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pranabdaspranabdas
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merge main and resove conflicts
2 parents ace0e50 + 10f5879 commit b745db0

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+1450
-132
lines changed

‎.github/workflows/cicd.yml

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@@ -8,7 +8,7 @@ concurrency:
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jobs:
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run-py-linter:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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python-version: [3.10.13]
@@ -33,7 +33,7 @@ jobs:
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run-py-tests:
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needs: run-py-linter
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runs-on: ubuntu-20.04
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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python-version:

‎dist/js/ArrayWithIds.d.ts

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import { RoundingOptions, ValueWithId } from "./ValueWithId";
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export declare class ArrayWithIds<T> {
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values: T[];
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ids: number[];
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constructor(values?: T[], ids?: number[]);
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static fromValues<U, C extends ArrayWithIds<U>>(this: new (values: U[], ids: number[]) => C, values: U[]): C;
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static fromObjects<U, C extends ArrayWithIds<U>>(this: new (values: U[], ids: number[]) => C, objects: {
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id: number;
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value: U;
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}[]): C;
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toJSON(): object[];
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toValueWithIdArray(): ValueWithId<T>[];
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getElementValueById(id: number): T | undefined;
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getElementValueByIndex(index: number): T | undefined;
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getElementIdByIndex(index: number): number | undefined;
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getElementIdByValue(value: T): number | undefined;
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filterByValues(valuesToKeep: T | T[]): void;
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filterByIndices(indices: number | number[]): void;
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filterByIds(ids: number | number[], invert?: boolean): void;
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equals(other: ArrayWithIds<T>): boolean;
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mapArrayInPlace(func: (value: T) => T): void;
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addItem(value: T, id?: number): void;
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removeItem(index: number, id?: number): void;
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}
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export declare class RoundedArrayWithIds<T> extends ArrayWithIds<T> {
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readonly roundingOptions: RoundingOptions;
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constructor(values?: T[], ids?: number[], options?: RoundingOptions);
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toJSON(): object[];
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}

‎dist/js/ArrayWithIds.js

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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.RoundedArrayWithIds = exports.ArrayWithIds = void 0;
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const ValueWithId_1 = require("./ValueWithId");
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class ArrayWithIds {
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constructor(values = [], ids = []) {
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if (values.length !== ids.length) {
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throw new Error("Values and IDs must have the same length");
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}
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this.values = [...values];
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this.ids = [...ids];
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}
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static fromValues(values) {
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const ids = values.map((_, i) => i);
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return new this(values, ids);
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}
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static fromObjects(objects) {
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const values = objects.map((obj) => obj.value);
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const ids = objects.map((obj) => obj.id);
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return new this(values, ids);
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}
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toJSON() {
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return this.values.map((value, index) => ({
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id: this.ids[index],
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value: value !== null &&
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typeof value === "object" &&
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"toJSON" in value &&
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typeof value.toJSON === "function"
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? value.toJSON()
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: value,
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}));
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}
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toValueWithIdArray() {
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return this.values.map((value, index) => ValueWithId_1.ValueWithId.fromValueAndId(value, this.ids[index]));
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}
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getElementValueById(id) {
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const index = this.ids.indexOf(id);
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return index !== -1 ? this.values[index] : undefined;
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}
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getElementValueByIndex(index) {
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return this.values[index];
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}
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getElementIdByIndex(index) {
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return this.ids[index] || undefined;
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}
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getElementIdByValue(value) {
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const index = this.values.findIndex((v) => Array.isArray(v) && Array.isArray(value)
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? v.length === value.length && v.every((val, idx) => val === value[idx])
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: v === value);
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return index !== -1 ? this.ids[index] : undefined;
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}
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filterByValues(valuesToKeep) {
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const toHash = (v) => (Array.isArray(v) ? JSON.stringify(v) : String(v));
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const keepSet = new Set(Array.isArray(valuesToKeep) ? valuesToKeep.map(toHash) : [toHash(valuesToKeep)]);
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const filtered = this.values
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.map((value, i) => [value, this.ids[i]])
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.filter(([value]) => keepSet.has(toHash(value)));
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this.values = filtered.map(([v]) => v);
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this.ids = filtered.map(([_, id]) => id);
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}
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filterByIndices(indices) {
62+
const keepSet = new Set(Array.isArray(indices) ? indices : [indices]);
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this.values = this.values.filter((_, i) => keepSet.has(i));
64+
this.ids = this.ids.filter((_, i) => keepSet.has(i));
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}
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filterByIds(ids, invert = false) {
67+
const idSet = new Set(Array.isArray(ids) ? ids : [ids]);
68+
const keep = invert
69+
? this.ids.map((id, i) => (idSet.has(id) ? -1 : i)).filter((i) => i >= 0)
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: this.ids.map((id, i) => (idSet.has(id) ? i : -1)).filter((i) => i >= 0);
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this.values = keep.map((i) => this.values[i]);
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this.ids = keep.map((i) => this.ids[i]);
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}
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equals(other) {
75+
if (!(other instanceof ArrayWithIds))
76+
return false;
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if (this.values.length !== other.values.length)
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return false;
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if (this.ids.length !== other.ids.length)
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return false;
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return (this.values.every((v, i) => {
82+
const ov = other.values[i];
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return Array.isArray(v) && Array.isArray(ov)
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? v.length === ov.length && v.every((val, idx) => val === ov[idx])
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: v === ov;
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}) && this.ids.every((id, i) => id === other.ids[i]));
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}
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mapArrayInPlace(func) {
89+
this.values = this.values.map(func);
90+
}
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addItem(value, id) {
92+
const newId = id !== null && id !== void 0 ? id : Math.max(-1, ...this.ids) + 1;
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this.values.push(value);
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this.ids.push(newId);
95+
}
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removeItem(index, id) {
97+
if (id !== undefined) {
98+
index = this.ids.indexOf(id);
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if (index === -1)
100+
throw new Error("ID not found");
101+
}
102+
if (index < 0 || index >= this.values.length) {
103+
throw new Error("Index out of range");
104+
}
105+
this.values.splice(index, 1);
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this.ids.splice(index, 1);
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}
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}
109+
exports.ArrayWithIds = ArrayWithIds;
110+
class RoundedArrayWithIds extends ArrayWithIds {
111+
constructor(values = [], ids = [], options = ValueWithId_1.defaultRoundingOptions) {
112+
super(values, ids);
113+
this.roundingOptions = options;
114+
}
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toJSON() {
116+
return this.values.map((value, index) => new ValueWithId_1.RoundedValueWithId(this.ids[index], value, this.roundingOptions).toJSON());
117+
}
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}
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exports.RoundedArrayWithIds = RoundedArrayWithIds;

‎dist/js/ValueWithId.d.ts

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import { ObjectWithIdAndValueSchema } from "@mat3ra/esse/dist/js/types";
2+
import { RoundingMethodEnum } from "./math";
3+
interface ValueWithIdSchema<T> {
4+
id: ObjectWithIdAndValueSchema["id"];
5+
value: T | null;
6+
}
7+
export declare class ValueWithId<T> {
8+
id: number;
9+
value: T | null;
10+
static defaultConfig: {
11+
id: number;
12+
value: null;
13+
};
14+
static fromValueAndId<U, C extends ValueWithId<U>>(this: new (args: {
15+
id: number;
16+
value: U;
17+
}) => C, value: U, id?: number): C;
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constructor({ id, value }?: ValueWithIdSchema<T>);
19+
/**
20+
* Converts the instance to a plain JavaScript object.
21+
*/
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toJSON(): object;
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/**
24+
* Checks if this instance is equal to another ValueWithId.
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*/
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equals<U>(other: ValueWithId<U>): boolean;
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}
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export interface RoundingOptions {
29+
precision: number;
30+
roundingMethod: RoundingMethodEnum;
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}
32+
export declare const defaultRoundingOptions: RoundingOptions;
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export declare class RoundedValueWithId<T> extends ValueWithId<T> {
34+
readonly precision: number;
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readonly roundingMethod: RoundingMethodEnum;
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constructor(id: number, value: T, options?: RoundingOptions);
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toJSON(): object;
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}
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export {};

‎dist/js/ValueWithId.js

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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.RoundedValueWithId = exports.defaultRoundingOptions = exports.ValueWithId = void 0;
4+
const math_1 = require("./math");
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class ValueWithId {
6+
static fromValueAndId(value, id = 0) {
7+
return new this({ id, value });
8+
}
9+
constructor({ id, value } = ValueWithId.defaultConfig) {
10+
this.id = id;
11+
this.value = value;
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}
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/**
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* Converts the instance to a plain JavaScript object.
15+
*/
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toJSON() {
17+
if (this.value !== null &&
18+
typeof this.value === "object" &&
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"toJSON" in this.value &&
20+
typeof this.value.toJSON === "function") {
21+
return { id: this.id, value: this.value.toJSON() };
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}
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return { id: this.id, value: this.value };
24+
}
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/**
26+
* Checks if this instance is equal to another ValueWithId.
27+
*/
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equals(other) {
29+
if (!(other instanceof ValueWithId))
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return false;
31+
// because U may differ from T, we cast to unknown when comparing
32+
const v1 = this.value;
33+
const v2 = other.value;
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if (Array.isArray(v1) && Array.isArray(v2)) {
35+
if (v1.length !== v2.length)
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return false;
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for (let i = 0; i < v1.length; i++) {
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if (v1[i] !== v2[i])
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return false;
40+
}
41+
return this.id === other.id;
42+
}
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return this.id === other.id && v1 === v2;
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}
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}
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exports.ValueWithId = ValueWithId;
47+
ValueWithId.defaultConfig = {
48+
id: 0,
49+
value: null,
50+
};
51+
exports.defaultRoundingOptions = {
52+
precision: 9,
53+
roundingMethod: math_1.RoundingMethodEnum.HalfAwayFromZero,
54+
};
55+
class RoundedValueWithId extends ValueWithId {
56+
constructor(id, value, options = exports.defaultRoundingOptions) {
57+
super({ id, value });
58+
this.precision = options.precision;
59+
this.roundingMethod = options.roundingMethod;
60+
}
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toJSON() {
62+
return {
63+
id: this.id,
64+
value: math_1.math.roundArrayOrNumber(this.value, this.precision, this.roundingMethod),
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};
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}
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}
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exports.RoundedValueWithId = RoundedValueWithId;

‎dist/js/constants.d.ts

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@@ -1,30 +1,51 @@
1-
export namespace coefficients {
2-
let EV_TO_RY: number;
3-
let BOHR_TO_ANGSTROM: number;
4-
let ANGSTROM_TO_BOHR: number;
5-
let EV_A_TO_RY_BOHR: number;
6-
}
7-
export namespace tolerance {
8-
let length: number;
9-
let lengthAngstrom: number;
10-
let pointsDistance: number;
11-
}
12-
export namespace units {
13-
let bohr: string;
14-
let angstrom: string;
15-
let degree: string;
16-
let radian: string;
17-
let alat: string;
18-
}
19-
export namespace ATOMIC_COORD_UNITS {
20-
let crystal: string;
21-
let cartesian: string;
22-
}
23-
export const HASH_TOLERANCE: 3;
24-
declare namespace _default {
25-
export { coefficients };
26-
export { tolerance };
27-
export { units };
28-
export { ATOMIC_COORD_UNITS };
29-
}
1+
export declare const coefficients: {
2+
EV_TO_RY: number;
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BOHR_TO_ANGSTROM: number;
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ANGSTROM_TO_BOHR: number;
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EV_A_TO_RY_BOHR: number;
6+
};
7+
export declare const tolerance: {
8+
length: number;
9+
lengthAngstrom: number;
10+
pointsDistance: number;
11+
};
12+
export declare const units: {
13+
bohr: string;
14+
angstrom: string;
15+
degree: string;
16+
radian: string;
17+
alat: string;
18+
};
19+
/**
20+
* @summary Coordinates units for a material's basis.
21+
*/
22+
export declare const ATOMIC_COORD_UNITS: {
23+
crystal: string;
24+
cartesian: string;
25+
};
26+
export declare const HASH_TOLERANCE = 3;
27+
declare const _default: {
28+
coefficients: {
29+
EV_TO_RY: number;
30+
BOHR_TO_ANGSTROM: number;
31+
ANGSTROM_TO_BOHR: number;
32+
EV_A_TO_RY_BOHR: number;
33+
};
34+
tolerance: {
35+
length: number;
36+
lengthAngstrom: number;
37+
pointsDistance: number;
38+
};
39+
units: {
40+
bohr: string;
41+
angstrom: string;
42+
degree: string;
43+
radian: string;
44+
alat: string;
45+
};
46+
ATOMIC_COORD_UNITS: {
47+
crystal: string;
48+
cartesian: string;
49+
};
50+
};
3051
export default _default;

‎dist/js/index.d.ts

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1+
import { ArrayWithIds, RoundedArrayWithIds } from "./ArrayWithIds";
12
import * as context from "./context";
23
import * as entity from "./entity";
34
import * as utils from "./utils";
4-
export declare const Code: {
5+
import { RoundedValueWithId, ValueWithId } from "./ValueWithId";
6+
import { RoundedVector3D, Vector3D } from "./vector";
7+
export { ArrayWithIds, ValueWithId, RoundedValueWithId, RoundedArrayWithIds, RoundedVector3D, Vector3D, };
8+
export { entity, context, utils };
9+
declare const Code: {
10+
ArrayWithIds: typeof ArrayWithIds;
11+
ValueWithId: typeof ValueWithId;
12+
RoundedArrayWithIds: typeof RoundedArrayWithIds;
13+
RoundedValueWithId: typeof RoundedValueWithId;
14+
RoundedVector3D: typeof RoundedVector3D;
15+
Vector3D: typeof Vector3D;
516
entity: typeof entity;
617
context: typeof context;
718
utils: typeof utils;
819
};
20+
export type CodeType = typeof Code;
21+
export default Code;

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