@mat3ra/made 2024.3.23-2 → 2024.3.25-1

package/.husky/post-checkout

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting '.git/hooks/post-checkout'.\n"; exit 2; }
+git lfs post-checkout "$@"

package/.husky/post-commit

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting '.git/hooks/post-commit'.\n"; exit 2; }
+git lfs post-commit "$@"

package/.husky/post-merge

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting '.git/hooks/post-merge'.\n"; exit 2; }
+git lfs post-merge "$@"

package/.husky/pre-commit

@@ -0,0 +1,6 @@
+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+npx lint-staged
+npm run transpile
+git add dist

package/.husky/pre-push

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting '.git/hooks/pre-push'.\n"; exit 2; }
+git lfs pre-push "$@"

package/dist/basis/basis.d.ts

@@ -57,7 +57,7 @@ export declare class Basis {
     labels, }: BasisProps);
     static get unitsOptionsConfig(): typeof ATOMIC_COORD_UNITS;
     static get unitsOptionsDefaultValue(): string;
-    static get defaultCell(): [import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema];
+    static get defaultCell(): [import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema];
     /**
      * Serialize class instance to JSON.
      * @example As below:
@@ -178,7 +178,12 @@ export declare class Basis {
      * Returns a nested array with elements and their corresponding coordinates
      * @example Output: [ ["Si", [0,0,0]], ["Si", [0.5,0.5,0.5]] ]
      */
-    get elementsAndCoordinatesArray(): [string, Coordinate, string][];
+    get elementsAndCoordinatesArray(): [string, Coordinate][];
+    /**
+     * Returns a nested array with elements and their corresponding coordinates with labels
+     * @example Output: [ ["Si", [0,0,0], ['1']], ["Si", [0.5,0.5,0.5]] , ['2']]
+     */
+    get elementsAndCoordinatesAndLabelsArray(): [string, Coordinate, string][];
     /**
      * @summary Concatenates elements and sorts them in alphanumeric order.
      * E.g.,

package/dist/basis/basis.js

@@ -276,6 +276,16 @@ class Basis {
      * @example Output: [ ["Si", [0,0,0]], ["Si", [0.5,0.5,0.5]] ]
      */
     get elementsAndCoordinatesArray() {
+        return this._elements.array.map((element, idx) => {
+            const coordinates = this.getCoordinateByIndex(idx);
+            return [element, coordinates];
+        });
+    }
+    /**
+     * Returns a nested array with elements and their corresponding coordinates with labels
+     * @example Output: [ ["Si", [0,0,0], ['1']], ["Si", [0.5,0.5,0.5]] , ['2']]
+     */
+    get elementsAndCoordinatesAndLabelsArray() {
         return this._elements.array.map((element, idx) => {
             const coordinates = this.getCoordinateByIndex(idx);
             const atomicLabel = this.atomicLabelsArray[idx];
@@ -297,7 +307,7 @@ class Basis {
         // make a copy to prevent modifying class values
         const clsInstance = new Basis(this.toJSON());
         clsInstance.toStandardRepresentation();
-        const standardRep = clsInstance.elementsAndCoordinatesArray.map((entry) => {
+        const standardRep = clsInstance.elementsAndCoordinatesAndLabelsArray.map((entry) => {
             const element = entry[0];
             const coordinate = entry[1];
             const atomicLabel = entry[2];
@@ -342,7 +352,7 @@ class Basis {
      * E.g., ``` ['Si 0 0 0', 'Li 0.5 0.5 0.5']```
      */
     get atomicPositions() {
-        return this.elementsAndCoordinatesArray.map((entry, idx) => {
+        return this.elementsAndCoordinatesAndLabelsArray.map((entry, idx) => {
             const element = entry[0];
             const coordinate = entry[1];
             const atomicLabel = this.atomicLabelsArray[idx];

package/dist/cell/cell.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Cell = void 0;
-const math_1 = require("@exabyte-io/code.js/dist/math");
+const math_1 = require("@mat3ra/code/dist/js/math");
 const constants_1 = __importDefault(require("../constants"));
 const MATRIX = math_1.math.matrix;
 const MULT = math_1.math.multiply;

package/dist/cell/conventional_cell.d.ts

@@ -1,4 +1,4 @@
-import { LatticeTypeSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeTypeSchema } from "@mat3ra/esse/dist/js/types";
 export declare const PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS: {
     CUB: number[][];
     FCC: number[][];

package/dist/cell/primitive_cell.d.ts

@@ -1,4 +1,4 @@
-import { LatticeImplicitSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeImplicitSchema } from "@mat3ra/esse/dist/js/types";
 import { VectorsAsArray } from "../lattice/types";
 /**
  * Returns lattice vectors for a primitive cell for a lattice.

package/dist/constants.d.ts

@@ -1,2 +1,2 @@
-export * from "@exabyte-io/code.js/dist/constants";
-export { default } from "@exabyte-io/code.js/dist/constants";
+export * from "@mat3ra/code/dist/js/constants";
+export { default } from "@mat3ra/code/dist/js/constants";

package/dist/constants.js

@@ -19,7 +19,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
 // TODO: adjust the imports and remove the need for re-exporting
-__exportStar(require("@exabyte-io/code.js/dist/constants"), exports);
+__exportStar(require("@mat3ra/code/dist/js/constants"), exports);
 // eslint-disable-next-line no-restricted-exports
-var constants_1 = require("@exabyte-io/code.js/dist/constants");
+var constants_1 = require("@mat3ra/code/dist/js/constants");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(constants_1).default; } });

package/dist/lattice/lattice.d.ts

@@ -1,4 +1,4 @@
-import { LatticeImplicitSchema, LatticeSchema, LatticeTypeExtendedSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeImplicitSchema, LatticeSchema, LatticeTypeExtendedSchema } from "@mat3ra/esse/dist/js/types";
 import { Cell } from "../cell/cell";
 import { FromVectorsProps, LatticeBravais } from "./lattice_bravais";
 import { BravaisConfigProps, LatticeVectors } from "./lattice_vectors";
@@ -61,7 +61,7 @@ export declare class Lattice extends LatticeBravais implements LatticeSchema {
     /**
      * Get lattice vectors as a nested array
      */
-    get vectorArrays(): [import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema];
+    get vectorArrays(): [import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema];
     get Cell(): Cell;
     /**
      * Get a short label for the type of the lattice, eg. "MCLC".

package/dist/lattice/lattice_bravais.d.ts

@@ -1,4 +1,4 @@
-import { LatticeImplicitSchema, LatticeTypeSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeImplicitSchema, LatticeTypeSchema } from "@mat3ra/esse/dist/js/types";
 import { Vector, VectorsAsArray } from "./types";
 export type Units = Required<LatticeImplicitSchema>["units"];
 export interface FromVectorsProps {

package/dist/lattice/lattice_vectors.d.ts

@@ -1,4 +1,4 @@
-import { LatticeExplicitUnit, LatticeImplicitSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeExplicitUnit, LatticeImplicitSchema } from "@mat3ra/esse/dist/js/types";
 import { Vector } from "./types";
 type RequiredLatticeExplicitUnit = Required<LatticeExplicitUnit>;
 export interface BravaisConfigProps extends Partial<LatticeImplicitSchema> {

package/dist/lattice/reciprocal/lattice_reciprocal.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ReciprocalLattice = void 0;
-const constants_1 = require("@exabyte-io/code.js/dist/constants");
+const constants_1 = require("@mat3ra/code/dist/js/constants");
 const array_almost_equal_1 = __importDefault(require("array-almost-equal"));
 const lodash_1 = __importDefault(require("lodash"));
 const math_1 = __importDefault(require("../../math"));

package/dist/lattice/types.d.ts

@@ -1,4 +1,4 @@
-import { ArrayOf3NumberElementsSchema, LatticeTypeSchema } from "@mat3ra/esse/lib/js/types";
+import { ArrayOf3NumberElementsSchema, LatticeTypeSchema } from "@mat3ra/esse/dist/js/types";
 export declare const DEFAULT_LATTICE_UNITS: {
     length: {
         angstrom: string;

package/dist/made.d.ts

@@ -20,10 +20,10 @@ export namespace Made {
         export { ArrayWithIds };
     }
 }
-import { coefficients } from "@exabyte-io/code.js/dist/constants";
-import { tolerance } from "@exabyte-io/code.js/dist/constants";
-import { units } from "@exabyte-io/code.js/dist/constants";
-import { ATOMIC_COORD_UNITS } from "@exabyte-io/code.js/dist/constants";
+import { coefficients } from "@mat3ra/code/dist/js/constants";
+import { tolerance } from "@mat3ra/code/dist/js/constants";
+import { units } from "@mat3ra/code/dist/js/constants";
+import { ATOMIC_COORD_UNITS } from "@mat3ra/code/dist/js/constants";
 import MadeMath from "./math";
 import { Material } from "./material";
 import { MaterialMixin } from "./material";

package/dist/material.d.ts

@@ -1,6 +1,6 @@
-import { HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity";
-import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory";
-import { ConsistencyCheck, DerivedPropertiesSchema, FileSourceSchema, MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity } from "@mat3ra/code/dist/js/entity";
+import { AnyObject } from "@mat3ra/code/dist/js/entity/in_memory";
+import { ConsistencyCheck, DerivedPropertiesSchema, FileSourceSchema, MaterialSchema } from "@mat3ra/esse/dist/js/types";
 import { ConstrainedBasis } from "./basis/constrained_basis";
 import { Constraint } from "./constraints/constraints";
 import { Lattice } from "./lattice/lattice";
@@ -194,6 +194,7 @@ export declare function MaterialMixin<T extends MaterialBaseEntityConstructor =
         };
         setProp: ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void);
         unsetProp: ((name: string) => void) & ((name: string) => void) & ((name: string) => void) & ((name: string) => void) & ((name: string) => void);
+        setProps: ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any);
         toJSONSafe: ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject);
         toJSONQuick: ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject);
         clone: ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any);
@@ -205,8 +206,8 @@ export declare function MaterialMixin<T extends MaterialBaseEntityConstructor =
         getClsName: (() => string) & (() => string) & (() => string) & (() => string) & (() => string);
         readonly slug: string;
         readonly isSystemEntity: boolean;
-        getAsEntityReference: ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema);
-        getEntityByName: ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity);
+        getAsEntityReference: ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema);
+        getEntityByName: ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity);
         metadata: object;
         updateMetadata(object: object): void;
         name: string;
@@ -397,6 +398,7 @@ export declare const Material: {
         };
         setProp: ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void) & ((name: string, value: unknown) => void);
         unsetProp: ((name: string) => void) & ((name: string) => void) & ((name: string) => void) & ((name: string) => void) & ((name: string) => void);
+        setProps: ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any) & ((json?: AnyObject | undefined) => any);
         toJSONSafe: ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject);
         toJSONQuick: ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject) & ((exclude?: string[] | undefined) => AnyObject);
         clone: ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any) & ((extraContext?: object | undefined) => any);
@@ -408,8 +410,8 @@ export declare const Material: {
         getClsName: (() => string) & (() => string) & (() => string) & (() => string) & (() => string);
         readonly slug: string;
         readonly isSystemEntity: boolean;
-        getAsEntityReference: ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/lib/js/types").EntityReferenceSchema);
-        getEntityByName: ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity) & ((entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string) => import("@exabyte-io/code.js/dist/entity").InMemoryEntity);
+        getAsEntityReference: ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema) & ((byIdOnly?: boolean | undefined) => import("@mat3ra/esse/dist/js/types").EntityReferenceSchema);
+        getEntityByName: ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity) & ((entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string) => import("@mat3ra/code/dist/js/entity").InMemoryEntity);
         metadata: object;
         updateMetadata(object: object): void;
         name: string;
@@ -447,14 +449,11 @@ export declare const Material: {
     consistencyChecks: object[];
     addConsistencyChecks(array: object[]): void;
     _json: AnyObject;
-    prop<T = undefined>(name: string, defaultValue: T): T; /**
-     * Converts basis to crystal/fractional coordinates.
-     */
-    prop<T_1 = undefined>(name: string): T_1 | undefined; /**
-     * Converts basis to crystal/fractional coordinates.
-     */
+    prop<T = undefined>(name: string, defaultValue: T): T;
+    prop<T_1 = undefined>(name: string): T_1 | undefined;
     setProp(name: string, value: unknown): void;
     unsetProp(name: string): void;
+    setProps(json?: AnyObject | undefined): any;
     toJSON(exclude?: string[] | undefined): AnyObject;
     toJSONSafe(exclude?: string[] | undefined): AnyObject;
     toJSONQuick(exclude?: string[] | undefined): AnyObject;
@@ -467,8 +466,8 @@ export declare const Material: {
     getClsName(): string;
     readonly slug: string;
     readonly isSystemEntity: boolean;
-    getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/lib/js/types").EntityReferenceSchema;
-    getEntityByName(entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string): import("@exabyte-io/code.js/dist/entity").InMemoryEntity;
+    getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/dist/js/types").EntityReferenceSchema;
+    getEntityByName(entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string): import("@mat3ra/code/dist/js/entity").InMemoryEntity;
 }) & (new (...args: any[]) => {
     metadata: object;
     updateMetadata(object: object): void;
@@ -477,9 +476,10 @@ export declare const Material: {
     prop<T_1_1 = undefined>(name: string): T_1_1 | undefined;
     setProp(name: string, value: unknown): void;
     unsetProp(name: string): void;
-    toJSON(exclude?: string[] | undefined): AnyObject; /**
-     * Returns material in POSCAR format. Pass `true` to ignore original poscar source and re-serialize.
+    setProps(json?: AnyObject | undefined): any; /**
+     * Returns a copy of the material with conventional cell constructed instead of primitive.
      */
+    toJSON(exclude?: string[] | undefined): AnyObject;
     toJSONSafe(exclude?: string[] | undefined): AnyObject;
     toJSONQuick(exclude?: string[] | undefined): AnyObject;
     clone(extraContext?: object | undefined): any;
@@ -491,8 +491,8 @@ export declare const Material: {
     getClsName(): string;
     readonly slug: string;
     readonly isSystemEntity: boolean;
-    getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/lib/js/types").EntityReferenceSchema;
-    getEntityByName(entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string): import("@exabyte-io/code.js/dist/entity").InMemoryEntity;
+    getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/dist/js/types").EntityReferenceSchema;
+    getEntityByName(entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string): import("@mat3ra/code/dist/js/entity").InMemoryEntity;
 }) & (new (...args: any[]) => {
     name: string;
     setName(name: string): void;
@@ -501,23 +501,21 @@ export declare const Material: {
     prop<T_1_2 = undefined>(name: string): T_1_2 | undefined;
     setProp(name: string, value: unknown): void;
     unsetProp(name: string): void;
+    setProps(json?: AnyObject | undefined): any;
     toJSON(exclude?: string[] | undefined): AnyObject;
     toJSONSafe(exclude?: string[] | undefined): AnyObject;
     toJSONQuick(exclude?: string[] | undefined): AnyObject;
     clone(extraContext?: object | undefined): any;
     validate(): void;
     clean(config: AnyObject): AnyObject;
-    isValid(): boolean; /**
-     * @summary a series of checks for the material and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
+    isValid(): boolean;
     id: string;
     readonly cls: string;
     getClsName(): string;
     readonly slug: string;
     readonly isSystemEntity: boolean;
-    getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/lib/js/types").EntityReferenceSchema;
-    getEntityByName(entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string): import("@exabyte-io/code.js/dist/entity").InMemoryEntity;
+    getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/dist/js/types").EntityReferenceSchema;
+    getEntityByName(entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string): import("@mat3ra/code/dist/js/entity").InMemoryEntity;
 }) & {
     new (...args: any[]): {
         readonly isDefault: boolean;
@@ -526,6 +524,7 @@ export declare const Material: {
         prop<T_1_3 = undefined>(name: string): T_1_3 | undefined;
         setProp(name: string, value: unknown): void;
         unsetProp(name: string): void;
+        setProps(json?: AnyObject | undefined): any;
         toJSON(exclude?: string[] | undefined): AnyObject;
         toJSONSafe(exclude?: string[] | undefined): AnyObject;
         toJSONQuick(exclude?: string[] | undefined): AnyObject;
@@ -538,11 +537,11 @@ export declare const Material: {
         getClsName(): string;
         readonly slug: string;
         readonly isSystemEntity: boolean;
-        getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/lib/js/types").EntityReferenceSchema;
-        getEntityByName(entities: import("@exabyte-io/code.js/dist/entity").InMemoryEntity[], entity: string, name: string): import("@exabyte-io/code.js/dist/entity").InMemoryEntity;
+        getAsEntityReference(byIdOnly?: boolean | undefined): import("@mat3ra/esse/dist/js/types").EntityReferenceSchema;
+        getEntityByName(entities: import("@mat3ra/code/dist/js/entity").InMemoryEntity[], entity: string, name: string): import("@mat3ra/code/dist/js/entity").InMemoryEntity;
     };
     readonly defaultConfig: object | null;
     createDefault(): any;
-} & typeof import("@exabyte-io/code.js/dist/entity").InMemoryEntity;
+} & typeof import("@mat3ra/code/dist/js/entity").InMemoryEntity;
 export type Material = InstanceType<typeof Material>;
 export {};

package/dist/material.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Material = exports.MaterialMixin = exports.defaultMaterialConfig = void 0;
-const entity_1 = require("@exabyte-io/code.js/dist/entity");
+const entity_1 = require("@mat3ra/code/dist/js/entity");
 const crypto_js_1 = __importDefault(require("crypto-js"));
 const constrained_basis_1 = require("./basis/constrained_basis");
 const conventional_cell_1 = require("./cell/conventional_cell");

package/dist/math.d.ts

@@ -17,7 +17,7 @@ declare const _default: {
     combinationsFromIntervals: (arrA: number[], arrB: number[], arrC: number[]) => number[][];
     calculateSegmentsBetweenPoints3D: (point1: (string | number)[], point2: (string | number)[], n: string | number) => number[][];
     roundValueToNDecimals: (value: number, decimals?: number | undefined) => number;
-    numberToPrecision: typeof import("@exabyte-io/code.js/dist/math").numberToPrecision;
+    numberToPrecision: typeof import("@mat3ra/code/dist/js/math").numberToPrecision;
     e: number;
     pi: number;
     i: number;

package/dist/math.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 // TODO: adjust the imports and remove the need for re-exporting
-const math_1 = require("@exabyte-io/code.js/dist/math");
+const math_1 = require("@mat3ra/code/dist/js/math");
 exports.default = {
     ...math_1.math,
 };

package/dist/parsers/espresso.d.ts

@@ -1,4 +1,4 @@
-import { MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
 /**
  * Construct textual representation of a materialOrConfig according to Quantum ESPRESSO pw.x input format.
  * @param materialOrConfig - material class instance or its config object

package/dist/parsers/xyz.d.ts

@@ -1,4 +1,4 @@
-import { MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { Constraint } from "../constraints/constraints";
 import { Vector } from "../lattice/types";
@@ -36,7 +36,7 @@ export interface BasisConfig {
  * @param units Coordinate units
  * @param cell Basis Cell
  */
-declare function toBasisConfig(txt: string, units?: string, cell?: [import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema]): BasisConfig;
+declare function toBasisConfig(txt: string, units?: string, cell?: [import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema]): BasisConfig;
 /**
  * Create XYZ from Basis class instance.
  * @param basisClsInstance Basis class instance.

package/dist/parsers/xyz_combinatorial_basis.d.ts

@@ -3,11 +3,11 @@ export class WrongBasisFormat extends Error {
     xyz: any;
 }
 export class CombinatorialBasis {
-    static toBasisConfig(array: any, units?: string, cell?: [import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema]): {
+    static toBasisConfig(array: any, units?: string, cell?: [import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema]): {
         elements: any[];
         coordinates: any[];
         units: string;
-        cell: [import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/lib/js/types").ArrayOf3NumberElementsSchema];
+        cell: [import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema, import("@mat3ra/esse/dist/js/types").ArrayOf3NumberElementsSchema];
     };
     /**
      * Creates Combinatorial basis

package/dist/tools/supercell.d.ts

@@ -13,7 +13,7 @@ declare function generateNewBasisWithinSupercell(basis: Basis, cell: Cell, super
 declare function generateConfig(material: Material, supercellMatrix: number[][]): {
     name: string;
     basis: import("../basis/basis").BasisSchema;
-    lattice: import("@mat3ra/esse/lib/js/types").LatticeImplicitSchema;
+    lattice: import("@mat3ra/esse/dist/js/types").LatticeImplicitSchema;
 };
 declare const _default: {
     generateConfig: typeof generateConfig;

package/dist/tools/surface.d.ts

@@ -5,6 +5,6 @@ export default _default;
 declare function generateConfig(material: any, millerIndices: any, numberOfLayers?: number, vx?: number, vy?: number): {
     name: string;
     basis: import("../basis/basis").BasisSchema;
-    lattice: import("@mat3ra/esse/lib/js/types").LatticeImplicitSchema;
+    lattice: import("@mat3ra/esse/dist/js/types").LatticeImplicitSchema;
     outOfPlaneAxisIndex: any;
 };

package/dist/types.d.ts

@@ -1,3 +1,3 @@
-import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory";
-import { MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { AnyObject } from "@mat3ra/code/dist/js/entity/in_memory";
+import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
 export type MaterialJSON = MaterialSchema & AnyObject;

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/made",
-    "version": "2024.3.23-2",
+    "version": "2024.3.25-1",
     "description": "MAterials DEsign library",
     "scripts": {
         "lint": "eslint --cache src/js tests/js && prettier --write src/js tests/js",
@@ -32,9 +32,9 @@
         "@babel/preset-react": "^7.16.7",
         "@babel/register": "^7.22.15",
         "@babel/runtime-corejs3": "^7.16.8",
-        "@exabyte-io/code.js": "2024.2.29-0",
         "@exabyte-io/eslint-config": "^2023.8.29-1",
-        "@mat3ra/esse": "2024.3.20-0",
+        "@mat3ra/code": "2024.3.25-3",
+        "@mat3ra/esse": "2024.3.25-6",
         "@mat3ra/tsconfig": "^2024.3.21-5",
         "@types/crypto-js": "^4.2.2",
         "@types/mathjs": "^3.21.1",
@@ -73,12 +73,13 @@
         "crypto-js": "4.2.0",
         "lodash": "^4.17.*",
         "mathjs": "12.4.1",
+        "ts-node": "^10.9.1",
         "typescript": "^4.5.5",
         "underscore": "^1.8.3",
         "underscore.string": "^3.3.4"
     },
     "peerDependencies": {
-        "@exabyte-io/code.js": "*",
+        "@mat3ra/code": "*",
         "@mat3ra/esse": "*"
     },
     "lint-staged": {

package/src/js/basis/basis.ts

@@ -362,7 +362,18 @@ export class Basis {
      * Returns a nested array with elements and their corresponding coordinates
      * @example Output: [ ["Si", [0,0,0]], ["Si", [0.5,0.5,0.5]] ]
      */
-    get elementsAndCoordinatesArray(): [string, Coordinate, string][] {
+    get elementsAndCoordinatesArray(): [string, Coordinate][] {
+        return this._elements.array.map((element, idx) => {
+            const coordinates = this.getCoordinateByIndex(idx);
+            return [element, coordinates];
+        });
+    }
+
+    /**
+     * Returns a nested array with elements and their corresponding coordinates with labels
+     * @example Output: [ ["Si", [0,0,0], ['1']], ["Si", [0.5,0.5,0.5]] , ['2']]
+     */
+    get elementsAndCoordinatesAndLabelsArray(): [string, Coordinate, string][] {
         return this._elements.array.map((element, idx) => {
             const coordinates = this.getCoordinateByIndex(idx);
             const atomicLabel = this.atomicLabelsArray[idx];
@@ -385,7 +396,7 @@ export class Basis {
         // make a copy to prevent modifying class values
         const clsInstance = new Basis(this.toJSON());
         clsInstance.toStandardRepresentation();
-        const standardRep = clsInstance.elementsAndCoordinatesArray.map((entry) => {
+        const standardRep = clsInstance.elementsAndCoordinatesAndLabelsArray.map((entry) => {
             const element = entry[0];
             const coordinate = entry[1];
             const atomicLabel = entry[2];
@@ -435,7 +446,7 @@ export class Basis {
      * E.g., ``` ['Si 0 0 0', 'Li 0.5 0.5 0.5']```
      */
     get atomicPositions(): string[] {
-        return this.elementsAndCoordinatesArray.map((entry, idx) => {
+        return this.elementsAndCoordinatesAndLabelsArray.map((entry, idx) => {
             const element = entry[0];
             const coordinate = entry[1];
             const atomicLabel = this.atomicLabelsArray[idx];

package/src/js/cell/cell.ts

@@ -1,4 +1,4 @@
-import { math } from "@exabyte-io/code.js/dist/math";
+import { math } from "@mat3ra/code/dist/js/math";
 
 import { Coordinate } from "../basis/types";
 import constants from "../constants";

package/src/js/cell/conventional_cell.ts

@@ -1,4 +1,4 @@
-import { LatticeTypeSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeTypeSchema } from "@mat3ra/esse/dist/js/types";
 
 /**
  * Routines for calculating conventional cell vectors from primitive cell Bravais parameters.

package/src/js/cell/primitive_cell.ts

@@ -1,5 +1,5 @@
 /* eslint no-unused-vars: 0 */
-import { LatticeImplicitSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeImplicitSchema } from "@mat3ra/esse/dist/js/types";
 
 import { VectorsAsArray } from "../lattice/types";
 import math from "../math";

package/src/js/constants.js

@@ -1,4 +1,4 @@
 // TODO: adjust the imports and remove the need for re-exporting
-export * from "@exabyte-io/code.js/dist/constants";
+export * from "@mat3ra/code/dist/js/constants";
 // eslint-disable-next-line no-restricted-exports
-export { default } from "@exabyte-io/code.js/dist/constants";
+export { default } from "@mat3ra/code/dist/js/constants";

package/src/js/lattice/lattice.ts

@@ -2,7 +2,7 @@ import {
     LatticeImplicitSchema,
     LatticeSchema,
     LatticeTypeExtendedSchema,
-} from "@mat3ra/esse/lib/js/types";
+} from "@mat3ra/esse/dist/js/types";
 import lodash from "lodash";
 import _ from "underscore";
 

package/src/js/lattice/lattice_bravais.ts

@@ -1,4 +1,4 @@
-import { LatticeImplicitSchema, LatticeTypeSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeImplicitSchema, LatticeTypeSchema } from "@mat3ra/esse/dist/js/types";
 
 import constants from "../constants";
 import math from "../math";

package/src/js/lattice/lattice_vectors.ts

@@ -1,4 +1,4 @@
-import { LatticeExplicitUnit, LatticeImplicitSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeExplicitUnit, LatticeImplicitSchema } from "@mat3ra/esse/dist/js/types";
 
 import { primitiveCell } from "../cell/primitive_cell";
 import constants from "../constants";

package/src/js/lattice/reciprocal/lattice_reciprocal.js

@@ -1,4 +1,4 @@
-import { ATOMIC_COORD_UNITS, units as UNITS } from "@exabyte-io/code.js/dist/constants";
+import { ATOMIC_COORD_UNITS, units as UNITS } from "@mat3ra/code/dist/js/constants";
 import almostEqual from "array-almost-equal";
 import lodash from "lodash";
 

package/src/js/lattice/reciprocal/symmetry_points.ts

@@ -4,7 +4,7 @@
  * This file contains information about the Brillouin zone symmetry points by lattice type.
  * [AFLOW](https://arxiv.org/abs/1004.2974) methodology is used for implementation.
  */
-import { LatticeImplicitSchema } from "@mat3ra/esse/lib/js/types";
+import { LatticeImplicitSchema } from "@mat3ra/esse/dist/js/types";
 
 import { Lattice } from "../lattice";
 

package/src/js/lattice/types.ts

@@ -1,4 +1,4 @@
-import { ArrayOf3NumberElementsSchema, LatticeTypeSchema } from "@mat3ra/esse/lib/js/types";
+import { ArrayOf3NumberElementsSchema, LatticeTypeSchema } from "@mat3ra/esse/dist/js/types";
 
 export const DEFAULT_LATTICE_UNITS = {
     // by default lattice vectors shall be measured in angstrom, angles - in degrees

package/src/js/material.ts

@@ -1,13 +1,13 @@
-import { HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity";
-import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory";
-// import MaterialJSONSchemaObject from "@mat3ra/esse/lib/js/schema/material.json";
+import { HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity } from "@mat3ra/code/dist/js/entity";
+import { AnyObject } from "@mat3ra/code/dist/js/entity/in_memory";
+// import MaterialJSONSchemaObject from "@mat3ra/esse/dist/js/schema/material.json";
 import {
     ConsistencyCheck,
     DerivedPropertiesSchema,
     FileSourceSchema,
     InChIRepresentationSchema,
     MaterialSchema,
-} from "@mat3ra/esse/lib/js/types";
+} from "@mat3ra/esse/dist/js/types";
 import CryptoJS from "crypto-js";
 
 import { ConstrainedBasis } from "./basis/constrained_basis";

package/src/js/math.js

@@ -1,5 +1,5 @@
 // TODO: adjust the imports and remove the need for re-exporting
-import { math as codeJSMath } from "@exabyte-io/code.js/dist/math";
+import { math as codeJSMath } from "@mat3ra/code/dist/js/math";
 
 export default {
     ...codeJSMath,

package/src/js/parsers/espresso.ts

@@ -1,4 +1,4 @@
-import { MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
 import _ from "underscore";
 import s from "underscore.string";
 

package/src/js/parsers/xyz.ts

@@ -1,4 +1,4 @@
-import { MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
 import _ from "underscore";
 import s from "underscore.string";
 

package/src/js/types.ts

@@ -1,4 +1,4 @@
-import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory";
-import { MaterialSchema } from "@mat3ra/esse/lib/js/types";
+import { AnyObject } from "@mat3ra/code/dist/js/entity/in_memory";
+import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
 
 export type MaterialJSON = MaterialSchema & AnyObject;