Merge branch 'dev' of git://github.com/galaxyproject/galaxy into tool…

…shed_decouple

Makefile

@@ -5,12 +5,47 @@ RELEASE_NEXT:=16.04
 #RELEASE_NEXT_BRANCH:=release_$(RELEASE_NEXT)
 RELEASE_NEXT_BRANCH:=dev
 RELEASE_UPSTREAM:=upstream
+# Location of virtualenv used for development.
+VENV?=.venv
+# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
+IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+PROJECT_URL?=https://github.com/galaxyproject/galaxy
 GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
 
 all: help
 	@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
 
-npm-deps:
+docs: ## generate Sphinx HTML documentation, including API docs
+	$(IN_VENV) $(MAKE) -C doc clean
+	$(IN_VENV) $(MAKE) -C doc html
+
+_open-docs:
+	open doc/_build/html/index.html || xdg-open doc/_build/html/index.html
+
+open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in browser
+
+open-project: ## open project on github
+	open $(PROJECT_URL) || xdg-open $(PROJECT_URL)
+
+lint: ## check style using tox and flake8 for Python 2 and Python 3
+	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
+
+release-issue: ## Create release issue on github
+	$(IN_VENV) python scripts/bootstrap_history.py --create-release-issue $(RELEASE_CURR)
+
+release-check-metadata: ## check github PR metadata for target release
+	$(IN_VENV) python scripts/bootstrap_history.py --check-release $(RELEASE_CURR)
+
+release-check-blocking-issues: ## Check github for release blocking issues
+	$(IN_VENV) python scripts/bootstrap_history.py --check-blocking-issues $(RELEASE_CURR)
+
+release-check-blocking-prs: ## Check github for release blocking PRs
+	$(IN_VENV) python scripts/bootstrap_history.py --check-blocking-prs $(RELEASE_CURR)
+
+release-bootstrap-history: ## bootstrap history for a new release
+	$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
+
+npm-deps: ## Install NodeJS dependencies.
 	cd client && npm install
 
 grunt: npm-deps ## Calls out to Grunt to build client
@@ -22,7 +57,7 @@ style: npm-deps ## Calls the style task of Grunt
 webpack: npm-deps ## Pack javascript
 	cd client && node_modules/webpack/bin/webpack.js -p
 
-client: grunt style webpack ## Process all client-side tasks
+client: grunt style webpack ## Rebuild all client-side artifacts
 
 grunt-docker-image: ## Build docker image for running grunt
 	docker build -t ${GRUNT_DOCKER_NAME} client
@@ -35,7 +70,7 @@ clean-grunt-docker-image: ## Remove grunt docker image
 
 
 # Release Targets
-create_release_rc: ## Create a release-candidate branch
+release-create-rc: ## Create a release-candidate branch 
 	git checkout dev
 	git pull --ff-only ${RELEASE_UPSTREAM} dev
 	git push origin dev

client/galaxy/scripts/layout/masthead.js

@@ -29,7 +29,6 @@ var View = Backbone.View.extend({
 
         // scratchbook
         Galaxy.frame = this.frame = new Scratchbook( { collection: this.collection } );
-        $( 'body' ).append( this.frame.$el );
 
         // set up the quota meter (And fetch the current user data from trans)
         // add quota meter to masthead

client/galaxy/scripts/layout/menu.js

@@ -41,23 +41,19 @@ var Collection = Backbone.Collection.extend({
             url             : 'library/index',
             tooltip         : 'Access published resources',
             menu            : [{
-                    title   : 'Data Libraries deprecated',
-                    url     : 'library/index'
-                },{
                     title   : 'Data Libraries',
-                    url     : 'library/list',
-                    divider : true
+                    url     : 'library/list'
                 },{
-                    title   : 'Published Histories',
+                    title   : 'Histories',
                     url     : 'history/list_published'
                 },{
-                    title   : 'Published Workflows',
+                    title   : 'Workflows',
                     url     : 'workflow/list_published'
                 },{
-                    title   : 'Published Visualizations',
+                    title   : 'Visualizations',
                     url     : 'visualization/list_published'
                 },{
-                    title   : 'Published Pages',
+                    title   : 'Pages',
                     url     : 'page/list_published'
             }]
         });

client/galaxy/scripts/layout/page.js

@@ -32,7 +32,8 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
         Galaxy.modal = this.modal = new Modal.View();
         this.masthead = new Masthead.View( this.options.config );
         this.$el.attr( 'scroll', 'no' );
-        this.$el.append( this._template() );
+        this.$el.html( this._template() );
+        this.$el.append( this.masthead.frame.$el );
         this.$el.append( this.masthead.$el );
         this.$el.append( this.modal.$el );
         this.$messagebox = this.$( '#messagebox' );
@@ -72,11 +73,11 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
     renderInactivityBox : function() {
         if( this.options.show_inactivity_warning ){
             var content = this.options.inactivity_box_content || '';
-            var verificationLink = $( '<a/>' ).attr( 'href', Galaxy.root + 'user/resend_verification' ).html( 'Resend verification.' );
+            var verificationLink = $( '<a/>' ).attr( 'href', Galaxy.root + 'user/resend_verification' ).text( 'Resend verification' );
             this.$el.addClass( 'has-inactivity-box' );
             this.$inactivebox
-                .html( content )
-                .append( ' ' + verificationLink )
+                .html( content + ' ' )
+                .append( verificationLink )
                 .toggle( !!content )
                 .show();
         } else {
@@ -93,10 +94,14 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
             if( _.has( page, panelId ) ){
                 page[ panelId ].setElement( '#' + panelId );
                 page[ panelId ].render();
-            } else if ( panelId !== 'center' ) {
-                page.center.$el.css( panelId, 0 );
             }
         });
+        if( !this.left ){
+            this.center.$el.css( 'left', 0 );
+        }
+        if( !this.right ){
+            this.center.$el.css( 'right', 0 );
+        }
         return this;
     },
 
@@ -106,27 +111,26 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
             '<div id="everything">',
                 '<div id="background"/>',
                 '<div id="messagebox"/>',
-                '<div id="inactivebox" class="panel-warning-message"/>',
-                '<div id="left"/>',
-                '<div id="center" class="inbound"/>',
-                '<div id="right"/>',
+                '<div id="inactivebox" class="panel-warning-message" />',
+                this.left?   '<div id="left" />' : '',
+                this.center? '<div id="center" class="inbound" />' : '',
+                this.right?  '<div id="right" />' : '',
             '</div>',
-            '<div id="dd-helper"/>',
-            '<noscript>',
-                '<div class="overlay overlay-background noscript-overlay">',
-                    '<div>',
-                        '<h3 class="title">Javascript Required for Galaxy</h3>',
-                        '<div>',
-                            'The Galaxy analysis interface requires a browser with Javascript enabled.<br>',
-                            'Please enable Javascript and refresh this page',
-                        '</div>',
-                    '</div>',
-                '</div>',
-            '</noscript>'
+            '<div id="dd-helper" />',
         ].join('');
     },
 
-    toString : function() { return 'PageLayoutView' }
+    /** hide both side panels if previously shown */
+    hideSidePanels : function(){
+        if( this.left ){
+            this.left.hide();
+        }
+        if( this.right ){
+            this.right.hide();
+        }
+    },
+
+    toString : function() { return 'PageLayoutView'; }
 });
 
 // ============================================================================