nbmolviz3d - npm Package Compare versions

Comparing version 0.1.2 to 0.1.3

example/js/bipyridine_styles.js

@@ -1,22 +0,22 @@
-export default [
-  { visualization_type: 'stick', color: '#fedcba' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#fedcba' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#abcdef' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-  { visualization_type: 'stick', color: '#bada55' },
-];
+export default {
+  0: { visualization_type: 'stick', color: '#fedcba' },
+  1: { visualization_type: 'stick', color: '#abcdef' },
+  2: { visualization_type: 'stick', color: '#abcdef' },
+  3: { visualization_type: 'stick', color: '#abcdef' },
+  4: { visualization_type: 'stick', color: '#abcdef' },
+  5: { visualization_type: 'stick', color: '#abcdef' },
+  6: { visualization_type: 'stick', color: '#abcdef' },
+  7: { visualization_type: 'stick', color: '#fedcba' },
+  8: { visualization_type: 'stick', color: '#abcdef' },
+  9: { visualization_type: 'stick', color: '#abcdef' },
+  10: { visualization_type: 'stick', color: '#abcdef' },
+  11: { visualization_type: 'stick', color: '#abcdef' },
+  12: { visualization_type: 'stick', color: '#bada55' },
+  13: { visualization_type: 'stick', color: '#bada55' },
+  14: { visualization_type: 'stick', color: '#bada55' },
+  15: { visualization_type: 'stick', color: '#bada55' },
+  16: { visualization_type: 'stick', color: '#bada55' },
+  17: { visualization_type: 'stick', color: '#bada55' },
+  18: { visualization_type: 'stick', color: '#bada55' },
+  19: { visualization_type: 'stick', color: '#bada55' },
+};

example/js/example_settings_view.js

@@ -35,4 +35,4 @@ import Backbone from 'backbone';
 
-  onBlurShape(event) {
-    this.model.set('shape', JSON.parse(event.target.value));
+  onBlurShapes(event) {
+    this.model.set('shapes', JSON.parse(event.target.value));
   },
@@ -102,3 +102,3 @@
     const shapesLabel = document.createElement('h4');
-    shapesLabel.innerHTML = 'shape';
+    shapesLabel.innerHTML = 'shapes';
     this.el.appendChild(shapesLabel);
@@ -108,4 +108,4 @@ const shapesTA = document.createElement('textarea');
     shapesTA.rows = '3';
-    shapesTA.value = JSON.stringify(this.model.get('shape'));
-    shapesTA.addEventListener('blur', this.onBlurShape.bind(this));
+    shapesTA.value = JSON.stringify(this.model.get('shapes'));
+    shapesTA.addEventListener('blur', this.onBlurShapes.bind(this));
     this.el.appendChild(shapesTA);
@@ -112,0 +112,0 @@

example/js/main.js

@@ -18,3 +18,3 @@ import 'babel-polyfill';
   styles,
-  shape: {
+  shapes: [{
     type: 'Arrow',
@@ -31,3 +31,3 @@ start: {
     },
-  },
+  }],
   selection_type: selectionTypesConstants.ATOM,
@@ -34,0 +34,0 @@ orbital,

package.json

 {
   "name": "nbmolviz3d",
-  "version": "0.1.2",
+  "version": "0.1.3",
   "description": "3D molecule visualization",
@@ -12,2 +12,3 @@ "main": "dist/bundle.js",
   "dependencies": {
+    "babel-polyfill": "^6.13.0",
     "backbone": "^1.3.3",
@@ -20,3 +21,2 @@ "jquery": "^3.1.0",
     "babel-loader": "^6.2.4",
-    "babel-polyfill": "^6.13.0",
     "babel-preset-es2015": "^6.6.0",
@@ -28,5 +28,5 @@ "chai": "^3.5.0",
     "eslint-loader": "^1.3.0",
-    "eslint-plugin-import": "^1.14.0",
+    "eslint-plugin-import": "^1.15.0",
     "eslint-plugin-jsx-a11y": "^2.2.2",
-    "eslint-plugin-react": "^6.2.0",
+    "eslint-plugin-react": "^6.2.2",
     "inline-environment-variables-webpack-plugin": "^1.1.0",
@@ -33,0 +33,0 @@ "karma": "^0.13.22",

README.md

@@ -120,2 +120,11 @@ # nbmolviz3d
 
+### Running Tests
+Unit tests can be run with:
+
+    npm test
+
+End-to-end tests can be run with:
+
+    npm run e2e
+
 ### Releasing a new version
@@ -128,2 +137,3 @@ A new version should be released via npm every time new code is merged to master.  Currently, this process is manual and obviously must be done by a collaborator of the npm package.
     git push origin master
+    git push origin --tags
     npm publish
@@ -130,0 +140,0 @@

src/main.js

@@ -19,2 +19,5 @@ /**
 import jquery from 'jquery';
+import MolWidget3DModel from './models/mol_widget_3d_model';
+import MolWidget3DView from './views/mol_widget_3d_view';
+
 if (window) {
@@ -25,5 +28,3 @@ window.jquery = jquery;
 
-import MolWidget3DModel from './models/mol_widget_3d_model';
-import MolWidget3DView from './views/mol_widget_3d_view';
 
 export { MolWidget3DModel, MolWidget3DView };

src/models/mol_widget_3d_model.js

@@ -31,11 +31,6 @@ /**
     },
-    styles: [],
+    styles: {},
     selected_atom_indices: [],
     selection_type: selectionTypesConstants.ATOM,
-    shape: {
-      type: '',
-      x: null,
-      y: null,
-      z: null,
-    },
+    shape: [],
     width: '500px',
@@ -42,0 +37,0 @@ },

src/utils/lib_utils.js

@@ -36,3 +36,8 @@ import shapeConstants from '../constants/shape_constants';
   getShapeSpec(shape, callback) {
-    const shapeSpec = {
+    let color;
+    if (shape.color) {
+      color = libUtils.colorStringToNumber(shape.color);
+    }
+
+    const shapeSpec = Object.assign({}, {
       alpha: 0.8,
@@ -43,3 +48,3 @@ callback,
       radius: shape.radius,
-    };
+    }, shape, { color });
 
@@ -46,0 +51,0 @@ if (shape.type === shapeConstants.ARROW) {

src/utils/molecule_utils.js

@@ -10,3 +10,3 @@ import selectionTypesConstants from '../constants/selection_types_constants';
   modelDataToCDJSON(modelData) {
-    const atoms = modelData.atoms.map((atom) => ({
+    const atoms = modelData.atoms.map(atom => ({
       l: atom.elem,
@@ -19,3 +19,3 @@ x: atom.positions[0],
 
-    const bonds = modelData.bonds.map((bond) => ({
+    const bonds = modelData.bonds.map(bond => ({
       b: bond.atom1_index,
@@ -22,0 +22,0 @@ e: bond.atom2_index,

src/views/mol_widget_3d_view.js

@@ -17,5 +17,2 @@ /**
 import Backbone from 'backbone';
-const jQuery = require('jquery');
-window.$ = jQuery;
-const $3Dmol = require('../vendor/3Dmol');
 import environmentConstants from '../constants/environment_constants';
@@ -25,2 +22,7 @@ import libUtils from '../utils/lib_utils';
 
+const jQuery = require('jquery');
+
+window.$ = jQuery;
+const $3Dmol = require('../vendor/3Dmol');
+
 const DEFAULT_VISUALIZATION_TYPE = 'stick';
@@ -49,3 +51,3 @@ const DEFAULT_FONT_SIZE = 14;
 
-    this.mydiv = this.mydiv || document.createElement('div');
+    this.mydiv = this.mydiv || window.document.createElement('div');
     this.mydiv.classList.add('nbmolviz3d');
@@ -125,7 +127,8 @@ this.mydiv.style.width = this.model.get('width');
 
-    // Shape
-    const shape = this.model.get('shape');
-    if (shape.type) {
-      glviewer[`add${shape.type}`](libUtils.getShapeSpec(shape, this.setSelectionTrait));
-    }
+    // Shapes
+    this.model.get('shapes').forEach((shape) => {
+      if (shape.type) {
+        glviewer[`add${shape.type}`](libUtils.getShapeSpec(shape, this.setSelectionTrait));
+      }
+    });
 
@@ -137,3 +140,3 @@ // Orbital
       glviewer.addIsosurface(volumeData, {
-        isoVal: orbital.iso_val,
+        isoval: orbital.iso_val,
         color: ORBITAL_COLOR_POSITIVE,
@@ -143,3 +146,3 @@ opacity: orbital.opacity,
       glviewer.addIsosurface(volumeData, {
-        isoVal: -orbital.iso_val,
+        isoval: -orbital.iso_val,
         color: ORBITAL_COLOR_NEGATIVE,
@@ -146,0 +149,0 @@ opacity: orbital.opacity,

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Fixed alerts

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Improved metrics

Total package byte prevSize

3422786

increased by40.37%

Dev dependency count

27

decreased by-3.57%

Lines of code

36708

increased by43.06%

Number of lines in readme file

151

increased by7.09%

Worsened metrics

Dependency count

4

increased by33.33%

Dependency changes

• + Addedbabel-polyfill@^6.13.0

• + Addedbabel-polyfill@6.26.0(transitive)

• + Addedbabel-runtime@6.26.0(transitive)

• + Addedcore-js@2.6.12(transitive)

• + Addedregenerator-runtime@0.10.50.11.1(transitive)