12 +1,6 @@
-/* eslint-disable max-len */
-import {IVP2WebWorker, solveIvp} from '../worker-tools';
-import {PipelineCreator} from './pipeline-creator';
-import {BasicModelPipelineCreator} from './basic-pipeline-creator';
-import {IVP} from '../scripting-tools';
-import {UpdatesModelPipelineCreator} from './updates-pipeline-creator';
-import {CyclicModelPipelineCreator} from './loops-pipeline-creator';
-
-
+import { IVP2WebWorker } from '../worker-tools';
+import { PipelineCreator } from './pipeline-creator';
+import { IVP } from '../scripting-tools';
 /**
  * Represents a wrapper for a single modeling step in a multi-stage simulation.
  *
@@ -15,11 +9,10 @@ import {CyclicModelPipelineCreator} from './loops-pipeline-creator';
  * @property out - A script that generates the output of the step.
  */
 export type Wrapper = {
-    preproc: string | null,
-    out: string | null,
-    postproc: string | null,
+    preproc: string | null;
+    out: string | null;
+    postproc: string | null;
 };
-
 /**
  * Represents a computational pipeline for multi-stage simulations.
  *
@@ -27,18 +20,9 @@ export type Wrapper = {
  * @property out - A script or specification that generates the final output of the pipeline.
  */
 export type Pipeline = {
-    wrappers: Wrapper[],
-    out: string | null,
+    wrappers: Wrapper[];
+    out: string | null;
 };
-
-/** Return concatenated arrays */
-function concat(arr1: Float64Array, arr2: Float64Array): Float64Array {
-  const result = new Float64Array(arr1.length + arr2.length);
-  result.set(arr1, 0);
-  result.set(arr2, arr1.length);
-  return result;
-}
-
 /** Apply pipeline to initial value problem with the source inputs, and return a solution
  * @param pipeline - computational pipeleine
  * @param ivp - initial value problem
@@ -136,70 +120,7 @@ function concat(arr1: Float64Array, arr2: Float64Array): Float64Array {
  *   console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
  * }
  */
-export function applyPipeline(pipeline: Pipeline, ivp: IVP2WebWorker, sourceInputs: Float64Array): Float64Array[] {
-  let solution: Float64Array[] = [];
-  let currentSolution: Float64Array[];
-  let func: Function;
-  let inputs = new Float64Array(sourceInputs);
-  const wrappers = pipeline.wrappers;
-  let step: Wrapper;
-  let isFirstSolverCall = true;
-
-  const stepsCount = wrappers.length;
-
-  if (stepsCount < 1)
-    throw new Error(`Incorrect solution pipeline: ${stepsCount} steps.`);
-
-  // Perform pipeline steps
-  for (let idx = 0; idx < stepsCount; ++idx) {
-    step = wrappers[idx];
-
-    // Pre-processing
-    if (step.preproc !== null) {
-      func = new Function(step.preproc);
-      inputs = func(solution, inputs);
-      //console.log('Pre');
-    }
-
-    //console.log(inputs);
-
-    // Solving a problem
-    currentSolution = solveIvp(ivp, inputs);
-
-    // Output from solution
-    if (step.out !== null) {
-      func = new Function(step.out);
-      currentSolution = func(currentSolution, inputs);
-    }
-
-    if (isFirstSolverCall) {
-      solution = currentSolution;
-      isFirstSolverCall = false;
-    } else
-      currentSolution.forEach((arr, kdx) => solution[kdx] = concat(solution[kdx], arr));
-
-    // Post-processing
-    if (step.postproc !== null) {
-      func = new Function(step.postproc);
-      inputs = func(solution, inputs);
-      //console.log('Pro');
-    }
-
-    //console.log(inputs);
-  }
-
-  // Compute final output
-  const out = pipeline.out;
-
-  if (out !== null) {
-    func = new Function(out);
-
-    return func(solution, sourceInputs);
-  }
-
-  return solution;
-} // performPipeline
-
+export declare function applyPipeline(pipeline: Pipeline, ivp: IVP2WebWorker, sourceInputs: Float64Array): Float64Array[];
 /** Return pipeline creator specified by the initial value problem
  * @param ivp - initial value problem
  * @returns a creator of computational pipeline corresponding to the given model
@@ -295,12 +216,4 @@ export function applyPipeline(pipeline: Pipeline, ivp: IVP2WebWorker, sourceInpu
  *   console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
  * }
  */
-export function getPipelineCreator(ivp: IVP): PipelineCreator {
-  if (ivp.updates !== null)
-    return new UpdatesModelPipelineCreator(ivp);
-
-  if (ivp.loop !== null)
-    return new CyclicModelPipelineCreator(ivp);
-
-  return new BasicModelPipelineCreator(ivp);
-}
+export declare function getPipelineCreator(ivp: IVP): PipelineCreator;

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