Merge pull request #1798 from papillot/remove-promisify

remove utils.promisify dependency

CHANGELOG.md

@@ -4,6 +4,7 @@ All notable changes to this project will be documented in this file, following t
 Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
 
 ## [Unreleased]
+- Dependencies: remove `utils.promisify` (#1797)
 - Fix circular dependency which causes crash in bundlers (#1791)
 - Add `putty` as a mol-view-spec representation.
 - Fix detecting sidechain-only structures as coarse-grained (#1420)

package.json

@@ -179,8 +179,7 @@
     "remark-gfm": "^4.0.1",
     "rxjs": "^7.8.2",
     "swagger-ui-dist": "^5.32.0",
-    "tslib": "^2.8.1",
+    "tslib": "^2.8.1"
-    "util.promisify": "^1.1.3"
   },
   "peerDependencies": {
     "@google-cloud/storage": "^7.14.0",

src/cli/chem-comp-dict/create-ions.ts

@@ -1,17 +1,16 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import * as argparse from 'argparse';
 import * as path from 'path';
-import util from 'util';
 import fs from 'fs';
-require('util.promisify').shim();
+const writeFileAsync = fs.promises.writeFile;
-const writeFile = util.promisify(fs.writeFile);
 
 import { DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
@@ -32,7 +31,7 @@ function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
 
 function writeIonNamesFile(filePath: string, ionNames: string[]) {
     const output = `/**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
@@ -41,7 +40,7 @@ function writeIonNamesFile(filePath: string, ionNames: string[]) {
 
 export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
 `;
-    writeFile(filePath, output);
+    writeFileAsync(filePath, output);
 }
 
 async function run(out: string, options = DefaultDataOptions) {

src/cli/chem-comp-dict/create-saccharides.ts

@@ -1,16 +1,15 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import * as argparse from 'argparse';
 import * as path from 'path';
-import util from 'util';
 import fs from 'fs';
-require('util.promisify').shim();
+const writeFileAsync = fs.promises.writeFile;
-const writeFile = util.promisify(fs.writeFile);
 
 import { DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
@@ -44,7 +43,7 @@ function writeSaccharideNamesFile(filePath: string, ionNames: string[]) {
 
 export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
 `;
-    writeFile(filePath, output);
+    writeFileAsync(filePath, output);
 }
 
 async function run(out: string, options = DefaultDataOptions) {

src/cli/chem-comp-dict/create-table.ts

@@ -1,16 +1,15 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import * as argparse from 'argparse';
-import * as util from 'util';
 import * as path from 'path';
 import * as fs from 'fs';
-require('util.promisify').shim();
+const writeFileAsync = fs.promises.writeFile;
-const writeFile = util.promisify(fs.writeFile);
 
 import { Database, Table, DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
@@ -250,14 +249,14 @@ async function run(out: string, binary = false, options = DefaultDataOptions, cc
     if (!fs.existsSync(path.dirname(out))) {
         fs.mkdirSync(path.dirname(out));
     }
-    writeFile(out, ccbCif);
+    writeFileAsync(out, ccbCif);
 
     if (!!ccaOut) {
         const ccaCif = getEncodedCif(CCA_TABLE_NAME, atoms, binary);
         if (!fs.existsSync(path.dirname(ccaOut))) {
             fs.mkdirSync(path.dirname(ccaOut));
         }
-        writeFile(ccaOut, ccaCif);
+        writeFileAsync(ccaOut, ccaCif);
     }
 }
 

src/cli/chem-comp-dict/util.ts

@@ -1,17 +1,16 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
-import * as util from 'util';
 import * as path from 'path';
 import * as fs from 'fs';
 import * as zlib from 'zlib';
 import fetch from 'node-fetch';
-require('util.promisify').shim();
+const readFileAsync = fs.promises.readFile;
-const readFile = util.promisify(fs.readFile);
+const writeFileAsync = fs.promises.writeFile;
-const writeFile = util.promisify(fs.writeFile);
 
 import { Progress } from '../../mol-task';
 import { Database } from '../../mol-data/db';
@@ -27,9 +26,9 @@ export async function ensureAvailable(path: string, url: string, forceDownload =
             fs.mkdirSync(DATA_DIR);
         }
         if (url.endsWith('.gz')) {
-            await writeFile(path, zlib.gunzipSync(await data.buffer()));
+            await writeFileAsync(path, zlib.gunzipSync(await data.buffer()));
         } else {
-            await writeFile(path, await data.text());
+            await writeFileAsync(path, await data.text());
         }
         console.log(`done downloading ${url}`);
     }
@@ -41,7 +40,7 @@ export async function ensureDataAvailable(options: DataOptions) {
 }
 
 export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
-    const parsed = await parseCif(await readFile(path, 'utf8'));
+    const parsed = await parseCif(await readFileAsync(path, 'utf8'));
     return CIF.toDatabaseCollection(schema, parsed.result);
 }
 

src/cli/cif2bcif/converter.ts

@@ -1,8 +1,9 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import { CIF, CifCategory, getCifFieldType, CifField, CifFile } from '../../mol-io/reader/cif';
@@ -22,7 +23,7 @@ function showProgress(p: Progress) {
     process.stdout.write(`\r${Progress.format(p)}`);
 }
 
-const readFileAsync = util.promisify(fs.readFile);
+const readFileAsync = fs.promises.readFile;
 const unzipAsync = util.promisify<zlib.InputType, Buffer>(zlib.unzip);
 
 async function readFile(ctx: RuntimeContext, filename: string): Promise<ReaderResult<CifFile>> {

src/cli/cif2bcif/index.ts

@@ -12,7 +12,6 @@ import * as fs from 'fs';
 import * as zlib from 'zlib';
 import { convert } from './converter';
 
-require('util.promisify').shim();
 
 async function process(srcPath: string, outPath: string, configPath?: string, filterPath?: string) {
     const config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;

src/cli/structure-info/helpers.ts

@@ -1,18 +1,17 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
-import * as util from 'util';
 import * as fs from 'fs';
 import fetch from 'node-fetch';
-require('util.promisify').shim();
 
 import { CIF } from '../../mol-io/reader/cif';
 import { Progress } from '../../mol-task';
 
-const readFileAsync = util.promisify(fs.readFile);
+const readFileAsync = fs.promises.readFile;
 
 async function readFile(path: string) {
     if (path.match(/\.bcif$/)) {

src/cli/structure-info/model.ts

@@ -7,7 +7,6 @@
  */
 
 import * as argparse from 'argparse';
-require('util.promisify').shim();
 
 import { CifFrame } from '../../mol-io/reader/cif';
 import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing, Trajectory } from '../../mol-model/structure';

src/cli/structure-info/volume.ts

@@ -1,14 +1,14 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import * as fs from 'fs';
 import * as argparse from 'argparse';
-import * as util from 'util';
 
 import { Volume } from '../../mol-model/volume';
 import { downloadCif } from './helpers';
@@ -20,8 +20,7 @@ import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
 import { Theme } from '../../mol-theme/theme';
 import { volumeFromDensityServerData, DscifFormat } from '../../mol-model-formats/volume/density-server';
 
-require('util.promisify').shim();
+const writeFileAsync = fs.promises.writeFile;
-const writeFileAsync = util.promisify(fs.writeFile);
 
 async function getVolume(url: string): Promise<Volume> {
     const cif = await downloadCif(url, true);

src/perf-tests/lookup3d.ts

@@ -1,4 +1,3 @@
-import * as util from 'util';
 import * as fs from 'fs';
 import { CIF } from '../mol-io/reader/cif';
 
@@ -10,8 +9,7 @@ import { OrderedSet } from '../mol-data/int';
 import { trajectoryFromMmCIF, MmcifFormat } from '../mol-model-formats/structure/mmcif';
 import { getBoundary } from '../mol-math/geometry/boundary';
 
-require('util.promisify').shim();
+const readFileAsync = fs.promises.readFile;
-const readFileAsync = util.promisify(fs.readFile);
 
 async function readData(path: string) {
     if (path.match(/\.bcif$/)) {

src/perf-tests/structure.ts

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import * as B from 'benchmark';
 
-import * as util from 'util';
 import * as fs from 'fs';
 import fetch from 'node-fetch';
 import { CIF } from '../mol-io/reader/cif';
@@ -20,9 +20,8 @@ import { trajectoryFromMmCIF, MmcifFormat } from '../mol-model-formats/structure
 // import { printUnits } from '../apps/structure-info/model';
 // import { EquivalenceClasses } from '../mol-data/util';
 
-require('util.promisify').shim();
+const readFileAsync = fs.promises.readFile;
-const readFileAsync = util.promisify(fs.readFile);
+const writeFileAsync = fs.promises.writeFile;
-const writeFileAsync = util.promisify(fs.writeFile);
 
 async function readData(path: string) {
     if (path.match(/\.bcif$/)) {

src/servers/model/properties/providers/wwpdb.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Paul Pillot <paul.pillot@tandemai.com>
  */
 
 import * as fs from 'fs';
-import * as util from 'util';
 import { AttachModelProperty } from '../../property-provider';
 import { CIF } from '../../../../mol-io/reader/cif';
 import { getParam } from '../../../common/util';
@@ -14,8 +14,7 @@ import { ComponentBond } from '../../../../mol-model-formats/structure/property/
 import { ComponentAtom } from '../../../../mol-model-formats/structure/property/atoms/chem_comp';
 import { CCD_Database, CCD_Schema } from '../../../../mol-io/reader/cif/schema/ccd';
 
-require('util.promisify').shim();
+const readFileAsync = fs.promises.readFile;
-const readFile = util.promisify(fs.readFile);
 
 export const wwPDB_chemCompBond: AttachModelProperty = async ({ model, params }) => {
     const table = await getChemCompBondTable(getBondTablePath(params));
@@ -25,7 +24,7 @@ export const wwPDB_chemCompBond: AttachModelProperty = async ({ model, params })
 };
 
 async function read(path: string) {
-    return path.endsWith('.bcif') ? new Uint8Array(await readFile(path)) : readFile(path, 'utf8');
+    return path.endsWith('.bcif') ? new Uint8Array(await readFileAsync(path)) : readFileAsync(path, 'utf8');
 }
 
 let chemCompBondTable: mmCIF_Database['chem_comp_bond'];

src/servers/model/server/structure-wrapper.ts

@@ -19,7 +19,6 @@ import { trajectoryFromMmCIF } from '../../../mol-model-formats/structure/mmcif'
 import { fetchRetry } from '../utils/fetch-retry';
 import { Task } from '../../../mol-task';
 
-require('util.promisify').shim();
 
 export enum StructureSourceType {
     File,
@@ -65,7 +64,7 @@ export async function createStructureWrapperFromJobEntry(entry: JobEntry, proper
 export const StructureCache = new Cache<StructureWrapper>(s => s.key, s => s.approximateSize);
 const perf = new PerformanceMonitor();
 
-const readFileAsync = util.promisify(fs.readFile);
+const readFileAsync = fs.promises.readFile;
 const unzipAsync = util.promisify<zlib.InputType, Buffer>(zlib.unzip);
 
 async function readFile(filename: string) {