Merge pull request #2 from galaxyproject/dev

Stays up-to-date with galaxy dev branch

CONTRIBUTORS.md

@@ -20,6 +20,7 @@ The following individuals have contributed code to Galaxy:
 * Dave Bouvier <dave@bx.psu.edu>
 * Adam Brenner <aebrenne@uci.edu>
 * Anthony Bretaudeau <anthony.bretaudeau@rennes.inra.fr> <abretaud@irisa.fr>
+* Christian Y. Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk>
 * Freek de Bruijn <freek.de.bruijn@nbic.nl>
 * Richard Burhans <burhans@bx.psu.edu>
 * Jennifer Cabral <jencabral@gmail.com>
@@ -37,14 +38,19 @@ The following individuals have contributed code to Galaxy:
 * Michael R. Crusoe <crusoe@ucdavis.edu>
 * Gianmauro Cuccuru <gmauro@crs4.it>
 * Frederik Delaere <frederik.delaere@gmail.com>
+* Matthias Desmet <matthias.desmet@ugent.be>
 * Olivia Doppelt <olivia.doppelt@pasteur.fr>
+* Shane Dowling <shane@shanedowling.com>
 * John Duddy <jduddy@illumina.com>
 * Carl Eberhard <carlfeberhard@gmail.com>
+* Mark Einon <mark.einon@gmail.com>
 * Kyle Ellrott <kellrott@gmail.com> <kellrott@soe.ucsc.edu>
 * Eric Enns <eric.enns@gmail.com>
+* fescudie <fescudie@toulouse.inra.fr>
 * Dorine Francheteau <dorine@bx.psu.edu>
 * Jaime Frey <jfrey@cs.wisc.edu>
 * Carrie Ganote <cganote@iu.edu>
+* Ryan Golhar <ngsbioinformatics@gmail.com>
 * Jeremy Goecks <jeremy.goecks@emory.edu> <jgoecks@gwu.edu>
 * Nuwan Goonasekera <nuwan.goonasekera@gmail.com>
 * Björn Grüning <bjoern.gruening@gmail.com> <bjoern@gruenings.eu>
@@ -67,27 +73,35 @@ The following individuals have contributed code to Galaxy:
 * Rory Kirchner <roryk@mit.edu>
 * Brad Langhorst <langhorst@neb.com>
 * Ross Lazarus <ross.lazarus@gmail.com> <rossl@bx.psu.edu>
+* Gildas Le Corguillé @lecorguille
 * Simone Leo <simone.leo@gmail.com>
 * Kanwei Li <kanwei@gmail.com>
 * Michael Li <michael.li@uwaterloo.ca>
+* Mikael Loaec <mikael.loaec@versailles.inra.fr>
 * Philip Mabon <philipmabon@gmail.com>
 * Remi Marenco <remi.marenco@gmail.com> <remimarenco@gmail.com>
+* Zipho Mashologu <zipho@trustpay.biz>
 * Thomas McGowan <mcgo0092@msi.umn.edu>
 * Scott McManus <scottmcmanus@emory.edu> <scottmcmanus@gatech.edu>
 * Hunter Moseley <hunter.moseley@louisville.edu>
+* Takao Nakaguchi <takao.nakaguchi@gmail.com>
 * Arjun Nath <arjun@bx.psu.edu>
 * Anton Nekrutenko <anton@bx.psu.edu> <anton@nekrut.org>
 * Eric Paniagua <paniagua.cshl@gmail.com>
 * Richard Park <rpark@bu.edu>
 * Lance Parsons <lparsons@princeton.edu>
 * Chinmay Rao <chinmay@bx.psu.edu>
+* Matt Ralston <mrals89@gmail.com>
 * Eric Rasche <esr@tamu.edu> <rasche.eric@gmail.com> <rasche.eric@yandex.ru>
 * Andrew Robinson <Andrew.Robinson@latrobe.edu.au>
+* Michael Sauria <crockopotamus@gmail.com>
 * Andrea Sbardellati <andrea.sbardellati@crs4.it>
 * Ian Schenck <ian@bx.psu.edu>
 * Nick Semenkovich <semenko@alum.mit.edu>
 * Matthew Shirley <mdshw5@gmail.com>
+* Sourav Singh <ssouravsingh12@gmail.com>
 * Clare Sloggett <sloc@unimelb.edu.au>
+* Eteri Sokhoyan @Sokhoyan
 * Nicola Soranzo <nicola.soranzo@tgac.ac.uk> <nsoranzo@tiscali.it> <soranzo@crs4.it>
 * Roy Storey <kiwiroy@gmail.com>
 * Hanfei Sun <ad9075@gmail.com>
@@ -97,13 +111,17 @@ The following individuals have contributed code to Galaxy:
 * David Trudgian <dave@trudgian.net> <david.trudgian@utsouthwestern.edu>
 * Nitesh Turaga <nitesh.turaga@gmail.com>
 * Clayton Turner <clayclay911@gmail.com>
+* Jesse c j van Dam <jesse.vandam@wur.nl>
 * Marek Vavruša <marek@vavrusa.com>
 * Martijn Vermaat <m.vermaat.hg@lumc.nl>
 * Kelly Vincent <kpvincent@bx.psu.edu>
 * Greg Von Kuster <greg@bx.psu.edu>
+* Pavan Videm <videmp@informatik.uni-freiburg.de>
 * Hiral Vora <hvora1@uncc.edu>
 * Andrew Warren <anwarren@vbi.vt.edu>
 * Trevor Wennblom <trevor@well.com>
+* Thomas Wollmann <thomas.s.wollmann@gmail.com> <thomas.wollmann@bioquant.uni-heidelberg.de>
+* Jay Young <xiaojay@gmail.com>
 * Yi Zhang <yizhang@bx.psu.edu>
 
 # Institutional sponsors

Makefile

@@ -5,6 +5,7 @@ RELEASE_NEXT:=16.04
 #RELEASE_NEXT_BRANCH:=release_$(RELEASE_NEXT)
 RELEASE_NEXT_BRANCH:=dev
 RELEASE_UPSTREAM:=upstream
+MY_UPSTREAM:=origin
 # Location of virtualenv used for development.
 VENV?=.venv
 # Source virtualenv to execute command (flake8, sphinx, twine, etc...)
@@ -63,10 +64,7 @@ grunt: npm-deps ## Calls out to Grunt to build client
 style: npm-deps ## Calls the style task of Grunt
 	cd client && node_modules/grunt-cli/bin/grunt style
 
-webpack: npm-deps ## Pack javascript
-	cd client && node_modules/webpack/bin/webpack.js -p
-
-client: grunt style webpack ## Rebuild all client-side artifacts
+client: grunt style ## Rebuild all client-side artifacts
 
 grunt-docker-image: ## Build docker image for running grunt
 	docker build -t ${GRUNT_DOCKER_NAME} client
@@ -79,12 +77,12 @@ clean-grunt-docker-image: ## Remove grunt docker image
 
 
 # Release Targets
-release-create-rc: release-ensure-upstream ## Create a release-candidate branch 
+release-create-rc: release-ensure-upstream ## Create a release-candidate branch
 	git checkout dev
 	git pull --ff-only $(RELEASE_UPSTREAM) dev
-	git push origin dev
+	git push $(MY_UPSTREAM) dev
 	git checkout -b release_$(RELEASE_CURR)
-	git push origin release_$(RELEASE_CURR)
+	git push $(MY_UPSTREAM) release_$(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
@@ -102,24 +100,25 @@ release-create-rc: release-ensure-upstream ## Create a release-candidate branch
 	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 push $(MY_UPSTREAM) version-$(RELEASE_CURR):version-$(RELEASE_CURR)
+	git push $(MY_UPSTREAM) version-$(RELEASE_NEXT).dev:version-$(RELEASE_NEXT).dev
 	git branch -d version-$(RELEASE_CURR)
 	git branch -d version-$(RELEASE_NEXT).dev
 	# TODO: Use hub to automate these PR creations or push directly.
 	@echo "Open a PR from version-$(RELEASE_CURR) of your fork to release_$(RELEASE_CURR)"
 	@echo "Open a PR from version-$(RELEASE_NEXT).dev of your fork to dev"
 
-create_release: release-ensure-upstream ## Create a release branch
+release-create: release-ensure-upstream ## Create a release branch
+	git checkout master
 	git pull --ff-only $(RELEASE_UPSTREAM) master
-	git push origin master
+	git push $(MY_UPSTREAM) master
 	git checkout release_$(RELEASE_CURR)
 	git pull --ff-only $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
-	#git push origin release_$(RELEASE_CURR)
+	#git push $(MY_UPSTREAM) release_$(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 push $(MY_UPSTREAM) dev
+	# Test run of merging. If there are conflicts, it will fail here.
 	git merge release_$(RELEASE_CURR)
 	git checkout release_$(RELEASE_CURR)
 	sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = None/" lib/galaxy/version.py
@@ -134,20 +133,20 @@ create_release: release-ensure-upstream ## Create a release branch
 	git commit -m "Merge branch 'release_$(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
+	#git push $(RELEASE_UPSTREAM) release_$(RELEASE_CURR):release_$(RELEASE_CURR)
+	#git push $(RELEASE_UPSTREAM) dev:dev
+	#git push $(RELEASE_UPSTREAM) master:master
+	#git push $(RELEASE_UPSTREAM) --tags
 
-create_point_release: ## Create a point release
+release-create-point: ## Create a point release
 	git pull --ff-only $(RELEASE_UPSTREAM) master
-	git push origin master
+	git push $(MY_UPSTREAM) master
 	git checkout release_$(RELEASE_CURR)
 	git pull --ff-only $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
-	#git push origin release_$(RELEASE_CURR)
+	#git push $(MY_UPSTREAM) release_$(RELEASE_CURR)
 	git checkout $(RELEASE_NEXT_BRANCH)
 	git pull --ff-only $(RELEASE_UPSTREAM) $(RELEASE_NEXT_BRANCH)
-	#git push origin $(RELEASE_NEXT_BRANCH)
+	#git push $(MY_UPSTREAM) $(RELEASE_NEXT_BRANCH)
 	git merge release_$(RELEASE_CURR)
 	git checkout release_$(RELEASE_CURR)
 	sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = \"$(RELEASE_CURR_MINOR_NEXT)\"/" lib/galaxy/version.py

README.rst

@@ -22,7 +22,7 @@ The latest information about Galaxy is available via `https://galaxyproject.org/
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 2.6 or 2.7. To check your python version, run:
+Galaxy requires Python 2.7 To check your python version, run:
 
 .. code:: console
 

client/bower.json

@@ -8,14 +8,14 @@
   ],
   "homepage": "usegalaxy.org",
   "dependencies": {
-    "jquery": "~1.11.1",
+    "jquery": "~1.12",
     "tracekit": "*",
-    "ravenjs": "~1.1.16",
-    "underscore": "~1.7.0",
-    "backbone": "~1.1.2",
+    "ravenjs": "~3",
+    "underscore": "~1",
+    "backbone": "~1.3",
     "bootstrap": "~3.3.2",
     "bootstrap-tour": "~0.10.2",
-    "d3": "~3.5.3",
+    "d3": "~3",
     "farbtastic": "~2.0.0-alpha.1",
     "toastr": "~2.1.0",
     "jQTouch": "git://github.com/senchalabs/jQTouch#~1.0.0",
@@ -31,11 +31,10 @@
     "jstree": "~3.0.9",
     "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2",
     "threedubmedia.jquery.event": "*",
-    "jquery-migrate": "~1.2.1",
-    "requirejs": "~2.1.17"
+    "jquery-migrate": "~1.4",
+    "requirejs": "~2"
   },
   "resolutions": {
-    "jquery": "~1.11.1"
-  },
-  "devDependencies": {}
+    "jquery": "~1.12"
+  }
 }