more ts conversions, fisrt test running with jest, docs with typedoc

Author: arose

lib/chroma.es6.js

@@ -13,20 +13,29 @@
     "prebuild": "npm run-script lint",
     "build": "rollup -c",
     "postbuild": "node ./scripts/makeScriptsList.js",
-    "pretest": "npm run build",
-    "test": "mocha",
+    "test": "./node_modules/.bin/jest",
     "preversion": "npm test",
     "version": "npm run-script build-min && git add -A dist",
     "postversion": "git push && git push --tags",
     "prepublish": "npm test",
     "devpublish": "npm publish --tag next",
-    "doc": "esdoc",
+    "doc": "./node_modules/.bin/typedoc --mode file --includes doc/usage/ --media doc/usage/ --out build/docs/ ./src/",
     "watch": "rollup -c -w",
     "deploy": "./scripts/deploy.sh prerelease",
     "gallery": "./scripts/gallery.sh",
     "prerelease": "./scripts/release.sh prerelease",
     "build-min": "rollup -c && uglifyjs build/js/ngl.dev.js -cm > dist/ngl.js && cp build/js/ngl.esm.js dist/ngl.esm.js"
   },
+  "jest": {
+    "moduleFileExtensions": [
+      "ts",
+      "js"
+    ],
+    "transform": {
+      "\\.ts$": "<rootDir>/node_modules/ts-jest/preprocessor.js"
+    },
+    "testRegex": "\\.spec\\.ts$"
+  },
   "homepage": "https://github.com/arose/ngl#readme",
   "repository": {
     "type": "git",
@@ -48,6 +57,7 @@
     "science"
   ],
   "devDependencies": {
+    "@types/chroma-js": "^1.3.1",
     "@types/jest": "^20.0.8",
     "@types/node": "^8.0.25",
     "@types/signals": "0.0.17",
@@ -59,9 +69,8 @@
     "babel-register": "^6.26.0",
     "babelrc-rollup": "^3.0.0",
     "chai": "^4.1.1",
-    "cheerio": "^1.0.0-rc.1",
-    "esdoc": "^1.0.2",
-    "esdoc-standard-plugin": "^1.0.0",
+    "chroma-js": "^1.3.4",
+    "jest": "^21.0.1",
     "mocha": "^3.5.0",
     "promise-polyfill": "^6.0.2",
     "rollup": "^0.49.2",
@@ -75,6 +84,8 @@
     "sprintf-js": "^1.1.1",
     "standard": "^10.0.3",
     "three": "^0.87.1",
+    "ts-jest": "^21.0.0",
+    "typedoc": "^0.8.0",
     "typescript": "^2.5.1",
     "uglify-js": "^3.0.28"
   },

package.json

@@ -57,6 +57,7 @@ export default {
     }),
     commonjs({
       namedExports: {
+        'node_modules/chroma-js/chroma.js': [ 'scale' ],
         'node_modules/signals/dist/signals.js': [ 'Signal' ],
         'node_modules/sprintf-js/src/sprintf.js': [ 'sprintf' ]
       }

rollup.config.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import Selection from '../selection/selection.js'
 import Alignment from './alignment.js'
 import Superposition from './superposition.js'

src/align/align-utils.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { Debug, Log } from '../globals.js'
+import { Debug, Log } from '../globals'
 
 // const nucleotides = 'ACTG';
 const aminoacidsX = 'ACDEFGHIKLMNPQRSTVWY'

src/align/alignment.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { Debug, Log } from '../globals.js'
+import { Debug, Log } from '../globals'
 import {
     Matrix, svd, meanRows, subRows, addRows, transpose,
     multiplyABt, invert3x3, multiply3x3, mat3x3determinant

src/align/superposition.js

@@ -6,8 +6,8 @@
 
 import { Vector3, Quaternion } from 'three'
 
-import { defaults, ensureVector3, ensureQuaternion } from '../utils.js'
-import { lerp, smoothstep } from '../math/math-utils.js'
+import { defaults, ensureVector3, ensureQuaternion } from '../utils'
+import { lerp, smoothstep } from '../math/math-utils'
 
 /**
  * Animation. Base animation class.

src/animation/animation.js

@@ -6,8 +6,8 @@
 
 import { Matrix4, Vector3, Group } from 'three'
 
-import { BufferRegistry } from '../globals.js'
-import { defaults } from '../utils.js'
+import { BufferRegistry } from '../globals'
+import { defaults } from '../utils'
 import Buffer from './buffer.js'
 import CylinderBuffer from './cylinder-buffer.js'
 import ConeBuffer from './cone-buffer.js'

src/buffer/arrow-buffer.js

@@ -6,7 +6,7 @@
 
 import { BoxBufferGeometry, Vector3 } from 'three'
 
-import { BufferRegistry } from '../globals.js'
+import { BufferRegistry } from '../globals'
 import GeometryBuffer from './geometry-buffer.js'
 
 const scale = new Vector3()

src/buffer/box-buffer.js

@@ -13,8 +13,8 @@ import {
     ShaderMaterial
 } from 'three'
 
-import { Log } from '../globals.js'
-import { defaults, getTypedArray, getUintArray } from '../utils.js'
+import { Log } from '../globals'
+import { defaults, getTypedArray, getUintArray } from '../utils'
 import { getShader } from '../shader/shader-utils.js'
 
 /**

src/buffer/buffer.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { BufferRegistry } from '../globals.js'
+import { BufferRegistry } from '../globals'
 import ConeGeometryBuffer from './conegeometry-buffer.js'
 
 /**

src/buffer/cone-buffer.js

@@ -6,7 +6,7 @@
 
 import { Matrix4, Vector3, ConeBufferGeometry } from 'three'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import { calculateCenterArray } from '../math/array-utils.js'
 import GeometryBuffer from './geometry-buffer.js'
 

src/buffer/conegeometry-buffer.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { BufferRegistry, ExtensionFragDepth } from '../globals.js'
+import { BufferRegistry, ExtensionFragDepth } from '../globals'
 import CylinderGeometryBuffer from './cylindergeometry-buffer.js'
 import CylinderImpostorBuffer from './cylinderimpostor-buffer.js'
 

src/buffer/cylinder-buffer.js

@@ -6,7 +6,7 @@
 
 import { Matrix4, Vector3, CylinderBufferGeometry } from 'three'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import { calculateCenterArray, serialBlockArray } from '../math/array-utils.js'
 import GeometryBuffer from './geometry-buffer.js'
 

src/buffer/cylindergeometry-buffer.js

@@ -9,7 +9,7 @@ import { Matrix4 } from 'three'
 import '../shader/CylinderImpostor.vert'
 import '../shader/CylinderImpostor.frag'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import MappedAlignedBoxBuffer from './mappedalignedbox-buffer.js'
 
 /**

src/buffer/cylinderimpostor-buffer.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { BufferRegistry } from '../globals.js'
+import { BufferRegistry } from '../globals'
 import EllipsoidGeometryBuffer from './ellipsoidgeometry-buffer.js'
 
 /**

src/buffer/ellipsoid-buffer.js

@@ -6,7 +6,7 @@
 
 import { IcosahedronBufferGeometry, Vector3 } from 'three'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import GeometryBuffer from './geometry-buffer.js'
 
 const scale = new Vector3()

src/buffer/ellipsoidgeometry-buffer.js

@@ -6,7 +6,7 @@
 
 import { Matrix4, Matrix3 } from 'three'
 
-import { getUintArray } from '../utils.js'
+import { getUintArray } from '../utils'
 import { serialBlockArray } from '../math/array-utils.js'
 import { applyMatrix3toVector3array, applyMatrix4toVector3array } from '../math/vector-utils.js'
 import MeshBuffer from './mesh-buffer.js'

src/buffer/geometry-buffer.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { ExtensionFragDepth } from '../globals.js'
+import { ExtensionFragDepth } from '../globals'
 import { calculateMinArray } from '../math/array-utils.js'
 import CylinderGeometryBuffer from './cylindergeometry-buffer.js'
 import HyperballStickImpostorBuffer from './hyperballstickimpostor-buffer.js'

src/buffer/hyperballstick-buffer.js

@@ -9,7 +9,7 @@ import { Matrix4 } from 'three'
 import '../shader/HyperballStickImpostor.vert'
 import '../shader/HyperballStickImpostor.frag'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import MappedBoxBuffer from './mappedbox-buffer.js'
 
 /**

src/buffer/hyperballstickimpostor-buffer.js

@@ -12,7 +12,7 @@ import {
 import '../shader/Image.vert'
 import '../shader/Image.frag'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import Buffer from './buffer.js'
 
 const quadIndices = new Uint16Array([

src/buffer/image-buffer.js

@@ -6,7 +6,7 @@
 
 import Buffer from './buffer.js'
 
-import { getUintArray } from '../utils.js'
+import { getUintArray } from '../utils'
 import { calculateCenterArray, serialArray } from '../math/array-utils.js'
 
 /**

src/buffer/mapped-buffer.js

@@ -6,7 +6,7 @@
 
 import { OctahedronBufferGeometry, Vector3 } from 'three'
 
-import { BufferRegistry } from '../globals.js'
+import { BufferRegistry } from '../globals'
 import GeometryBuffer from './geometry-buffer.js'
 
 const scale = new Vector3()

src/buffer/octahedron-buffer.js

@@ -9,9 +9,9 @@ import { DataTexture } from 'three'
 import '../shader/Point.vert'
 import '../shader/Point.frag'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import { serialArray } from '../math/array-utils.js'
-import { smoothstep } from '../math/math-utils.js'
+import { smoothstep } from '../math/math-utils'
 import Buffer from './buffer.js'
 
 function distance (x0, y0, x1, y1) {

src/buffer/point-buffer.js

@@ -6,7 +6,7 @@
 
 import '../shader/Ribbon.vert'
 
-import { getUintArray } from '../utils.js'
+import { getUintArray } from '../utils'
 import { serialArray } from '../math/array-utils.js'
 import MeshBuffer from './mesh-buffer.js'
 

src/buffer/ribbon-buffer.js

@@ -4,7 +4,7 @@
  * @private
  */
 
-import { BufferRegistry, ExtensionFragDepth } from '../globals.js'
+import { BufferRegistry, ExtensionFragDepth } from '../globals'
 import SphereGeometryBuffer from './spheregeometry-buffer.js'
 import SphereImpostorBuffer from './sphereimpostor-buffer.js'
 

src/buffer/sphere-buffer.js

@@ -6,7 +6,7 @@
 
 import { IcosahedronBufferGeometry, Vector3 } from 'three'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import GeometryBuffer from './geometry-buffer.js'
 
 const scale = new Vector3()

src/buffer/spheregeometry-buffer.js

@@ -6,7 +6,7 @@
 
 import { TetrahedronBufferGeometry, Vector3 } from 'three'
 
-import { BufferRegistry } from '../globals.js'
+import { BufferRegistry } from '../globals'
 import GeometryBuffer from './geometry-buffer.js'
 
 const scale = new Vector3()

src/buffer/tetrahedron-buffer.js

@@ -9,8 +9,8 @@ import { Color, CanvasTexture } from 'three'
 import '../shader/SDFFont.vert'
 import '../shader/SDFFont.frag'
 
-import { Browser, BufferRegistry } from '../globals.js'
-import { defaults } from '../utils.js'
+import { Browser, BufferRegistry } from '../globals'
+import { defaults } from '../utils'
 import MappedQuadBuffer from './mappedquad-buffer.js'
 import { IgnorePicker } from '../utils/picker.js'
 

src/buffer/text-buffer.js

@@ -6,8 +6,8 @@
 
 import { TorusBufferGeometry, Vector3 } from 'three'
 
-import { BufferRegistry } from '../globals.js'
-import { defaults } from '../utils.js'
+import { BufferRegistry } from '../globals'
+import { defaults } from '../utils'
 import GeometryBuffer from './geometry-buffer.js'
 
 const scale = new Vector3()

src/buffer/torus-buffer.js

@@ -7,7 +7,7 @@
 import '../shader/Line.vert'
 import '../shader/Line.frag'
 
-import { Log } from '../globals.js'
+import { Log } from '../globals'
 import Buffer from './buffer.js'
 
 /**

src/buffer/trace-buffer.js

@@ -6,7 +6,7 @@
 
 import { Vector3 } from 'three'
 
-import { defaults, getUintArray } from '../utils.js'
+import { defaults, getUintArray } from '../utils'
 import { serialArray } from '../math/array-utils.js'
 import MeshBuffer from './mesh-buffer.js'
 

src/buffer/tubemesh-buffer.js

@@ -9,7 +9,7 @@ import { Color } from 'three'
 import '../shader/Line.vert'
 import '../shader/Line.frag'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import { uniformArray3 } from '../math/array-utils.js'
 import Buffer from './buffer.js'
 

src/buffer/vector-buffer.js

@@ -9,7 +9,7 @@ import { Vector2, Matrix4 } from 'three'
 import '../shader/WideLine.vert'
 import '../shader/WideLine.frag'
 
-import { defaults } from '../utils.js'
+import { defaults } from '../utils'
 import MappedQuadBuffer from './mappedquad-buffer.js'
 
 /**