Feature/SOF-7750 Update: Mat3ra namespace

.gitignore

@@ -16,4 +16,5 @@ __pycache__/
 *.egg-info/
 .coverage
 htmlcov/
+.python-version
 

.husky/pre-commit

@@ -2,3 +2,5 @@
 . "$(dirname "$0")/_/husky.sh"
 
 npx lint-staged
+npm run transpile
+git add dist/

.nycrc

@@ -8,6 +8,8 @@
     "exclude": [
         "tests/**/*",
         "src/js/generated/**/*",
+        "dist/**/*",
+        "build/**/*",
         "**/*.test.ts",
         "**/*.spec.ts",
         "**/*.d.ts"

dist/js/index.d.ts

@@ -1,2 +1,20 @@
 export { default as PropertyFactory } from "./PropertyFactory";
 export { PropertyName, PropertyType } from "./settings";
+export { default as Property } from "./Property";
+export { default as MetaProperty } from "./MetaProperty";
+export { default as PseudopotentialMetaProperty } from "./meta_properties/PseudopotentialMetaProperty";
+export { default as FinalStructureProperty } from "./properties/non-scalar/FinalStructureProperty";
+export { default as BandGapsProperty } from "./properties/non-scalar/BandGapsProperty";
+export { default as IsRelaxedProperty } from "./properties/non-scalar/IsRelaxedProperty";
+export { default as PressureProperty } from "./properties/scalar/PressureProperty";
+export { default as ReactionEnergyBarrierProperty } from "./properties/scalar/ReactionEnergyBarrierProperty";
+export { default as SurfaceEnergyProperty } from "./properties/scalar/SurfaceEnergyProperty";
+export { default as TotalEnergyProperty } from "./properties/scalar/TotalEnergyProperty";
+export { default as BandStructureProperty } from "./properties/non-scalar/BandStructureProperty";
+export { default as ChargeDensityProfileProperty } from "./properties/non-scalar/ChargeDensityProfileProperty";
+export { default as PotentialProfileProperty } from "./properties/non-scalar/PotentialProfileProperty";
+export { default as ReactionEnergyProfileProperty } from "./properties/non-scalar/ReactionEnergyProfileProperty";
+export { protoPropertyHolderMixin } from "./holders/mixins/ProtoPropertyHolderMixin";
+export { propertyHolderMixin } from "./holders/mixins/PropertyHolderMixin";
+export { metaPropertyHolderMixin } from "./holders/mixins/MetaPropertyHolderMixin";
+export * from "./types";

dist/js/index.js

@@ -1,12 +1,60 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PropertyType = exports.PropertyName = exports.PropertyFactory = void 0;
-// Add exports here
+exports.metaPropertyHolderMixin = exports.propertyHolderMixin = exports.protoPropertyHolderMixin = exports.ReactionEnergyProfileProperty = exports.PotentialProfileProperty = exports.ChargeDensityProfileProperty = exports.BandStructureProperty = exports.TotalEnergyProperty = exports.SurfaceEnergyProperty = exports.ReactionEnergyBarrierProperty = exports.PressureProperty = exports.IsRelaxedProperty = exports.BandGapsProperty = exports.FinalStructureProperty = exports.PseudopotentialMetaProperty = exports.MetaProperty = exports.Property = exports.PropertyType = exports.PropertyName = exports.PropertyFactory = void 0;
 var PropertyFactory_1 = require("./PropertyFactory");
 Object.defineProperty(exports, "PropertyFactory", { enumerable: true, get: function () { return __importDefault(PropertyFactory_1).default; } });
 var settings_1 = require("./settings");
 Object.defineProperty(exports, "PropertyName", { enumerable: true, get: function () { return settings_1.PropertyName; } });
 Object.defineProperty(exports, "PropertyType", { enumerable: true, get: function () { return settings_1.PropertyType; } });
+var Property_1 = require("./Property");
+Object.defineProperty(exports, "Property", { enumerable: true, get: function () { return __importDefault(Property_1).default; } });
+var MetaProperty_1 = require("./MetaProperty");
+Object.defineProperty(exports, "MetaProperty", { enumerable: true, get: function () { return __importDefault(MetaProperty_1).default; } });
+var PseudopotentialMetaProperty_1 = require("./meta_properties/PseudopotentialMetaProperty");
+Object.defineProperty(exports, "PseudopotentialMetaProperty", { enumerable: true, get: function () { return __importDefault(PseudopotentialMetaProperty_1).default; } });
+var FinalStructureProperty_1 = require("./properties/non-scalar/FinalStructureProperty");
+Object.defineProperty(exports, "FinalStructureProperty", { enumerable: true, get: function () { return __importDefault(FinalStructureProperty_1).default; } });
+var BandGapsProperty_1 = require("./properties/non-scalar/BandGapsProperty");
+Object.defineProperty(exports, "BandGapsProperty", { enumerable: true, get: function () { return __importDefault(BandGapsProperty_1).default; } });
+var IsRelaxedProperty_1 = require("./properties/non-scalar/IsRelaxedProperty");
+Object.defineProperty(exports, "IsRelaxedProperty", { enumerable: true, get: function () { return __importDefault(IsRelaxedProperty_1).default; } });
+var PressureProperty_1 = require("./properties/scalar/PressureProperty");
+Object.defineProperty(exports, "PressureProperty", { enumerable: true, get: function () { return __importDefault(PressureProperty_1).default; } });
+var ReactionEnergyBarrierProperty_1 = require("./properties/scalar/ReactionEnergyBarrierProperty");
+Object.defineProperty(exports, "ReactionEnergyBarrierProperty", { enumerable: true, get: function () { return __importDefault(ReactionEnergyBarrierProperty_1).default; } });
+var SurfaceEnergyProperty_1 = require("./properties/scalar/SurfaceEnergyProperty");
+Object.defineProperty(exports, "SurfaceEnergyProperty", { enumerable: true, get: function () { return __importDefault(SurfaceEnergyProperty_1).default; } });
+var TotalEnergyProperty_1 = require("./properties/scalar/TotalEnergyProperty");
+Object.defineProperty(exports, "TotalEnergyProperty", { enumerable: true, get: function () { return __importDefault(TotalEnergyProperty_1).default; } });
+var BandStructureProperty_1 = require("./properties/non-scalar/BandStructureProperty");
+Object.defineProperty(exports, "BandStructureProperty", { enumerable: true, get: function () { return __importDefault(BandStructureProperty_1).default; } });
+var ChargeDensityProfileProperty_1 = require("./properties/non-scalar/ChargeDensityProfileProperty");
+Object.defineProperty(exports, "ChargeDensityProfileProperty", { enumerable: true, get: function () { return __importDefault(ChargeDensityProfileProperty_1).default; } });
+var PotentialProfileProperty_1 = require("./properties/non-scalar/PotentialProfileProperty");
+Object.defineProperty(exports, "PotentialProfileProperty", { enumerable: true, get: function () { return __importDefault(PotentialProfileProperty_1).default; } });
+var ReactionEnergyProfileProperty_1 = require("./properties/non-scalar/ReactionEnergyProfileProperty");
+Object.defineProperty(exports, "ReactionEnergyProfileProperty", { enumerable: true, get: function () { return __importDefault(ReactionEnergyProfileProperty_1).default; } });
+var ProtoPropertyHolderMixin_1 = require("./holders/mixins/ProtoPropertyHolderMixin");
+Object.defineProperty(exports, "protoPropertyHolderMixin", { enumerable: true, get: function () { return ProtoPropertyHolderMixin_1.protoPropertyHolderMixin; } });
+var PropertyHolderMixin_1 = require("./holders/mixins/PropertyHolderMixin");
+Object.defineProperty(exports, "propertyHolderMixin", { enumerable: true, get: function () { return PropertyHolderMixin_1.propertyHolderMixin; } });
+var MetaPropertyHolderMixin_1 = require("./holders/mixins/MetaPropertyHolderMixin");
+Object.defineProperty(exports, "metaPropertyHolderMixin", { enumerable: true, get: function () { return MetaPropertyHolderMixin_1.metaPropertyHolderMixin; } });
+__exportStar(require("./types"), exports);

dist/js/types.d.ts

@@ -0,0 +1,14 @@
+export type { PropertySchemaJSON, PropertyRowValue } from "./Property";
+export type { PropertyHolderSourceSchema, PropertyHolderMixin, PropertyInMemoryEntity, } from "./holders/mixins/PropertyHolderMixin";
+export type { ProtoPropertyHolderMixin, ProtoPropertyInMemoryEntity, } from "./holders/mixins/ProtoPropertyHolderMixin";
+export type { ProtoPropertySchemaJSON } from "./holders/mixins/ProtoPropertyHolderMixin";
+export type { MetaPropertyHolderMixin, MetaPropertyInMemoryEntity, } from "./holders/mixins/MetaPropertyHolderMixin";
+export type { MetaPropertySchemaJSON } from "./holders/mixins/MetaPropertyHolderMixin";
+export type { default as AtomicForcesProperty } from "./properties/tensor/AtomicForcesProperty";
+export type { default as MagneticMomentsProperty } from "./properties/tensor/MagneticMomentsProperty";
+export type { default as StressTensorProperty } from "./properties/tensor/StressTensorProperty";
+export type { default as AveragePotentialProfileProperty } from "./properties/non-scalar/AveragePotentialProfileProperty";
+export type { default as DensityOfStatesProperty } from "./properties/non-scalar/DensityOfStatesProperty";
+export type { default as DielectricTensorProperty } from "./properties/non-scalar/DielectricTensorProperty";
+export type { default as PhononDispersionsProperty } from "./properties/non-scalar/PhononDispersionsProperty";
+export type { default as PhononDOSProperty } from "./properties/non-scalar/PhononDOSProperty";

dist/js/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package.json

@@ -1,5 +1,5 @@
 {
-    "name": "@exabyte-io/prode.js",
+    "name": "@mat3ra/prode",
     "version": "0.0.0",
     "description": "PROperty DEfinitions",
     "scripts": {
@@ -18,21 +18,32 @@
     },
     "repository": {
         "type": "git",
-        "url": "https://github.com/Exabyte-io/prode.js.git"
+        "url": "https://github.com/Exabyte-io/prode.git"
     },
     "main": "dist/js/index.js",
+    "types": "dist/js/index.d.ts",
     "files": [
         "/dist",
         "/src/js",
         ".babelrc",
         "tsconfig.json"
     ],
+    "exports": {
+        ".": {
+            "types": "./dist/js/index.d.ts",
+            "default": "./dist/js/index.js"
+        },
+        "./types": {
+            "types": "./dist/js/types.d.ts",
+            "default": "./dist/js/types.js"
+        }
+    },
     "author": "Exabyte Inc.",
     "bugs": {
-        "url": "https://github.com/Exabyte-io/prode.js/issues"
+        "url": "https://github.com/Exabyte-io/prode/issues"
     },
     "license": "Apache-2.0",
-    "homepage": "https://github.com/Exabyte-io/prode.js",
+    "homepage": "https://github.com/Exabyte-io/prode",
     "dependencies": {
         "@types/highcharts": "^5.0.44",
         "lodash": "^4.17.21"

src/js/index.ts

@@ -1,3 +1,21 @@
-// Add exports here
 export { default as PropertyFactory } from "./PropertyFactory";
 export { PropertyName, PropertyType } from "./settings";
+export { default as Property } from "./Property";
+export { default as MetaProperty } from "./MetaProperty";
+export { default as PseudopotentialMetaProperty } from "./meta_properties/PseudopotentialMetaProperty";
+export { default as FinalStructureProperty } from "./properties/non-scalar/FinalStructureProperty";
+export { default as BandGapsProperty } from "./properties/non-scalar/BandGapsProperty";
+export { default as IsRelaxedProperty } from "./properties/non-scalar/IsRelaxedProperty";
+export { default as PressureProperty } from "./properties/scalar/PressureProperty";
+export { default as ReactionEnergyBarrierProperty } from "./properties/scalar/ReactionEnergyBarrierProperty";
+export { default as SurfaceEnergyProperty } from "./properties/scalar/SurfaceEnergyProperty";
+export { default as TotalEnergyProperty } from "./properties/scalar/TotalEnergyProperty";
+export { default as BandStructureProperty } from "./properties/non-scalar/BandStructureProperty";
+export { default as ChargeDensityProfileProperty } from "./properties/non-scalar/ChargeDensityProfileProperty";
+export { default as PotentialProfileProperty } from "./properties/non-scalar/PotentialProfileProperty";
+export { default as ReactionEnergyProfileProperty } from "./properties/non-scalar/ReactionEnergyProfileProperty";
+export { protoPropertyHolderMixin } from "./holders/mixins/ProtoPropertyHolderMixin";
+export { propertyHolderMixin } from "./holders/mixins/PropertyHolderMixin";
+export { metaPropertyHolderMixin } from "./holders/mixins/MetaPropertyHolderMixin";
+
+export * from "./types";

src/js/types.ts

@@ -0,0 +1,24 @@
+export type { PropertySchemaJSON, PropertyRowValue } from "./Property";
+export type {
+    PropertyHolderSourceSchema,
+    PropertyHolderMixin,
+    PropertyInMemoryEntity,
+} from "./holders/mixins/PropertyHolderMixin";
+export type {
+    ProtoPropertyHolderMixin,
+    ProtoPropertyInMemoryEntity,
+} from "./holders/mixins/ProtoPropertyHolderMixin";
+export type { ProtoPropertySchemaJSON } from "./holders/mixins/ProtoPropertyHolderMixin";
+export type {
+    MetaPropertyHolderMixin,
+    MetaPropertyInMemoryEntity,
+} from "./holders/mixins/MetaPropertyHolderMixin";
+export type { MetaPropertySchemaJSON } from "./holders/mixins/MetaPropertyHolderMixin";
+export type { default as AtomicForcesProperty } from "./properties/tensor/AtomicForcesProperty";
+export type { default as MagneticMomentsProperty } from "./properties/tensor/MagneticMomentsProperty";
+export type { default as StressTensorProperty } from "./properties/tensor/StressTensorProperty";
+export type { default as AveragePotentialProfileProperty } from "./properties/non-scalar/AveragePotentialProfileProperty";
+export type { default as DensityOfStatesProperty } from "./properties/non-scalar/DensityOfStatesProperty";
+export type { default as DielectricTensorProperty } from "./properties/non-scalar/DielectricTensorProperty";
+export type { default as PhononDispersionsProperty } from "./properties/non-scalar/PhononDispersionsProperty";
+export type { default as PhononDOSProperty } from "./properties/non-scalar/PhononDOSProperty";

tests/js/properties/convergence_ionic.test.ts

@@ -0,0 +1,20 @@
+import type { ConvergenceIonicPropertySchema } from "@mat3ra/esse/dist/js/types";
+import { expect } from "chai";
+
+import ConvergenceIonicProperty from "../../../src/js/properties/non-scalar/convergence/ConvergenceIonicProperty";
+import { PropertyName, PropertyType } from "../../../src/js/settings";
+
+describe("ConvergenceIonicProperty", () => {
+    it("should create a convergence ionic property", () => {
+        const config: Omit<ConvergenceIonicPropertySchema, "name"> = {
+            units: "eV",
+            data: [{ energy: -100.5 }, { energy: -100.6 }],
+        };
+
+        const property = new ConvergenceIonicProperty(config);
+
+        expect(property).to.be.instanceOf(ConvergenceIonicProperty);
+        expect(ConvergenceIonicProperty.propertyType).equal(PropertyType.non_scalar);
+        expect(ConvergenceIonicProperty.propertyName).equal(PropertyName.convergence_ionic);
+    });
+});

tests/js/properties/hubbard_u.test.ts

@@ -0,0 +1,27 @@
+import type { HubbardUParametersPropertySchema } from "@mat3ra/esse/dist/js/types";
+import { expect } from "chai";
+
+import HubbardUProperty from "../../../src/js/properties/non-scalar/HubbardUProperty";
+import { PropertyName, PropertyType } from "../../../src/js/settings";
+
+describe("HubbardUProperty", () => {
+    it("should create a hubbard u property with correct constructor, propertyType, and propertyName", () => {
+        const config: Omit<HubbardUParametersPropertySchema, "name"> = {
+            units: "eV",
+            values: [
+                {
+                    id: 0,
+                    atomicSpecies: "Fe",
+                    orbitalName: "3d",
+                    value: 4.0,
+                },
+            ],
+        };
+
+        const hubbardUProperty = new HubbardUProperty(config);
+
+        expect(hubbardUProperty).to.be.instanceOf(HubbardUProperty);
+        expect(HubbardUProperty.propertyType).equal(PropertyType.non_scalar);
+        expect(HubbardUProperty.propertyName).equal(PropertyName.hubbard_u);
+    });
+});

tests/js/properties/phonon_dos.test.ts

@@ -0,0 +1,28 @@
+import type { PhononDensityOfStatesPropertySchema } from "@mat3ra/esse/dist/js/types";
+import { expect } from "chai";
+
+import PhononDOSProperty from "../../../src/js/properties/non-scalar/PhononDOSProperty";
+import { PropertyName, PropertyType } from "../../../src/js/settings";
+
+describe("PhononDOSProperty", () => {
+    it("should create a phonon dos property with correct constructor, propertyType, and propertyName", () => {
+        const config: Omit<PhononDensityOfStatesPropertySchema, "name"> = {
+            xAxis: {
+                label: "frequency" as const,
+                units: "cm-1",
+            },
+            yAxis: {
+                label: "Phonon DOS" as const,
+                units: "states/cm-1",
+            },
+            xDataArray: [0.0, 100.0, 200.0, 300.0],
+            yDataSeries: [[0.1, 0.2, 0.3, 0.4] as [number, ...number[]]],
+        };
+
+        const phononDOSProperty = new PhononDOSProperty(config);
+
+        expect(phononDOSProperty).to.be.instanceOf(PhononDOSProperty);
+        expect(PhononDOSProperty.propertyType).equal(PropertyType.non_scalar);
+        expect(PhononDOSProperty.propertyName).equal(PropertyName.phonon_dos);
+    });
+});

tests/js/proto_properties/atomic_constraints.test.ts

@@ -0,0 +1,23 @@
+import type { AtomicConstraintsPropertySchema } from "@mat3ra/esse/dist/js/types";
+import { expect } from "chai";
+
+import AtomicConstraintsProperty from "../../../src/js/proto_properties/AtomicConstraintsProperty";
+import { PropertyName } from "../../../src/js/settings";
+
+describe("AtomicConstraintsProperty", () => {
+    it("should create an atomic constraints property with correct constructor and propertyName", () => {
+        const config: Omit<AtomicConstraintsPropertySchema, "name"> = {
+            values: [
+                {
+                    id: 0,
+                    value: [true, true, false],
+                },
+            ],
+        };
+
+        const atomicConstraintsProperty = new AtomicConstraintsProperty(config);
+
+        expect(atomicConstraintsProperty).to.be.instanceOf(AtomicConstraintsProperty);
+        expect(AtomicConstraintsProperty.propertyName).equal(PropertyName.atomic_constraints);
+    });
+});