Merge pull request #359 from phovea/release-5.1.0

Release 5.1.0

Author: dvvanessastoiber

generators/_init-hybrid/index.js

@@ -37,22 +37,8 @@ class Generator extends Base {
   }
 
   default() {
-    this.composeWith('phovea:_node', {
-      options: this.options
-    }, {
-      local: require.resolve('../_node')
-    });
     const types = this.config.get('type').split('-');
-    this.composeWith('phovea:init-' + types[1], {
-      options: this.options
-    }, {
-      local: require.resolve('../init-' + types[1])
-    });
-    this.composeWith('phovea:init-' + types[0], {
-      options: this.options
-    }, {
-      local: require.resolve('../init-' + types[0])
-    });
+    this.composeWith(['phovea:_node', 'phovea:init-' + types[1], 'phovea:init-' + types[0]], {options: this.options})
   }
 
   end() {

generators/_init-hybrid/templates/package.tmpl.json

@@ -22,7 +22,7 @@
     "pretest": "echo hybrid",
     "posttest:web": "npm run lint",
     "posttest": "echo hybrid",
-    "test:web": "test ! $(find tests -name \"*.ts\") || karma start",
+    "test:web": "test ! $(find tests -name \"*.ts\") || jest",
     "test:python": "test ! $(find tests -name \"*.py\") || python setup.py test",
     "test": "npm run test:web && npm run test:python",
     "prebuild:python": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test:python",

generators/_init-python/index.js

@@ -61,8 +61,6 @@ class Generator extends Base {
     }
     this.composeWith('phovea:_node', {
       options: this.options
-    }, {
-      local: require.resolve('../_node')
     });
   }
 

generators/_init-web/index.js

@@ -1,5 +1,6 @@
 'use strict';
 const _ = require('lodash');
+const chalk = require('chalk');
 const Base = require('yeoman-generator');
 const {writeTemplates, patchPackageJSON, stringifyAble, useDevVersion} = require('../../utils');
 const fs = require('fs');
@@ -109,8 +110,6 @@ class Generator extends Base {
     }
     this.composeWith('phovea:_node', {
       options: this.options
-    }, {
-      local: require.resolve('../_node')
     });
   }
 
@@ -134,9 +133,10 @@ class Generator extends Base {
     });
     this.fs.copy(this.templatePath('_gitignore'), this.destinationPath('.gitignore'));
     writeTemplates.call(this, config);
-    // don't overwrite existing registry file
-    if (!fs.existsSync(this.destinationPath('phovea.js'))) {
-      this.fs.copyTpl(this.templatePath('phovea.tmpl.js'), this.destinationPath('phovea.js'), stringifyAble(config));
+
+    // do not overwrite existing registry file
+    if (!fs.existsSync(this.destinationPath('src/phovea.ts'))) {
+      this.fs.copyTpl(this.templatePath('phovea.tmpl.ts'), this.destinationPath('src/phovea.ts'), stringifyAble(config));
     }
   }
 
@@ -147,6 +147,16 @@ class Generator extends Base {
       });
     }
   }
+
+  end() {
+    if(fs.existsSync(this.destinationPath('phovea.js'))) {
+      this.log('\r\n');
+      this.log(chalk.red(`ACTION REQUIRED!`));
+      this.log(chalk.default(`Please migrate the content of`), chalk.yellow(`phovea.js`), chalk.default(`to`), chalk.yellow(`/src/phovea.ts`) + chalk.default(` now!`));
+      this.log(chalk.default(`Afterwards you can remove the`), chalk.yellow(`phovea.js`), chalk.default(`file from this plugin repository.`));
+      this.log(chalk.default(`If you do not migrate the content the registered extension points will be unavailable.`));
+    }
+  }
 }
 
 module.exports = Generator;

generators/_init-web/templates/package.tmpl.json

@@ -16,9 +16,9 @@
     "docs": "typedoc --options typedoc.json src/",
     "prebuild": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test",
     "pretest": "npm run compile",
-    "test": "test ! -d tests || karma start",
+    "test": "jest",
     "posttest": "npm run lint",
-    "test:watch": "karma start --autoWatch=true --singleRun=false",
+    "test:watch": "jest --watch",
     "build:dev": "webpack",
     "build": "webpack --env prod",
     "start": "webpack-dev-server --inline",
@@ -31,26 +31,21 @@
     "dist": "mkdir dist && cd build && tar cvzf ../dist/<%-name%>.tar.gz *"
   },
   "devDependencies": {
-    "@types/jasmine": "2.5.47",
+    "@types/jest": "24.9.1",
     "awesome-typescript-loader": "3.1.2",
     "cache-loader": "1.2.0",
     "css-loader": "0.28.0",
     "extract-text-webpack-plugin": "2.1.0",
     "extract-loader": "0.1.0",
+    "identity-obj-proxy": "^3.0.0",
     "ifdef-loader": "2.0.0",
     "file-loader": "0.11.1",
     "fork-ts-checker-webpack-plugin": "0.4.4",
     "html-loader": "0.4.5",
     "imports-loader": "0.7.1",
-    "jasmine": "2.5.3",
+    "jest": "24.9.0",
+    "jest-raw-loader": "1.0.1",
     "json-loader": "0.5.4",
-    "karma": "1.5.0",
-    "karma-chrome-launcher": "2.0.0",
-    "karma-firefox-launcher": "1.0.1",
-    "karma-jasmine": "1.1.0",
-    "karma-junit-reporter": "2.0.0",
-    "karma-sourcemap-loader": "0.3.7",
-    "karma-webpack": "2.0.3",
     "node-sass": "^4.13.1",
     "null-loader": "0.1.1",
     "raw-loader": "0.5.1",
@@ -60,6 +55,7 @@
     "ts-loader": "4.0.1",
     "tslib": "~1.11.0",
     "tslint": "5.9.1",
+    "ts-jest": "24.3.0",
     "typedoc": "~0.16.10",
     "typescript": "~3.8.2",
     "url-loader": "0.5.8",

generators/_init-web/templates/phovea.tmpl.js

@@ -0,0 +1,18 @@
+/* *****************************************************************************
+ * Caleydo - Visualization for Molecular Biology - http://caleydo.org
+ * Copyright (c) The Caleydo Team. All rights reserved.
+ * Licensed under the new BSD license, available at http://caleydo.org/license
+ **************************************************************************** */
+
+import {IRegistry} from 'phovea_core/src/plugin';
+
+export default function (registry: IRegistry) {
+  /// #if include('extension-type', 'extension-id')
+  // registry.push('extension-type', 'extension-id', () => System.import('./extension_impl'), {});
+  /// #endif
+
+  // generator-phovea:begin
+  <%- extensions.map((d) => `   registry.push('${d.type}', '${d.id}', () => System.import('./src/${d.module}'), ${stringify(d.extras, ' ')});`).join('\n\n') %>
+  // generator-phovea:end
+}
+

generators/_init-web/templates/phovea.tmpl.ts

@@ -0,0 +1,56 @@
+// test dependencies that require transformation
+let pluginsToTransform = [
+  'tdp_*',
+  'phovea_*',
+  'lineupjs'
+].join('|');
+
+if(pluginsToTransform.length > 0) {
+ /**  Attention: Negative Lookahead! This regex adds the specified repos to a whitelist that holds plugins that are excluded from the transformIgnorePatterns.
+  * This means that pluginsToTransform should contain all repos that export ts files. They can only be handled by the transformation. */
+    pluginsToTransform = `(?!${pluginsToTransform})`;
+}
+
+/**
+ * TODO check if we can process inline webpack loaders (e.g. as found in https://github.com/phovea/phovea_ui/blob/master/src/_bootstrap.ts)
+ * see also https://jestjs.io/docs/en/webpack#mocking-css-modules
+ */
+module.exports = {
+  transform: {
+    "^.+\\.tsx?$": "ts-jest",
+    "\\.xml$": "jest-raw-loader"
+  },
+  testRegex: "(.*(test|spec))\\.(tsx?)$",
+  moduleFileExtensions: [
+    "ts",
+    "tsx",
+    "js",
+    "jsx",
+    "json",
+    "node"
+  ],
+  testURL: "http://localhost",
+  modulePaths: [
+    "src",
+    "../node_modules",
+    "../"
+  ],
+  transformIgnorePatterns: [`../node_modules/${pluginsToTransform}`, `node_modules/${pluginsToTransform}`],
+  globals: {
+    "__VERSION__": "TEST_VERSION",
+    "__APP_CONTEXT__": "TEST_CONTEXT",
+    'ts-jest': {
+      // has to be set to true, otherwise i18n import fails
+      "tsConfig": {
+        "esModuleInterop": true,
+      }
+    }
+  },
+  moduleNameMapper: {
+    "^.+\\.(css|less|scss|sass|png|jpg|gif)$": "identity-obj-proxy",
+    "imports-loader?.*": "imports-loader",
+    "raw-loader?.*": "raw-loader",
+    "file-loader?.*": "file-loader",
+    "script-loader?.*": "script-loader"
+  }
+}

generators/_init-web/templates/plain/jest.config.js

@@ -24,6 +24,10 @@ declare module "*.html" {
   const content:string;
   export default content;
 }
+declare module "*.xml" {
+  const content:string;
+  export default content;
+}
 //allow json dependencies
 declare module "*.json";
 //allow file dependencies