Update loaders, drop use of external jquery/etc.

config/plugins/visualizations/hyphyvision/package.json

@@ -1,13 +1,11 @@
 {
   "devDependencies": {
-    "css-loader": "^0.28.11",
-    "file-loader": "^1.1.11",
-    "mini-css-extract-plugin": "^0.4.0",
-    "style-loader": "^0.21.0",
-    "url-loader": "^1.0.1",
-    "webpack": "^4.12.0",
-    "webpack-cli": "^3.0.4",
-    "webpack-dev-server": "^3.1.4"
+    "css-loader": "^3.4.2",
+    "file-loader": "^5.0.2",
+    "mini-css-extract-plugin": "^0.9.0",
+    "style-loader": "^1.1.3",
+    "webpack": "^4.41.6",
+    "webpack-cli": "^3.3.11"
   },
   "dependencies": {
     "hyphy-vision": "2.6.3"
@@ -17,6 +15,6 @@
   "main": "index.js",
   "license": "MIT",
   "scripts": {
-    "build": "webpack --mode=production"
+    "build": "webpack -p"
   }
 }

config/plugins/visualizations/hyphyvision/src/index.js

@@ -1,9 +1,5 @@
-window.jQuery = window.$ = $;
-window.d3 = d3;
-import "bootstrap/dist/css/bootstrap.css";
-import "font-awesome/css/font-awesome.css";
-const hyphyVision = require("hyphy-vision");
-require("phylotree.css");
-require("hyphy-vision.css");
+import "hyphy-vision/dist/hyphyvision.css"
+import "hyphy-vision/dist/hyphyvision.js"
+
 window.renderHyPhyVision = hyphyVision.renderHyPhyVision;
-window.render_branch_selection = hyphyVision.render_branch_selection;
+window.render_branch_selection = hyphyVision.render_branch_selection;

config/plugins/visualizations/hyphyvision/webpack.config.js

@@ -3,19 +3,12 @@ const webpack = require("webpack"),
     MiniCssExtractPlugin = require("mini-css-extract-plugin");
 
 module.exports = {
-    entry: "index.js",
+    entry: path.resolve(__dirname, "src/index.js"),
     output: {
         filename: "bundle.js",
-        path: path.resolve(__dirname, "..", "static")
+        path: path.resolve(__dirname, "static")
     },
     plugins: [
-        /*
-    new webpack.ProvidePlugin({
-      $: "jquery",
-      d3: "d3",
-      _: "underscore"
-    }),
-    */
         new MiniCssExtractPlugin()
     ],
     module: {
@@ -43,9 +36,9 @@ module.exports = {
         ]
     },
     resolve: {
-        modules: ["src"],
+        modules: ["node_modules"],
         alias: {
-            "phylotree.css": __dirname + "/node_modules/phylotree/phylotree.css",
+            "phylotree.css": __dirname + "/node_modules/phylotree/build/phylotree.css",
             "hyphy-vision.css": __dirname + "/node_modules/hyphy-vision/dist/hyphyvision.css"
         }
     }