@mat3ra/esse 2024.3.20-0 → 2024.3.25-0

package/.eslintrc.json

@@ -1,6 +1,6 @@
 {
     "extends": ["@exabyte-io/eslint-config"],
-    "ignorePatterns": ["lib/js/**/*.js", "lib/js/**/*.ts"],
+    "ignorePatterns": ["dist/js/**/*.js", "dist/js/**/*.ts"],
     "settings": {
         "import/resolver": {
           "node": {

package/{build_schemas.js → build_schemas.ts}

@@ -3,8 +3,9 @@
  * at build time and writes them out to a single schemas.js file for
  * downstream consumption to avoid FS calls in the browser.
  */
-const fs = require("fs");
-const JSONSchemasGenerator = require("./lib/js/esse/JSONSchemasGenerator").default;
+import * as fs from "fs";
+
+import JSONSchemasGenerator from "./src/js/esse/JSONSchemasGenerator";
 
 // JS Modules
 

package/compile_ts.ts

@@ -1,3 +1,3 @@
 import compileTS from "./src/js/scripts/compileTs";
 
-compileTS("./lib/js/schema", `./lib/js/types.ts`);
+compileTS("./dist/js/schema", `./dist/js/types.ts`);

package/{lib → dist}/js/esse/utils.js

@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseIncludeReferenceStatementsByDir = exports.parseIncludeReferenceStatements = void 0;
+// @ts-ignore
 const json_schema_deref_sync_1 = __importDefault(require("json-schema-deref-sync"));
 const path_1 = __importDefault(require("path"));
 const json_include_1 = require("../json_include");

package/{lib → dist}/js/utils/ajv.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.validateAndClean = exports.validate = exports.getValidator = void 0;
 const ajv_1 = __importDefault(require("ajv"));
+const ajv_formats_1 = __importDefault(require("ajv-formats"));
 const schemaUtils_1 = require("../esse/schemaUtils");
 function addAdditionalPropertiesToSchema(schema, additionalProperties = false) {
     return (0, schemaUtils_1.mapObjectDeep)(schema, (object) => {
@@ -37,6 +38,9 @@ const ajvValidatorAndCleanerWithCoercingTypes = new ajv_1.default({
     removeAdditional: true,
     coerceTypes: true,
 });
+(0, ajv_formats_1.default)(ajvValidator);
+(0, ajv_formats_1.default)(ajvValidatorAndCleaner);
+(0, ajv_formats_1.default)(ajvValidatorAndCleanerWithCoercingTypes);
 function getAjvInstance({ clean, coerceTypes }) {
     if (clean && coerceTypes) {
         return ajvValidatorAndCleanerWithCoercingTypes;

package/package.json

@@ -1,20 +1,18 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2024.3.20-0",
+    "version": "2024.3.25-0",
     "description": "Mat3ra's Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D",
     "scripts": {
-        "prepublishOnly": "rm -rf lib; npm run transpile",
-        "transpile": "tsc && BUILD_ASSETS=true BUILD_PATH='./lib/js' node build_schemas.js",
-        "transpile-and-build-assets": "npm run transpile && ts-node compile_ts.ts",
-        "build:assets": "node build_schemas.js",
-        "build:js-and-python-modules": "BUILD_PYTHON_MODULES=true node build_schemas.js",
-        "build:assets-with-docs": "BUILD_ASSETS=true node build_schemas.js",
-        "test": "npm run set-schema-ids && npm run transpile-and-build-assets && nyc --reporter=text mocha --bail",
-        "test-only": "nyc --reporter=text mocha --bail",
+        "prepublishOnly": "rm -rf dist; npm run transpile",
+        "transpile": "tsc -p tsconfig-transpile.json",
+        "build-schemas": "BUILD_ASSETS=true BUILD_PYTHON_MODULES=true BUILD_PATH='./dist/js' ts-node build_schemas.ts",
+        "compile-types": "ts-node compile_ts.ts",
+        "transpile-and-build-assets": "npm run transpile && npm run build-schemas && npm run compile-types",
+        "test": "npm run build-schemas && nyc --reporter=text mocha --recursive --bail tests/js",
+        "test-only": "nyc --reporter=text mocha --recursive --bail tests/js",
         "lint": "eslint src/js && prettier --write src/js",
         "lint:fix": "eslint --fix --cache src/js && prettier --write src/js",
         "prettier": "prettier --check src/js",
-        "postinstall": "npm run transpile-and-build-assets",
         "prepare": "husky install || exit 0",
         "set-schema-ids": "ts-node set_schema_ids.ts"
     },
@@ -22,7 +20,7 @@
         "type": "git",
         "url": "https://github.com/Exabyte-io/esse.git"
     },
-    "main": "lib/js/esse/index.js",
+    "main": "dist/js/esse/index.js",
     "author": "Mat3ra.com",
     "email": "info@mat3ra.com",
     "bugs": {
@@ -31,6 +29,7 @@
     "homepage": "https://github.com/Exabyte-io/esse",
     "devDependencies": {
         "@exabyte-io/eslint-config": "^2023.8.29-1",
+        "@mat3ra/tsconfig": "^2024.3.25-3",
         "@typescript-eslint/eslint-plugin": "^5.9.1",
         "@typescript-eslint/parser": "^5.9.1",
         "chai": "4.3.4",
@@ -50,7 +49,7 @@
         "eslint-plugin-simple-import-sort": "^7.0.0",
         "husky": "^7.0.4",
         "lint-staged": "^12.1.2",
-        "mocha": "^9.2.0",
+        "mocha": "10.3.0",
         "nyc": "15.1.0",
         "prettier": "^2.5.1",
         "prettyjson": "^1.1.3",
@@ -60,7 +59,7 @@
     "license": "Apache-2.0",
     "dependencies": {
         "@babel/cli": "7.16.0",
-        "@babel/core": "7.16.0",
+        "@babel/core": "7.24.1",
         "@babel/eslint-parser": "7.16.3",
         "@babel/plugin-proposal-class-properties": "7.16.0",
         "@babel/preset-env": "7.16.4",
@@ -68,13 +67,12 @@
         "@babel/preset-typescript": "^7.22.5",
         "@babel/register": "^7.16.0",
         "@babel/runtime-corejs3": "7.16.8",
-        "@tsconfig/node14": "^14.1.0",
-        "@tsconfig/node20": "^20.1.2",
         "@types/chai": "^4.3.11",
+        "@types/js-yaml": "^4.0.9",
         "@types/json-schema-merge-allof": "^0.6.5",
         "@types/mocha": "^10.0.6",
-        "@types/js-yaml": "^4.0.9",
         "ajv": "^8.12.0",
+        "ajv-formats": "^2.1.1",
         "js-yaml": "^4.1.0",
         "json-schema": "^0.4.0",
         "json-schema-deref-sync": "0.14.0",
@@ -83,20 +81,28 @@
         "lodash": "4.17.21"
     },
     "engines": {
-        "node": ">=12.0.0"
+        "node": ">=14.0.0"
     },
     "lint-staged": {
         "*.js": "eslint --cache --fix",
         "*.{js,css}": "prettier --write"
     },
     "exports": {
-        "./lib/js/schema/*": "./lib/js/schema/*",
-        "./lib/js/example/*": "./lib/js/example/*",
-        "./lib/js/utils/*": "./lib/js/utils/*.js",
-        "./lib/js/esse/*": "./lib/js/esse/*.js",
-        "./lib/js/json_include/*": "./lib/js/json_include/*.js",
-        "./lib/js/scripts/*": "./lib/js/scripts/*.js",
-        "./lib/js/types.ts": "./lib/js/types.ts",
-        "./lib/js/schemas.json": "./lib/js/schemas.ts"
+        "./lib/js/schema/*.json": "./dist/js/schema/*.json",
+        "./lib/js/example/*": "./dist/js/example/*.js",
+        "./lib/js/utils/*": "./dist/js/utils/*.js",
+        "./lib/js/esse/*": "./dist/js/esse/*.js",
+        "./lib/js/json_include/*": "./dist/js/json_include/*.js",
+        "./lib/js/scripts/*": "./dist/js/scripts/*.js",
+        "./lib/js/types": "./dist/js/types.ts",
+        "./lib/js/schemas.json": "./dist/js/schemas.json",
+        "./dist/schema/*.json": "./dist/js/schema/*.json",
+        "./dist/example/*": "./dist/js/example/*.js",
+        "./dist/utils/*": "./dist/js/utils/*.js",
+        "./dist/esse/*": "./dist/js/esse/*.js",
+        "./dist/json_include/*": "./dist/js/json_include/*.js",
+        "./dist/scripts/*": "./dist/js/scripts/*.js",
+        "./dist/types": "./dist/js/types.ts",
+        "./dist/schemas.json": "./dist/js/schemas.json"
     }
 }

package/schema/system/timestampable.json

@@ -15,24 +15,10 @@
             "format": "date-time"
         },
         "createdBy": {
-            "oneOf": [
-                {
-                    "type": "string"
-                },
-                {
-                    "type": "number"
-                }
-            ]
+            "type": "string"
         },
         "updatedBy": {
-            "oneOf": [
-                {
-                    "type": "string"
-                },
-                {
-                    "type": "number"
-                }
-            ]
+            "type": "string"
         }
     }
 }

package/src/js/esse/utils.ts

@@ -1,4 +1,5 @@
 import { JSONSchema7, JSONSchema7Definition } from "json-schema";
+// @ts-ignore
 import deref from "json-schema-deref-sync";
 import path from "path";
 

package/src/js/utils/ajv.ts

@@ -1,6 +1,6 @@
-import type {} from "ajv"; // @see https://github.com/microsoft/TypeScript/issues/47663
 import Ajv, { SchemaObject } from "ajv";
 import { AnyValidateFunction } from "ajv/dist/core";
+import addFormats from "ajv-formats";
 
 import { mapObjectDeep } from "../esse/schemaUtils";
 import { AnyObject } from "../esse/types";
@@ -43,6 +43,10 @@ const ajvValidatorAndCleanerWithCoercingTypes = new Ajv({
     coerceTypes: true,
 });
 
+addFormats(ajvValidator);
+addFormats(ajvValidatorAndCleaner);
+addFormats(ajvValidatorAndCleanerWithCoercingTypes);
+
 interface AjvInstanceOptions {
     clean: boolean;
     coerceTypes: boolean;

package/tsconfig-transpile.json

@@ -0,0 +1,3 @@
+{
+    "extends": "@mat3ra/tsconfig/tsconfig-js-py-transpile.json"
+}

package/tsconfig.json

@@ -1,34 +1,3 @@
 {
-  "compilerOptions": {
-    "target": "ES2018",
-    "jsx": "react",
-    "lib": ["ES2019"],
-    "allowJs": true,
-    "module": "commonjs",
-    "moduleResolution": "Node",
-    "declaration": true,
-    "outDir": "./lib",
-    "noEmitOnError": false,
-    "isolatedModules": true,
-    "esModuleInterop": true,
-    "resolveJsonModule": true,
-    "forceConsistentCasingInFileNames": true,
-    "strict": true,
-    "skipLibCheck": true,
-    "types": ["mocha", "node"],
-    "rootDir": "./src",
-    "baseUrl": "./",
-  },
-  "include": [ 
-    "./src",
-    "modules.d.ts"
-  ],
-  "exclude": [
-      "node_modules",
-      "lib"
-  ],
-  "ts-node": {
-    "files": true,
-    "compilerOptions": {}
-  },
+    "extends": "@mat3ra/tsconfig/tsconfig-js-py-dev.json"
 }

package/lib/js/example/3pse/db/nist_jarvis/2024.3.13/db_entry.json

@@ -1,91 +0,0 @@
-{
-    "phi": {
-        "nelect": 48,
-        "phi": 4.73414095269429,
-        "scf_vbm": -1.6519,
-        "scf_cbm": -1.6472,
-        "Ef": -1.97822464,
-        "scf_gap": 0,
-        "avg_max": 2.7559163126942896,
-        "scf_dir": false
-    },
-    "atoms": {
-        "lattice_mat": [
-            [
-                3.353617811446221,
-                0,
-                0
-            ],
-            [
-                0,
-                6.273423021773385,
-                0
-            ],
-            [
-                0,
-                0,
-                33.313518
-            ]
-        ],
-        "coords": [
-            [
-                0,
-                0.6004615456553349,
-                0.2002745956304112
-            ],
-            [
-                0.5,
-                0.9651745521229684,
-                0.205389889617873
-            ],
-            [
-                0,
-                0.8600702878546368,
-                0.2642586539633663
-            ],
-            [
-                0.5,
-                0.3508476059345406,
-                0.2471701152668883
-            ],
-            [
-                0.5,
-                0.7055702442093444,
-                0.1414059027438078
-            ],
-            [
-                0,
-                0.2147957642231673,
-                0.1584938427776558
-            ]
-        ],
-        "elements": [
-            "Mo",
-            "Mo",
-            "Te",
-            "Te",
-            "Te",
-            "Te"
-        ],
-        "abc": [
-            3.35362,
-            6.27342,
-            33.31352
-        ],
-        "angles": [
-            90,
-            90,
-            90
-        ],
-        "cartesian": false,
-        "props": [
-            "",
-            "",
-            "",
-            "",
-            "",
-            ""
-        ]
-    },
-    "jid": "JVASP-677"
-}

package/lib/js/example/3pse/file/applications/espresso/7.2/pw.x.json

@@ -1,94 +0,0 @@
-{
-    "&CONTROL": {
-        "calculation": "scf",
-        "title": "",
-        "verbosity": "low",
-        "restart_mode": "from_scratch",
-        "wf_collect": true,
-        "tstress": true,
-        "tprnfor": true,
-        "outdir": "{{ JOB_WORK_DIR }}/outdir",
-        "wfcdir": "{{ JOB_WORK_DIR }}/outdir",
-        "prefix": "__prefix__",
-        "pseudo_dir": "{{ JOB_WORK_DIR }}/pseudo"
-    },
-    "&SYSTEM": {
-        "ibrav": 0,
-        "nat": 2,
-        "ntyp": 2,
-        "ecutwfc": 40,
-        "ecutrho": 200,
-        "occupations": "smearing",
-        "degauss": 0.005,
-        "starting_magnetization": [
-            0.01,
-            0.02
-        ],
-        "Hubbard_occ": [
-            [
-                1,
-                1,
-                0
-            ],
-            [
-                1,
-                2,
-                0.02
-            ]
-        ]
-    },
-    "&ELECTRONS": {
-        "diagonalization": "david",
-        "diago_david_ndim": 4,
-        "diago_full_acc": true,
-        "mixing_beta": 0.3,
-        "startingwfc": "atomic+random"
-    },
-    "&IONS": null,
-    "&CELL": null,
-    "ATOMIC_SPECIES": {
-        "values": [
-            {
-                "X": "Cs",
-                "Mass_X": 132.90543,
-                "PseudoPot_X": "Cs.upf"
-            },
-            {
-                "X": "Cl",
-                "Mass_X": 35.4527,
-                "PseudoPot_X": "Cl.upf"
-            }
-        ]
-    },
-    "CELL_PARAMETERS": {
-        "card_option": "angstrom",
-        "values": {
-            "v1": [
-                4.324582724,
-                0,
-                2.496799
-            ],
-            "v2": [
-                1.441527575,
-                4.077255694,
-                2.496799
-            ],
-            "v3": [
-                0,
-                0,
-                4.993598
-            ]
-        }
-    },
-    "K_POINTS": {
-        "card_option": "automatic",
-        "values": {
-            "nk1": 2,
-            "nk2": 2,
-            "nk3": 2,
-            "sk1": 0,
-            "sk2": 0,
-            "sk3": 0
-        }
-    }
-}

package/lib/js/example/core/abstract/2d_data.json

@@ -1,19 +0,0 @@
-{
-    "xDataArray": [
-        0,
-        1,
-        2
-    ],
-    "yDataSeries": [
-        [
-            0,
-            0.5,
-            1
-        ],
-        [
-            0,
-            2.5,
-            5
-        ]
-    ]
-}

package/lib/js/example/core/abstract/2d_plot.json

@@ -1,26 +0,0 @@
-{
-    "xAxis": {
-        "label": "kpoint index"
-    },
-    "xDataArray": [
-        0,
-        1,
-        2
-    ],
-    "yAxis": {
-        "label": "eigenvalues",
-        "units": "eV"
-    },
-    "yDataSeries": [
-        [
-            0,
-            0.5,
-            1
-        ],
-        [
-            0,
-            2.5,
-            5
-        ]
-    ]
-}

package/lib/js/example/core/abstract/3d_grid.json

@@ -1,12 +0,0 @@
-{
-    "dimensions": [
-        2,
-        2,
-        2
-    ],
-    "shifts": [
-        0,
-        0,
-        0
-    ]
-}

package/lib/js/example/core/abstract/3d_tensor.json

@@ -1,17 +0,0 @@
-[
-    [
-        1,
-        0,
-        0
-    ],
-    [
-        0,
-        1,
-        0
-    ],
-    [
-        0,
-        0,
-        1
-    ]
-]

package/lib/js/example/core/abstract/3d_vector_basis.json

@@ -1,17 +0,0 @@
-{
-    "a": [
-        5,
-        0,
-        0
-    ],
-    "b": [
-        0,
-        5,
-        0
-    ],
-    "c": [
-        0,
-        0,
-        5
-    ]
-}

package/lib/js/example/core/abstract/point.json

@@ -1,5 +0,0 @@
-[
-    0,
-    5.5,
-    0
-]

package/lib/js/example/core/abstract/vector.json

@@ -1,5 +0,0 @@
-[
-    1,
-    0,
-    0
-]

package/lib/js/example/core/primitive/1d_data_series.json

@@ -1,12 +0,0 @@
-[
-    [
-        0,
-        0.5,
-        1
-    ],
-    [
-        0,
-        2.5,
-        5
-    ]
-]

package/lib/js/example/core/primitive/3d_lattice.json

@@ -1,8 +0,0 @@
-{
-    "a": 5.14,
-    "alpha": 90,
-    "b": 5.14,
-    "beta": 90,
-    "c": 5.14,
-    "gamma": 90
-}

package/lib/js/example/core/primitive/array_of_3_booleans.json

@@ -1,5 +0,0 @@
-[
-    true,
-    false,
-    false
-]

package/lib/js/example/core/primitive/array_of_3_numbers.json

@@ -1,5 +0,0 @@
-[
-    1,
-    0,
-    0
-]

package/lib/js/example/core/primitive/array_of_ids.json

@@ -1,8 +0,0 @@
-[
-    {
-        "id": 1
-    },
-    {
-        "id": 2
-    }
-]

package/lib/js/example/core/primitive/axis.json

@@ -1,4 +0,0 @@
-{
-    "label": "energy",
-    "units": "eV"
-}

package/lib/js/example/core/primitive/scalar.json

@@ -1,3 +0,0 @@
-{
-    "value": 0.1
-}

package/lib/js/example/core/primitive/string.json

@@ -1,3 +0,0 @@
-{
-    "value": "example string"
-}

package/lib/js/example/core/reference/experiment/condition.json

@@ -1,12 +0,0 @@
-{
-    "name": "pressure",
-    "scalar": [
-        {
-            "value": "1.2"
-        },
-        {
-            "value": "3.3"
-        }
-    ],
-    "units": "kbar"
-}

package/lib/js/example/core/reference/experiment/location.json

@@ -1,4 +0,0 @@
-{
-    "latitude": 24.3423424,
-    "longitude": 43.234232
-}