Changes to build system.

Disable amd when importing external sources so they populate the
namespace as expected.  Otherwise we lose access to them in request
based projects (like jupyter).

I'm pulling in UPNG now to support creation of animated pngs in py3Dmol.

3Dmol/3dmol.js

@@ -657,6 +657,14 @@ $3Dmol.getPropertyRange = function (atomlist, prop) {
 
 //hackish way to work with requirejs - doesn't actually work yet
 //since we don't use the require optimizer to combine modules
+if(typeof(_3dmol_saved_define) !== 'undefined') {
+    /** When pulling in external sources, disable amd to ensure they
+     * populate the global namespace as expected.  Restore it so code
+     * using amd still works. */
+    /*global _3dmol_saved_define, _3dmol_saved_require, define:true, require:true */
+    define = _3dmol_saved_define;
+    require = _3dmol_saved_require;
+}
 if( typeof(define) === 'function' && define.amd) {
     define('$3Dmol',[], function() { return $3Dmol; });
 }

gulpfile.js

@@ -9,7 +9,7 @@ del = require('del');
 jsdoc = require('gulp-jsdoc3');
 
 coresrc = ['3Dmol/3dmol.js','3Dmol/WebGL/math.js','3Dmol/WebGL/shapes.js','3Dmol/WebGL/core.js','3Dmol/WebGL/**.js','3Dmol/**.js','!3Dmol/SurfaceWorker.js','3Dmol/SurfaceWorker.js'];
-extsrc = ['js/mmtf.js','node_modules/pako/dist/pako.js','node_modules/netcdfjs/dist/netcdfjs.js','node_modules/upng-js/UPNG.js'];
+extsrc = ['js/disable_amd.js','js/mmtf.js','node_modules/pako/dist/pako.js','node_modules/netcdfjs/dist/netcdfjs.js','node_modules/upng-js/UPNG.js'];
 uisrc = ['3Dmol/ui/ui.js', '3Dmol/ui/state.js', '3Dmol/ui/icon.js', '3Dmol/ui/form.js', '3Dmol/ui/defaultValues.js'];
 jqsrc = ['node_modules/jquery/dist/jquery.js'];
 
@@ -49,7 +49,8 @@ function check() {
 		    'MMTF': false,
 		    'TextDecoder': false,
 		    'FileReader': false,
-	            'define':false}}))
+	            'define':false,
+		    'require':false}}))
     .pipe(jshint.reporter('default'))
     .pipe(jshint.reporter('fail'));
 }

js/disable_amd.js

@@ -0,0 +1,8 @@
+
+if(typeof define !== 'undefined') {
+  // UPNG checks the existence of require, not define, so need to do both
+  var _3dmol_saved_define = define;
+  var _3dmol_saved_require = require;
+  define = null;
+  require = null;
+}