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

.ci/first_startup.sh

@@ -0,0 +1,6 @@
+echo "Testing for correct startup:"
+bash run.sh --daemon && sleep 30s && curl -I localhost:8080
+EXIT_CODE=$?
+echo "exit code:$EXIT_CODE, showing startup log:"
+cat paster.log
+exit $EXIT_CODE

.gitignore

@@ -86,12 +86,13 @@ tool-data/genome/*
 tool-data/*.sample
 tool-data/testtoolshed.g2.bx.psu.edu/
 tool-data/toolshed.g2.bx.psu.edu/
-
+tool-data/**/*.fa 
 
 # Test output
 test-data-cache
 run_framework_tests.html
 run_functional_tests.html
+run_toolshed_tests.html
 run_api_tests.html
 test/tool_shed/tmp/*
 .coverage

.travis.yml

@@ -1,15 +1,33 @@
 language: python
 python: 2.7
+os:
+  - linux
 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:
+  include:
+  - os: osx
+    env: TOX_ENV=first_startup
+    language: generic
+  - os: osx
+    env: TOX_ENV=py27-unit
+    language: generic
+
+before_install:
+  - if [ `uname` == "Darwin"  ]; then bash -c "brew update && brew install python"; fi
 
 install:
   - pip install tox
   - if [ "$TOX_ENV" == "qunit" ]; then bash -c 'cd test/qunit && npm install'; fi
+  - if [ "$TOX_ENV" == "first_startup" ]; then bash -c "bash scripts/common_startup.sh && wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite && mv db_gx_rev_0127.sqlite database/universe.sqlite && bash manage_db.sh -c ./config/galaxy.ini.sample upgrade"; fi
 
 script: tox -e $TOX_ENV
 
+notifications:
+  email: false

Makefile

@@ -1,3 +1,6 @@
+RELEASE_CURR:=16.01
+RELEASE_NEXT:=16.04
+RELEASE_UPSTREAM:=upstream
 GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
 
 all:
@@ -25,3 +28,31 @@ grunt-docker: grunt-docker-image
 
 clean-grunt-docker-image:
 	docker rmi ${GRUNT_DOCKER_NAME}
+
+
+# Release Targets
+create_release_rc:
+	git checkout dev
+	git pull ${RELEASE_UPSTREAM} dev
+	git push origin dev
+	git checkout -b release_$(RELEASE_CURR)
+	git push origin release_$(RELEASE_CURR)
+	git push ${RELEASE_UPSTREAM} release_$(RELEASE_CURR)
+	git checkout -b version-$(RELEASE_CURR)
+	sed -i "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_CURR)\"/" lib/galaxy/version.py
+	sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = \"rc1\"/" lib/galaxy/version.py
+	git add lib/galaxy/version.py
+	git commit -m "Update version to $(RELEASE_CURR).rc1"
+	git checkout dev
+
+	git checkout -b version-$(RELEASE_NEXT).dev
+	sed -i "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_NEXT)\"/" lib/galaxy/version.py
+	git add lib/galaxy/version.py
+	git commit -m "Update version to $(RELEASE_NEXT).dev"
+
+	git merge version-$(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

client/GruntFile.js

@@ -24,5 +24,5 @@ module.exports = function(grunt) {
     // see the sub directory grunt-tasks/ for individual task definitions
     grunt.loadTasks( 'grunt-tasks' );
     // note: 'handlebars' *not* 'templates' since handlebars doesn't call uglify
-    grunt.registerTask( 'default', [ 'check-modules', 'handlebars', 'uglify' ] );
+    grunt.registerTask( 'default', [ 'check-modules', 'uglify', 'webpack' ] );
 };

client/README.md

@@ -46,19 +46,31 @@ This will:
 
 1. compress the files in client/galaxy/scripts and place them in static/scripts
 2. generate source maps and place them in static/maps
+3. rebuild the webpack-based client apps
 
 
-Templates
-=========
+Rebuilding Scripts Only
+=======================
 
-You can change and recompile the templates by using:
+To re-minify all the individual javascript files:
 
-    grunt templates
+    grunt scripts
 
-This will:
 
-1. recompile the templates in client/galaxy/scripts/templates to client/galaxy/scripts/templates/compiled
-2. minify and generate source maps for the compiled templates
+Rebuilding Webpack Apps
+=======================
+
+To rebuild the webpack bundles for apps (compressed for production):
+
+    grunt webpack
+
+To rebuild the apps without compression:
+
+    grunt webpack-dev
+
+To rebuild without compression and watch and rebuild when scripts change:
+
+    grunt webpack-watch
 
 
 Changing Styles/CSS

client/bower.json

@@ -14,6 +14,7 @@
     "underscore": "~1.7.0",
     "backbone": "~1.1.2",
     "bootstrap": "~3.3.2",
+    "bootstrap-tour": "~0.10.2",
     "d3": "~3.5.3",
     "farbtastic": "~2.0.0-alpha.1",
     "toastr": "~2.1.0",
@@ -30,7 +31,6 @@
     "jstree": "~3.0.9",
     "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2",
     "threedubmedia.jquery.event": "*",
-    "handlebars": "~3.0.0",
     "jquery-migrate": "~1.2.1",
     "requirejs": "~2.1.17"
   },

client/galaxy/scripts/apps/analysis.js

@@ -7,7 +7,8 @@ var jQuery = require( 'jquery' ),
     ToolPanel = require( './tool-panel' ),
     HistoryPanel = require( './history-panel' ),
     PAGE = require( 'layout/page' ),
-    ToolForm = require( 'mvc/tool/tool-form' );
+    ToolForm = require( 'mvc/tool/tool-form' ),
+    Tours = require( 'mvc/tours' );
 
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
  *  * has a masthead
@@ -30,7 +31,6 @@ window.app = function app( options, bootstrapped ){
         toolPanel = new ToolPanel({
             el                  : '#left',
             userIsAnonymous     : Galaxy.user.isAnonymous(),
-            spinner_url         : config.spinner_url,
             search_url          : config.search_url,
             toolbox             : config.toolbox,
             toolbox_in_panel    : config.toolbox_in_panel,
@@ -100,6 +100,16 @@ window.app = function app( options, bootstrapped ){
             '(/)' : 'home',
             // TODO: remove annoying 'root' from root urls
             '(/)root*' : 'home',
+            '(/)tours(/:tour_id)' : 'show_tours',
+        },
+
+        show_tours : function( tour_id ){
+            if (tour_id){
+                Tours.giveTour(tour_id);
+            }
+            else{
+                centerPanel.display( new Tours.ToursView() );
+            }
         },
 
         /**  */

client/galaxy/scripts/apps/tool-panel.js

@@ -17,7 +17,6 @@ var ToolPanel = LeftPanel.extend({
 
         // create tool search, tool panel, and tool panel view.
         var tool_search = new Tools.ToolSearch({
-            spinner_url : options.spinner_url,
             search_url  : options.search_url,
             hidden      : false
         });