mat3ra-esse 2024.1.25.post7__tar.gz → 2024.1.26.post0__tar.gz

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/.github/workflows/cicd.yml

@@ -40,9 +40,9 @@ jobs:
     strategy:
       matrix:
         python-version:
+          # Enable 3.10 after resolving Cython/PyYAML issue https://github.com/yaml/pyyaml/issues/724
           - 3.8.6
           - 3.9.x
-          # Enable after resolving Cython/PyYAML issue https://github.com/yaml/pyyaml/issues/724
           - 3.10.x
           - 3.11.x
           # Enable after: AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/.husky/pre-commit

@@ -5,10 +5,8 @@ SRC_PATTERN="\.json$"
 if git diff --cached --name-only | grep --quiet -E "$SRC_PATTERN"
 then
   echo "JSON assets changed. Running build scripts."
-  echo "Re-building JS assets."
-  npm run build:assets
-  echo "Re-building Python assets: requires virtual environment and dependencies (pip install .'[tests]')."
-  python build_schemas.py
+  echo "Re-building JS and PY assets using JS script."
+  npm run build:js-and-python-modules
 fi
 
 npx lint-staged

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mat3ra-esse
-Version: 2024.1.25.post7
+Version: 2024.1.26.post0
 Summary: Excellent Source of Schemas and Examples.
 Author-email: "Exabyte Inc." <info@mat3ra.com>
 License: # LICENSE

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/build_schemas.js

@@ -8,8 +8,10 @@ const path = require("path");
 const mergeAllOf = require("json-schema-merge-allof");
 const { ESSE } = require("./lib/js/esse");
 
+// JS Modules
+
 const esse = new ESSE();
-const { schemas, wrappedExamples } = esse;
+const { schemas, wrappedExamples, propertiesManifest, results } = esse;
 const schema = esse.buildGlobalSchema();
 
 fs.writeFileSync(
@@ -20,19 +22,47 @@ fs.writeFileSync(
 
 fs.writeFileSync("./schema.js", "module.exports = " + JSON.stringify(schema), "utf8");
 
+if (process.env.BUILD_PYTHON_MODULES === "true") {
+    // PY Modules
+    fs.writeFileSync(
+        "./src/py/mat3ra/esse/data/examples.py",
+        ["import json", `EXAMPLES = json.loads(r'''${JSON.stringify(wrappedExamples)}''')`].join(
+            "\n",
+        ),
+        "utf8",
+    );
+    fs.writeFileSync(
+        "./src/py/mat3ra/esse/data/schemas.py",
+        ["import json", `SCHEMAS = json.loads(r'''${JSON.stringify(schemas)}''')`].join("\n"),
+        "utf8",
+    );
+    fs.writeFileSync(
+        "./src/py/mat3ra/esse/data/properties.py",
+        [
+            "import json",
+            `PROPERTIES_MANIFEST = json.loads(r'''${JSON.stringify(propertiesManifest)}''')`,
+            `RESULTS = json.loads(r'''${JSON.stringify(results)}''')`,
+        ].join("\n"),
+        "utf8",
+    );
+}
+
 if (process.env.BUILD_ASSETS !== "true") {
     process.exit(0);
 }
 
 const subfolder = process.env.BUILD_PATH || "./docs/js/";
 schemas.forEach((s) => {
+    let mergedSchema = s;
     if (process.env.SKIP_MERGE_ALLOF !== "true") {
-        s = mergeAllOf(s, { resolvers: { defaultResolver: mergeAllOf.options.resolvers.title } });
+        mergedSchema = mergeAllOf(s, {
+            resolvers: { defaultResolver: mergeAllOf.options.resolvers.title },
+        });
     }
-    const id_as_path = s.$id.replace("-", "_");
+    const id_as_path = mergedSchema.$id.replace("-", "_");
     const full_path = `${subfolder}/schema/${id_as_path}.json`;
     fs.mkdirSync(path.dirname(full_path), { recursive: true });
-    fs.writeFileSync(full_path, JSON.stringify(s, null, 4), "utf8");
+    fs.writeFileSync(full_path, JSON.stringify(mergedSchema, null, 4), "utf8");
 });
 wrappedExamples.forEach((e) => {
     const id_as_path = e.path.replace("-", "_");

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/package.json

@@ -7,6 +7,7 @@
         "transpile": "mkdir -p lib; babel src/js --out-dir lib/js; node build_schemas.js",
         "transpile-and-build-assets": "mkdir -p lib; babel src/js --out-dir lib/js; BUILD_ASSETS=true BUILD_PATH='./lib/js' node build_schemas.js",
         "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": "nyc --reporter=text mocha --bail --require @babel/register tests/js/",
         "lint": "eslint src/js && prettier --write src/js",

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/src/js/esse/index.js

@@ -1,17 +1,27 @@
 import Ajv from "ajv";
+import fs from "fs";
+import yaml from "js-yaml";
 
 import { buildSchemaDefinitions } from "./schemaUtils";
-import { EXAMPLES_DIR, SCHEMAS_DIR } from "./settings";
+import { EXAMPLES_DIR, PROPERTIES_MANIFEST_PATH, SCHEMAS_DIR } from "./settings";
 import { parseIncludeReferenceStatementsByDir } from "./utils";
 
 const SCHEMAS = parseIncludeReferenceStatementsByDir(SCHEMAS_DIR);
 const EXAMPLES = parseIncludeReferenceStatementsByDir(EXAMPLES_DIR, true);
+const PROPERTIES_MANIFEST = yaml.load(
+    fs.readFileSync(PROPERTIES_MANIFEST_PATH, { encoding: "utf-8" }),
+);
+const RESULTS = Object.entries(PROPERTIES_MANIFEST)
+    .map((k) => (k[1].isResult ? k[0] : null))
+    .filter((x) => x);
 
 export class ESSE {
-    constructor() {
-        this.schemas = SCHEMAS;
-        this.wrappedExamples = EXAMPLES;
-        this.examples = EXAMPLES.map((example) => example.data);
+    constructor(config = {}) {
+        this.schemas = config.schemas || SCHEMAS;
+        this.wrappedExamples = config.wrappedExamples || EXAMPLES;
+        this.examples = this.wrappedExamples.map((example) => example.data);
+        this.propertiesManifest = config.propertiesManifest || PROPERTIES_MANIFEST;
+        this.results = config.results || RESULTS;
     }
 
     getSchemaById(schemaId) {

{mat3ra-esse-2024.1.25.post7 → mat3ra-esse-2024.1.26.post0}/src/js/esse/settings.js

@@ -2,3 +2,7 @@ import path from "path";
 
 export const SCHEMAS_DIR = path.resolve(__dirname, "../../../schema");
 export const EXAMPLES_DIR = path.resolve(__dirname, "../../../example");
+export const PROPERTIES_MANIFEST_PATH = path.resolve(
+    __dirname,
+    "../../../manifest/properties.yaml",
+);

mat3ra-esse-2024.1.26.post0/src/py/mat3ra/esse/data/examples.py

@@ -0,0 +1,2 @@
+import json
+EXAMPLES = json.loads(r'''[{"data":{"properties":[{"name":"atomic_radius","value":4},{"name":"electronegativity","value":1.1},{"name":"ionization_potential","value":7.7}],"symbol":"Si"},"path":"element"},{"data":{"_id":"FPjAaKfuYAL7tiHbm","_material":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Material","slug":"silicon-fcc"},"_project":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Project","slug":"project-default"},"compute":{"arguments":{"nband":1,"npools":1,"ntg":1},"cluster":{"fqdn":"master-1-staging.exabyte.io","jid":"1234.master-1-staging.exabyte.io"},"email":"demo@exabyte.io","errors":[{"domain":"rupy","message":"File Not Found: /home/demo/data/project1/job-123/job-config.json","reason":"FileNotFound"}],"excludeFilesPattern":"^.*.txt$","maxCPU":36,"nodes":1,"notify":"abe","ppn":1,"queue":"OF","timeLimit":"00:05:00"},"createdAt":"2018-11-19 06:41:46.877Z","creator":{"_id":"HtxACY2wX4b2hS8Rv","cls":"User","slug":"exadmin"},"name":"job","owner":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Account","slug":"exabyte"},"schemaVersion":"0.2.0","slug":"job","status":"pre-submission","workflow":{"_id":"FPjAaKfuYAL7tiHbm","createdAt":"2018-11-19 06:41:46.877Z","creator":{"_id":"HtxACY2wX4b2hS8Rv","cls":"User","slug":"exadmin"},"exabyteId":"qKtTzu9utCo6ac4n7","hash":"f4fd707d2e47c15f8d786cf159040954","isDefault":true,"name":"workflow","owner":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Account","slug":"exabyte"},"properties":["band_structure"],"schemaVersion":"0.2.0","slug":"workflow","subworkflows":[{"_id":"LCthJ6E2QabYCZqf4","application":{"name":"espresso","shortName":"qe","summary":"Quantum Espresso","version":"5.1.1","hasAdvancedComputeOptions":true},"model":{"method":{"data":{"pseudo":[]},"subtype":"us","type":"pseudopotential"},"subtype":"gga","type":"dft"},"name":"Band Structure","properties":["band_structure"],"units":[{"flowchartId":"pw-scf","head":true,"name":"pw_scf","status":"idle","type":"execution","tags":["test-tags"]}]}],"tags":["workflow"],"units":[{"_id":"LCthJ6E2QabYCZqf4","flowchartId":"05c362dc27ff1bb98d16fd60","type":"subworkflow"}]}},"path":"job"},{"data":{"_id":"LCthJ6E2QabYCZqf3","basis":{"coordinates":[{"id":1,"value":[0,0,0]},{"id":2,"value":[0.25,0.25,0.25]}],"elements":[{"id":1,"value":"Si"},{"id":2,"value":"Si"}],"name":"basis","units":"crystal"},"createdAt":"2016-04-03T05:25:37.430Z","creator":{"_id":"HtxACY2wX4b2hS8Rv","cls":"User","slug":"exadmin"},"derivedProperties":[{"name":"volume","units":"angstrom^3","value":131.1},{"name":"density","units":"g/cm^3","value":2.33},{"name":"symmetry","spaceGroupSymbol":"Fd-3m","tolerance":{"units":"angstrom","value":0.3}},{"degree":10,"name":"p-norm","value":0.71},{"element":"Si","name":"elemental_ratio","value":0.71},{"name":"inchi","value":""},{"name":"inchi_key","value":""}],"exabyteId":"RKiswuxHKkF3uvLyA","formula":"Si","hash":"4ac3fa057e3530628eb1295c77110eaa","isDefault":false,"isNonPeriodic":false,"lattice":{"name":"lattice","vectors":{"a":[5,0.000121312,0.000131415],"alat":1,"b":[0.000121312,5,0.000121314],"c":[0.000121313,0.000121312,5],"units":"angstrom"},"a":5.14,"alpha":90,"b":5.14,"beta":90,"c":5.14,"gamma":90,"type":"CUB","units":{"angle":"degree","length":"angstrom"}},"name":"Silicon FCC","owner":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Account","slug":"exabyte"},"scaledHash":"5bd4eb168e3530628eb1295d88221cbb","schemaVersion":"0.2.0","slug":"silicon-fcc","unitCellFormula":"Si2","updatedAt":"2016-04-04T17:58:42.867Z"},"path":"material"},{"data":{"data":{"pseudo":[]},"subtype":"us","type":"pseudopotential"},"path":"method"},{"data":{"method":{"data":{"pseudo":[]},"subtype":"us","type":"pseudopotential"},"subtype":"gga","type":"dft"},"path":"model"},{"data":{"_id":"tvFyik5699io8khi8","chargeRate":{"rate":2},"createdAt":"2019-01-03T23:52:26.809Z","creator":{"_id":"HtxACY2wX4b2hS8Rv","cls":"User","slug":"exadmin"},"description":"Default project","gid":3000000,"isDefault":true,"name":"Default","owner":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Account","slug":"exabyte"},"schemaVersion":"0.2.0","slug":"exadmin-default","tags":[],"updatedAt":"2019-01-04T00:12:37.316Z"},"path":"project"},{"data":{"_id":"FPjAaKfuYAL7tiHbm","createdAt":"2018-11-19 06:41:46.877Z","creator":{"_id":"HtxACY2wX4b2hS8Rv","cls":"User","slug":"exadmin"},"exabyteId":"qKtTzu9utCo6ac4n7","hash":"f4fd707d2e47c15f8d786cf159040954","isDefault":true,"name":"workflow","owner":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Account","slug":"exabyte"},"properties":["band_structure"],"schemaVersion":"0.2.0","slug":"workflow","subworkflows":[{"_id":"LCthJ6E2QabYCZqf4","application":{"name":"espresso","shortName":"qe","summary":"Quantum Espresso","version":"5.1.1","hasAdvancedComputeOptions":true},"model":{"method":{"data":{"pseudo":[]},"subtype":"us","type":"pseudopotential"},"subtype":"gga","type":"dft"},"name":"Band 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}}/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}}},"path":"3pse/file/applications/espresso/7.2/pw.x"},{"data":{"_id":"nDAavgjrT5ezwFgod","owner":{"_id":"HtxACY2wX4b2hS8Rv","cls":"Account","slug":"exabyte"},"title":"My Calculation"},"path":"core/reference"},{"data":{"xDataArray":[0,1,2],"yDataSeries":[[0,0.5,1],[0,2.5,5]]},"path":"core/abstract/2d_data"},{"data":{"xAxis":{"label":"kpoint 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mat3ra-esse-2024.1.26.post0/src/py/mat3ra/esse/data/properties.py

@@ -0,0 +1,3 @@
+import json
+PROPERTIES_MANIFEST = json.loads(r'''{"convergence_ionic":{"defaults":{"units":"eV"},"schemaId":"properties-directory/workflow/convergence/ionic","isMonitor":true},"convergence_electronic":{"defaults":{"units":"eV"},"schemaId":"properties-directory/workflow/convergence/electronic","isMonitor":true},"pressure":{"defaults":{"units":"kbar"},"schemaId":"properties-directory/scalar/pressure","isResult":true},"total_energy":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/total-energy","isResult":true},"surface_energy":{"defaults":{"units":"eV/A^2"},"schemaId":"properties-directory/scalar/surface-energy","isResult":true},"fermi_energy":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/fermi-energy","isResult":true},"total_force":{"defaults":{"units":"eV/angstrom"},"schemaId":"properties-directory/scalar/total-force","isResult":true},"zero_point_energy":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/zero-point-energy","isResult":true},"reaction_energy_barrier":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/reaction-energy-barrier","isResult":true},"electron_affinity":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/electron-affinity","isResult":true},"ionization_potential":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/ionization-potential","isResult":true},"valence_band_offset":{"defaults":{"units":"eV"},"schemaId":"properties-directory/scalar/valence-band-offset"},"phonon_dos":{"defaults":{"xAxis":{"label":"frequency","units":"cm-1"},"yAxis":{"label":"Phonon DOS","units":"states/cm-1"}},"schemaId":"properties-directory/non-scalar/phonon-dos","isResult":true},"phonon_dispersions":{"defaults":{"xAxis":{"label":"qpoints","units":"crystal"},"yAxis":{"label":"frequency","units":"cm-1"}},"schemaId":"properties-directory/non-scalar/phonon-dispersions","isResult":true},"total_energy_contributions":{"defaults":{"units":"eV"},"schemaId":"properties-directory/non-scalar/total-energy-contributions","isResult":true},"band_gaps":{"types":["direct","indirect"],"defaults":{"units":"eV"},"schemaId":"properties-directory/non-scalar/band-gaps","isResult":true},"stress_tensor":{"defaults":{"units":"kbar"},"schemaId":"properties-directory/non-scalar/stress-tensor","isResult":true},"band_structure":{"defaults":{"xAxis":{"label":"kpoints","units":"crystal"},"yAxis":{"label":"energy","units":"eV"}},"schemaId":"properties-directory/non-scalar/band-structure","isResult":true},"density_of_states":{"defaults":{"xAxis":{"label":"energy","units":"eV"},"yAxis":{"label":"density of states","units":"states/unitcell"}},"schemaId":"properties-directory/non-scalar/density-of-states","isResult":true},"reaction_energy_profile":{"defaults":{"xAxis":{"label":"reaction coordinate"},"yAxis":{"label":"energy","units":"eV"}},"schemaId":"properties-directory/non-scalar/reaction-energy-profile","isResult":true},"potential_profile":{"defaults":{"xAxis":{"label":"z coordinate"},"yAxis":{"label":"energy","units":"eV"}},"schemaId":"properties-directory/non-scalar/potential-profile","isResult":true},"charge_density_profile":{"defaults":{"xAxis":{"label":"z coordinate"},"yAxis":{"label":"charge density","units":"e/A"}},"schemaId":"properties-directory/non-scalar/charge-density-profile","isResult":true},"vibrational_spectrum":{"defaults":{"xAxis":{"label":"wavenumber","units":"cm-1"},"yAxis":{"label":"Absorption coefficient","units":"km/mol"}},"schemaId":"properties-directory/non-scalar/vibrational-spectrum","isResult":true},"file_content":{"schemaId":"properties-directory/non-scalar/file-content","isResult":true},"average_potential_profile":{"defaults":{"xAxis":{"label":"z coordinate","units":"angstrom"},"yAxis":{"label":"energy","units":"eV"}},"schemaId":"properties-directory/non-scalar/average-potential-profile","isResult":true},"dielectric_tensor":{"schemaId":"properties-directory/non-scalar/dielectric-tensor","isResult":true},"basis":{"defaults":{"units":"angstrom"},"schemaId":"properties-directory/structural/basis"},"lattice":{"defaults":{"units":"angstrom"},"schemaId":"properties-directory/structural/lattice"},"atomic_forces":{"defaults":{"units":"eV/angstrom"},"schemaId":"properties-directory/structural/atomic-forces","isResult":true},"atomic_constraints":{"schemaId":"properties-directory/structural/basis/atomic-constraints"},"p-norm":{"schemaId":"properties-directory/structural/p-norm"},"volume":{"defaults":{"units":"angstrom^3"},"schemaId":"properties-directory/structural/volume"},"symmetry":{"defaults":{"units":"angstrom"},"schemaId":"properties-directory/structural/symmetry"},"elemental_ratio":{"schemaId":"properties-directory/structural/elemental-ratio"},"density":{"defaults":{"units":"g/cm^3"},"schemaId":"properties-directory/structural/density"},"magnetic_moments":{"defaults":{"units":"uB"},"schemaId":"properties-directory/structural/magnetic-moments","isResult":true},"bonds":{"defaults":{"units":"angstrom"},"schemaId":"properties-directory/structural/basis/bonds"},"inchi":{"schemaId":"properties-directory/structural/inchi"},"inchi_key":{"schemaId":"properties-directory/structural/inchi-key"},"material":{"schemaId":"material"},"hubbard_u":{"defaults":{"units":"eV"},"schemaId":"properties-directory/non-scalar/hubbard-u","isResult":true},"hubbard_v":{"defaults":{"units":"eV"},"schemaId":"properties-directory/non-scalar/hubbard-v","isResult":true},"hubbard_v_nn":{"defaults":{"units":"eV"},"schemaId":"properties-directory/non-scalar/hubbard-v-nn","isResult":true}}''')
+RESULTS = json.loads(r'''["pressure","total_energy","surface_energy","fermi_energy","total_force","zero_point_energy","reaction_energy_barrier","electron_affinity","ionization_potential","phonon_dos","phonon_dispersions","total_energy_contributions","band_gaps","stress_tensor","band_structure","density_of_states","reaction_energy_profile","potential_profile","charge_density_profile","vibrational_spectrum","file_content","average_potential_profile","dielectric_tensor","atomic_forces","magnetic_moments","hubbard_u","hubbard_v","hubbard_v_nn"]''')