sdf-parser - npm Package Compare versions

Comparing version 4.0.2 to 5.0.0

package.json

 {
   "name": "sdf-parser",
-  "version": "4.0.2",
+  "version": "5.0.0",
   "description": "SDF parser",
-  "main": "./src/index.js",
+  "main": "lib/index.js",
+  "module": "src/index.js",
   "files": [
+    "lib",
     "src"
   ],
   "scripts": {
-    "eslint": "eslint src __tests__",
+    "build": "npm run compile && cheminfo-build --root SDFParser",
+    "compile": "rollup -c",
+    "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
+    "prepack": "npm run compile",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
     "test": "npm run test-coverage && npm run eslint",
@@ -21,3 +28,3 @@ "test-coverage": "jest --coverage",
     "type": "git",
-    "url": "https://github.com/cheminfo-js/sdf-parser.git"
+    "url": "https://github.com/cheminfo/sdf-parser.git"
   },
@@ -29,2 +36,3 @@ "keywords": [
     "v2000",
+    "v3000",
     "mdl"
@@ -35,23 +43,22 @@ ],
   "bugs": {
-    "url": "https://github.com/cheminfo-js/sdf-parser/issues"
+    "url": "https://github.com/cheminfo/sdf-parser/issues"
   },
-  "homepage": "https://github.com/cheminfo-js/sdf-parser",
+  "homepage": "https://github.com/cheminfo/sdf-parser",
   "devDependencies": {
+    "@babel/plugin-transform-modules-commonjs": "^7.15.4",
     "babel-eslint": "^10.1.0",
     "callback-stream": "^1.1.0",
-    "eslint": "^7.3.1",
-    "eslint-config-cheminfo": "^4.0.0",
-    "eslint-plugin-import": "^2.22.0",
-    "eslint-plugin-jest": "^23.17.1",
-    "eslint-plugin-prettier": "^3.1.4",
-    "jest": "^26.1.0",
-    "openchemlib": "^7.2.3",
-    "prettier": "^2.0.5"
+    "cheminfo-build": "^1.1.11",
+    "eslint": "^7.32.0",
+    "eslint-config-cheminfo": "^6.0.1",
+    "jest": "^27.2.5",
+    "openchemlib": "^7.4.3",
+    "prettier": "^2.4.1"
   },
   "dependencies": {
     "pumpify": "^2.0.1",
-    "split2": "^3.1.1",
-    "through2": "^3.0.2",
+    "split2": "^3.2.2",
+    "through2": "^4.0.2",
     "through2-filter": "^3.0.0"
   }
 }

README.md

@@ -20,3 +20,3 @@ # sdf-parser
 
-var parse = require('sdf-parser');
+var { parse } = require('sdf-parser');
 
@@ -48,12 +48,12 @@ var fs = require('fs');
   modifiers: {
-    CLogP: function(field) {
+    CLogP: function (field) {
       return {
         low: field * 1 - 0.2,
-        high: field * 1 + 0.2
+        high: field * 1 + 0.2,
       };
-    }
+    },
   },
-  filter: function(entry) {
+  filter: (entry) => {
     return entry.CLogP && entry.CLogP.low > 4;
-  }
+  },
 });
@@ -103,5 +103,5 @@ ```
 [npm-url]: https://www.npmjs.com/package/sdf-parser
-[travis-image]: https://img.shields.io/travis/cheminfo-js/sdf-parser/master.svg?style=flat-square
-[travis-url]: https://travis-ci.org/cheminfo-js/sdf-parser
+[travis-image]: https://img.shields.io/travis/cheminfo/sdf-parser/master.svg?style=flat-square
+[travis-url]: https://travis-ci.org/cheminfo/sdf-parser
 [download-image]: https://img.shields.io/npm/dm/sdf-parser.svg?style=flat-square
 [download-url]: https://www.npmjs.com/package/sdf-parser

src/index.js

@@ -1,7 +0,2 @@
-'use strict';
-
-const parse = require('./parse');
-const stream = require('./stream');
-
-module.exports = parse;
-parse.stream = stream;
+export * from './parse';
+export * from './stream';

src/parse.js

@@ -1,4 +0,4 @@
-'use strict';
+import { getEntriesBoundaries } from './getEntriesBoundaries';
 
-function parse(sdf, options = {}) {
+export function parse(sdf, options = {}) {
   const {
@@ -31,3 +31,3 @@ include,
 
-  let sdfParts = sdf.split(new RegExp(`${eol}\\$\\$\\$\\$.*${eol}`));
+  let entriesBoundaries = getEntriesBoundaries(sdf, `${eol}$$$$`, eol);
   let molecules = [];
@@ -38,4 +38,4 @@ let labels = {};
 
-  for (let i = 0; i < sdfParts.length; i++) {
-    let sdfPart = sdfParts[i];
+  for (let i = 0; i < entriesBoundaries.length; i++) {
+    let sdfPart = sdf.substring(...entriesBoundaries[i]);
     let parts = sdfPart.split(`${eol}>`);
@@ -63,4 +63,8 @@ if (parts.length > 0 && parts[0].length > 5) {
             labels[label].keep = true;
-            if (modifiers[label]) labels[label].modifier = modifiers[label];
-            if (forEach[label]) labels[label].forEach = forEach[label];
+            if (modifiers[label]) {
+              labels[label].modifier = modifiers[label];
+            }
+            if (forEach[label]) {
+              labels[label].forEach = forEach[label];
+            }
           }
@@ -114,4 +118,8 @@ }
           molecules[j][label] = value;
-          if (value > currentLabel.maxValue) currentLabel.maxValue = value;
-          if (value < currentLabel.minValue) currentLabel.minValue = value;
+          if (value > currentLabel.maxValue) {
+            currentLabel.maxValue = value;
+          }
+          if (value < currentLabel.minValue) {
+            currentLabel.minValue = value;
+          }
         }
@@ -145,3 +153,1 @@ }
 }
-
-module.exports = parse;

src/stream.browser.js

@@ -1,3 +0,3 @@
-'use strict';
+const empty = {};
 
-module.exports = {};
+export default empty;

src/stream.js

@@ -1,10 +0,8 @@
-'use strict';
+import pipeline from 'pumpify';
+import split2 from 'split2';
+import through2 from 'through2';
+import filter from 'through2-filter';
 
-const pipeline = require('pumpify');
-const split2 = require('split2');
-const through2 = require('through2');
-const filter = require('through2-filter');
+import { parse } from './parse';
 
-const parse = require('./parse');
-
 const filterStream = filter.bind(null, { objectMode: true });
@@ -15,7 +13,7 @@ function filterCb(chunk) {
 
-function entries() {
+export function entries() {
   return pipeline.obj(
     split2(/\r?\n\${4}.*\r?\n/),
     filterStream(filterCb),
-    through2({ objectMode: true }, function (value, encoding, callback) {
+    through2({ objectMode: true }, function process(value, encoding, callback) {
       const eol = value.includes('\r\n') ? '\r\n' : '\n';
@@ -28,6 +26,6 @@ this.push(`${value + eol}$$$$${eol}`);
 
-function molecules(options) {
+export function molecules(options) {
   return pipeline.obj(
     entries(),
-    through2({ objectMode: true }, function (value, encoding, callback) {
+    through2({ objectMode: true }, function process(value, encoding, callback) {
       try {
@@ -49,6 +47,1 @@ const parsed = parse(value, options);
 }
-
-module.exports = {
-  entries,
-  molecules,
-};

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Major refactor

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Filesystem access

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Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Fixed alerts

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New author

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Improved metrics

Total package byte prevSize

355284

increased by2708.57%

Dev dependency count

9

decreased by-10%

Number of package files

18

increased by125%

Lines of code

659

increased by260.11%

Worsened metrics

Number of low supply chain risk alerts

6

increased byInfinity%

Dependency changes

• - Removedthrough2@3.0.2(transitive)

• Updatedsplit2@^3.2.2

• Updatedthrough2@^4.0.2