Merge remote-tracking branch 'upstream/dev' into api.batch

.ci/flake8_blacklist.txt

@@ -4,12 +4,3 @@ database/
 doc/patch.py
 doc/source/conf.py
 lib/galaxy/util/jstree.py
-scripts/api/
-scripts/data_libraries/
-scripts/loc_files/
-scripts/microbes/
-scripts/others/
-scripts/scramble/
-scripts/tool_shed/
-scripts/tools/
-scripts/transfer.py

.ci/py3_sources.txt

@@ -12,3 +12,6 @@ lib/galaxy/tools/toolbox/
 lib/galaxy/tools/parser/
 lib/galaxy/jobs/metrics/
 lib/galaxy/objectstore/
+scripts/api/common.py
+scripts/api/display.py
+scripts/api/workflow_execute_parameters.py

.travis.yml

@@ -5,9 +5,7 @@ os:
 env:
   - TOX_ENV=py34-lint
   - TOX_ENV=py27-lint
-  - TOX_ENV=py26-lint
   - TOX_ENV=py27-unit
-  - TOX_ENV=py26-unit
   - TOX_ENV=qunit
   - TOX_ENV=first_startup
 matrix:

Makefile

@@ -1,39 +1,43 @@
 RELEASE_CURR:=16.01
+RELEASE_CURR_MINOR_NEXT:=$(shell expr `awk '$$1 == "VERSION_MINOR" {print $$NF}' lib/galaxy/version.py | tr -d \" | sed 's/None/0/;s/dev/0/;' ` + 1)
 RELEASE_NEXT:=16.04
+# TODO: This needs to be updated with create_release_rc
+#RELEASE_NEXT_BRANCH:=release_$(RELEASE_NEXT)
+RELEASE_NEXT_BRANCH:=dev
 RELEASE_UPSTREAM:=upstream
 GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
 
-all:
+all: help
 	@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
 
 npm-deps:
 	cd client && npm install
 
-grunt: npm-deps
+grunt: npm-deps ## Calls out to Grunt to build client
 	cd client && node_modules/grunt-cli/bin/grunt
 
-style: npm-deps
+style: npm-deps ## Calls the style task of Grunt
 	cd client && node_modules/grunt-cli/bin/grunt style
 
-webpack: npm-deps
+webpack: npm-deps ## Pack javascript
 	cd client && node_modules/webpack/bin/webpack.js -p
 
-client: grunt style webpack
+client: grunt style webpack ## Process all client-side tasks
 
-grunt-docker-image:
+grunt-docker-image: ## Build docker image for running grunt
 	docker build -t ${GRUNT_DOCKER_NAME} client
 
-grunt-docker: grunt-docker-image
+grunt-docker: grunt-docker-image ## Run grunt inside docker
 	docker run -it -v `pwd`:/data ${GRUNT_DOCKER_NAME}
 
-clean-grunt-docker-image:
+clean-grunt-docker-image: ## Remove grunt docker image
 	docker rmi ${GRUNT_DOCKER_NAME}
 
 
 # Release Targets
-create_release_rc:
+create_release_rc: ## Create a release-candidate branch
 	git checkout dev
-	git pull ${RELEASE_UPSTREAM} dev
+	git pull --ff-only ${RELEASE_UPSTREAM} dev
 	git push origin dev
 	git checkout -b release_$(RELEASE_CURR)
 	git push origin release_$(RELEASE_CURR)
@@ -50,9 +54,73 @@ create_release_rc:
 	git add lib/galaxy/version.py
 	git commit -m "Update version to $(RELEASE_NEXT).dev"
 
-	git merge version-$(RELEASE_CURR)
+	-git merge version-$(RELEASE_CURR)
 	git checkout --ours lib/galaxy/version.py
 	git add lib/galaxy/version.py
 	git commit -m "Merge branch 'version-$(RELEASE_CURR)' into version-$(RELEASE_NEXT).dev"
 	git push origin version-$(RELEASE_CURR):version-$(RELEASE_CURR)
 	git push origin version-$(RELEASE_NEXT).dev:version-$(RELEASE_NEXT).dev
+	git branch -d version-$(RELEASE_CURR)
+	git branch -d version-$(RELEASE_NEXT).dev
+
+create_release: ## Create a release branch
+	git pull --ff-only $(RELEASE_UPSTREAM) master
+	git push origin master
+	git checkout release_$(RELEASE_CURR)
+	git pull --ff-only $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
+	#git push origin release_$(RELEASE_CURR)
+	git checkout dev
+	git pull --ff-only $(RELEASE_UPSTREAM) dev
+	#git push origin dev
+	# Test run of merging. If there are conflicts, it will fail here here.
+	git merge release_$(RELEASE_CURR)
+	git checkout release_$(RELEASE_CURR)
+	sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = None/" lib/galaxy/version.py
+	git add lib/galaxy/version.py
+	git commit -m "Update version to $(RELEASE_CURR)"
+	git tag -m "Tag version $(RELEASE_CURR)" v$(RELEASE_CURR)
+
+	git checkout dev
+	-git merge release_$(RELEASE_CURR)
+	git checkout --ours lib/galaxy/version.py
+	git add lib/galaxy/version.py
+	git commit -m "Merge branch 'release_$(RELEASE_CURR)' into dev"
+	git checkout master
+	git merge release_$(RELEASE_CURR)
+	#git push origin release_$(RELEASE_CURR):release_$(RELEASE_CURR)
+	#git push origin dev:dev
+	#git push origin master:master
+	#git push origin --tags
+
+create_point_release: ## Create a point release
+	git pull --ff-only $(RELEASE_UPSTREAM) master
+	git push origin master
+	git checkout release_$(RELEASE_CURR)
+	git pull --ff-only $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
+	#git push origin release_$(RELEASE_CURR)
+	git checkout $(RELEASE_NEXT_BRANCH)
+	git pull --ff-only $(RELEASE_UPSTREAM) $(RELEASE_NEXT_BRANCH)
+	#git push origin $(RELEASE_NEXT_BRANCH)
+	git merge release_$(RELEASE_CURR)
+	git checkout release_$(RELEASE_CURR)
+	sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = \"$(RELEASE_CURR_MINOR_NEXT)\"/" lib/galaxy/version.py
+	git add lib/galaxy/version.py
+	git commit -m "Update version to $(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)"
+	git tag -m "Tag version $(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)" v$(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)
+	git checkout $(RELEASE_NEXT_BRANCH)
+	-git merge release_$(RELEASE_CURR)
+	git checkout --ours lib/galaxy/version.py
+	git add lib/galaxy/version.py
+	git commit -m "Merge branch 'release_$(RELEASE_CURR)' into $(RELEASE_NEXT_BRANCH)"
+	git checkout master
+	git merge release_$(RELEASE_CURR)
+	#git push origin release_$(RELEASE_CURR):release_$(RELEASE_CURR)
+	#git push origin $(RELEASE_NEXT_BRANCH):release_$(RELEASE_NEXT_BRANCH)
+	#git push origin master:master
+	#git push origin --tags
+	git checkout release_$(RELEASE_CURR)
+
+.PHONY: help
+
+help:
+	@egrep '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'

client/galaxy/scripts/apps/analysis.js

@@ -100,7 +100,7 @@ window.app = function app( options, bootstrapped ){
             '(/)' : 'home',
             // TODO: remove annoying 'root' from root urls
             '(/)root*' : 'home',
-            '(/)tours(/:tour_id)' : 'show_tours',
+            '(/)tours(/)(:tour_id)' : 'show_tours',
         },
 
         show_tours : function( tour_id ){
@@ -116,9 +116,13 @@ window.app = function app( options, bootstrapped ){
         home : function( params ){
             // TODO: to router, remove Globals
             // load a tool by id (tool_id) or rerun a previous tool execution (job_id)
-            if( ( params.tool_id || params.job_id ) && params.tool_id !== 'upload1' ){
-                this._loadToolForm( params );
-
+            if( params.tool_id || params.job_id ) {
+                if ( params.tool_id === 'upload1' ) {
+                    Galaxy.upload.show();
+                    this._loadCenterIframe( 'welcome' );
+                } else {
+                    this._loadToolForm( params );
+                }
             } else {
                 // show the workflow run form
                 if( params.workflow_id ){

client/galaxy/scripts/galaxy.library.js

@@ -181,7 +181,7 @@ var GalaxyLibrary = Backbone.View.extend({
             if (Galaxy.libraries.datasetView){
                 Galaxy.libraries.datasetView.$el.unbind('click');
             }
-            Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
+            Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_version: false, show_permissions: false});
         });
 
         this.library_router.on( 'route:dataset_version', function(folder_id, dataset_id, ldda_id){

client/galaxy/scripts/layout/masthead.js

@@ -63,7 +63,7 @@ var View = Backbone.View.extend({
     render: function() {
         this.$navbarBrandTitle.html( 'Galaxy ' + ( this.options.brand && '/ ' + this.options.brand || '' ) );
         this.$navbarBrandLink.attr( 'href', this.options.logo_url );
-        this.$navbarBrandImage.attr( 'src', Galaxy.root + 'static/images/galaxyIcon_noText.png' );
+        this.$navbarBrandImage.attr( 'src', this.options.logo_src );
         this.quotaMeter.render();
         return this;
     },
@@ -90,4 +90,4 @@ return {
     View: View
 };
 
-});
+});

client/galaxy/scripts/layout/menu.js

@@ -144,15 +144,15 @@ var Collection = Backbone.Collection.extend({
                     target  : '_blank'
                 },{
                     title   : 'Interactive Tours',
+                    url     : 'tours',
                     onclick : function(){
                         if (Galaxy.app){
                             Galaxy.app.display(new Tours.ToursView());
                         } else {
                             // Redirect and use clientside routing to go to tour index
-                            window.location = Galaxy.root + "#/tours";
+                            window.location = Galaxy.root + "tours";
                         }
-                    },
-                    target  : 'galaxy_main'
+                    }
             }]
         };
         options.terms_url && helpTab.menu.push({

client/galaxy/scripts/layout/scratchbook.js

@@ -156,4 +156,4 @@ return Backbone.View.extend({
     }
 });
 
-});
+});