Updates to address new SharedArrayBuffer requirements.

CHANGELOG.md

 Changes
 =======
 
+1.0.3
+-----
+
+* Due to a recent browser update, web servers hosting Webina must now send the
+  `Cross-Origin-Embedder-Policy: require-corp` and `Cross-Origin-Opener-Policy:
+  same-origin` headers.
+  * Updated `README.md` to explain the need for these new headers.
+  * The webina.zip file now includes a simple Python3 server that provides the
+    required headers, to facilitate testing on users' local machines.
+* Starting with this version, we will no longer generate technical documentation
+  describing the Webina source code. Documentation describing basic usage,
+  compilation, etc. can be found in the `README.md` file.
+
 1.0.2
 -----
 

README.md

-# Webina 1.0.2 #
+# Webina 1.0.3 #
 
 ## Introduction ##
 
@@ -257,15 +257,19 @@ these instructions:
 2. Uncompress the file: `unzip webina.zip`
 3. Change to the new `webina/` directory: `cd webina`
 4. Start a local server.
-   * You can use `Node.js` and `npm`:
-     * `npm install -g http-server`
-     * `http-server`
-   * [With some
-     coding](https://curiousprog.com/2018/10/08/serving-webassembly-files-with-a-development-web-server/),
-     you can also use Python 2.7's built-in server:
-     * `python -m SimpleHTTPServer 8000`
-5. Access the server from your web-browser (e.g., `http://localhost:8000/`,
-   `http://0.0.0.0:8000/`, etc.)
+   * Webina uses `SharedArrayBuffer` to leverage multiple processors, so your
+     server must send the [following
+     headers](https://developer.chrome.com/blog/enabling-shared-array-buffer/): 
+      * `Cross-Origin-Embedder-Policy: require-corp`
+      * `Cross-Origin-Opener-Policy: same-origin`
+   * To simplify testing on users' local machines, the Webina download includes
+     a Python3 web-server script.
+      * The script is named `simple-server.py.txt` (with a `.txt` extension) for
+        security purposes, so first rename it to `simple-server.py`
+        * `mv simple-server.py.txt simple-server.py`
+      * Then run from the command line:
+        * `python3 simple-server.py`
+5. Access the server from your web-browser.
 
 Running Webina on other operating systems (e.g., Windows) should be similar.
 

package.json

 {
     "name": "webina",
-    "version": "1.0.2",
+    "version": "1.0.3",
     "description": "",
     "private": true,
     "scripts": {
@@ -20,7 +20,6 @@
         "css-loader": "^3.5.1",
         "duplicate-package-checker-webpack-plugin": "^3.0.0",
         "file-loader": "^4.3.0",
-        "google-closure-compiler": "^20190929.0.0",
         "html-webpack-plugin": "^3.2.0",
         "jquery": "^3.4.1",
         "mini-css-extract-plugin": "^0.8.2",
@@ -43,6 +42,7 @@
         "bootstrap": "^4.4.1",
         "bootstrap-vue": "^2.11.0",
         "file-saver": "^2.0.2",
+        "google-closure-compiler": "^20210601.0.0",
         "popper.js": "^1.16.1",
         "vue": "^2.6.11"
     }

src/UI/Tabs/VinaExistingOutput.ts

@@ -39,7 +39,7 @@ let methodsFunctions = {
                     val: this.$store.state["crystalContentsExample"]
                 });
 
-                resolve();
+                resolve(undefined);
             }, 100);
         })
 

src/UI/ThreeDMol.ts

@@ -155,7 +155,10 @@ let methodsFunctions = {
                         // console.log(this["type"], "Adding " + typeStr, pdb.length);
                         this[typeStr + "PdbOfLoaded"] = pdb;
 
-                        this["viewer"].removeModel(this[typeStr + "Mol"]);
+                        let prevModel = this[typeStr + "Mol"];
+                        if (prevModel !== undefined) {
+                            this["viewer"].removeModel(prevModel);
+                        }
                         this["viewer"].resize();
 
                         this[typeStr + "Mol"] = this["viewer"].addModel(pdb, "pdb", {"keepH": true});
@@ -562,68 +565,68 @@ let methodsFunctions = {
 let watchFunctions = {
     /**
      * Watch when the receptorContents computed property.
-     * @param  {string} oldReceptorContents  The old value of the property.
      * @param  {string} newReceptorContents  The new value of the property.
+     * @param  {string} oldReceptorContents  The old value of the property.
      * @returns void
      */
-    "receptorContents": function (oldReceptorContents: string, newReceptorContents: string): void {
+    "receptorContents": function (newReceptorContents: string, oldReceptorContents: string): void {
         // The purpose of this is to react when new receptorContents
         // are added.
 
-        let duration: number = (newReceptorContents === "") ? 0 : 500;
+        let duration: number = (oldReceptorContents === "") ? 0 : 500;
         this.modelAdded(duration);
         // this.updateBox();  // So when invalid pdb loaded, can recover with valid pdb.
     },
 
     /**
      * Watch when the ligandContents computed property.
-     * @param  {string} oldLigandContents  The old value of the property.
      * @param  {string} newLigandContents  The new value of the property.
+     * @param  {string} oldLigandContents  The old value of the property.
      * @returns void
      */
-    "ligandContents": function (oldLigandContents: string, newLigandContents: string): void {
+    "ligandContents": function (newLigandContents: string, oldLigandContents: string): void {
         // The purpose of this is to react when new ligandContents are
         // added.
 
-        let duration: number = (newLigandContents === "") ? 0 : 500;
+        let duration: number = (oldLigandContents === "") ? 0 : 500;
         this.modelAdded(duration);
     },
 
     /**
      * Watch when the dockedContents computed property.
-     * @param  {string} oldDockedContents  The old value of the property.
      * @param  {string} newDockedContents  The new value of the property.
+     * @param  {string} oldDockedContents  The old value of the property.
      * @returns void
      */
-    "dockedContents": function (oldDockedContents: string, newDockedContents: string): void {
+    "dockedContents": function (newDockedContents: string, oldDockedContents: string): void {
         // The purpose of this is to react when new dockedContents are
         // added.
 
-        let duration: number = (newDockedContents === "") ? 0 : 500;
+        let duration: number = (oldDockedContents === "") ? 0 : 500;
         this.modelAdded(duration);
     },
 
     /**
      * Watch when the crystalContents computed property.
-     * @param  {string} oldCrystalContents  The old value of the property.
      * @param  {string} newCrystalContents  The new value of the property.
+     * @param  {string} oldCrystalContents  The old value of the property.
      * @returns void
      */
-    "crystalContents": function (oldCrystalContents: string, newCrystalContents: string): void {
+    "crystalContents": function (newCrystalContents: string, oldCrystalContents: string): void {
         // The purpose of this is to react when new dockedContents are
         // added.
 
-        let duration: number = (newCrystalContents === "") ? 0 : 500;
+        let duration: number = (oldCrystalContents === "") ? 0 : 500;
         this.modelAdded(duration);
     },
 
     /**
      * Watch when the vinaParams computed property.
-     * @param  {string} oldVinaParams  The old value of the property.
      * @param  {string} newVinaParams  The new value of the property.
+     * @param  {string} oldVinaParams  The old value of the property.
      * @returns void
      */
-    vinaParams(oldVinaParams: string, newVinaParams: string): void {
+    vinaParams(newVinaParams: string, oldVinaParams: string): void {
         // For updating the docking box...
         if (this["type"] !== "receptor") {
             return;

src/Utils.ts

@@ -67,6 +67,7 @@ export function curPath(): string {
     }
     return url;
 }
+
 /**
  * Given a filename, replace its extension.
  * @param  {string} filename  The original filename.

src/Version.ts

@@ -2,4 +2,4 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-export let VERSION = "1.0.2";
+export let VERSION = "1.0.3";

src/index.ts

@@ -6,11 +6,10 @@
 import * as UI from "./UI/UI";
 import * as VueSetup from "./Vue/Setup";
 import { VERSION } from "./Version";
+declare var ga;
 
 console.log("Webina Web App " + VERSION);
 
-declare var ga;
-
 VueSetup.setup();
 UI.setup();
 

utils/build/after_build.sh

@@ -44,13 +44,16 @@ ls app.*js | awk '{print "cat t > " $1 ".tmp; cat " $1 " >> " $1 ".tmp; mv " $1
 rm t
 cd -
 
+# Copy simple python server.
+cp ./utils/simple-server.py ./dist/simple-server.py.txt
+
 # Also create a ZIP file of the dist directory, for convenient distribution.
 mv dist webina
 zip -r webina.zip webina
 mv webina dist
 
 # Build the docs while you're at it.
-. utils/build/make_docs.sh
+# . utils/build/make_docs.sh
 
 # Let the user know that compilation is finished. Works only on macOS.
 say "Beep"

utils/build/make_docs.sh

 rm -rf technical_docs
-typedoc --out technical_docs --exclude "**/*.js" --ignoreCompilerErrors --mode modules --hideGenerator src
+# typedoc --out technical_docs --exclude "**/*.js" --ignoreCompilerErrors --mode modules --hideGenerator src
+
+# typedoc \
+#     --exclude "**/*.old" --exclude "**/*.js" --out technical_docs \
+#     --categorizeByGroup --hideGenerator --excludePrivate --excludeProtected --theme minimal \
+#     --sort alphabetical --plugin none \
+#     ../../src/index.ts
+
+cd ../../src/
+
+typedoc \
+    --exclude "**/*.old" --exclude "**/*.js" --out technical_docs \
+    --categorizeByGroup --hideGenerator --theme minimal \
+    --sort alphabetical --plugin none \
+    --moduleResolution node \
+    ./
+
+
+    # --entryPoints ../../src/index.ts
+
+    # --entryPoints $(find ../../src/ -name "*.ts" | awk '{print $1}' | grep -v "\.old" | grep -v "\.d\.ts" | awk '{printf $1 " "}') \
+# --readme ../../USAGE.md
\ No newline at end of file