Merge pull request #1 from galaxyproject/dev

Staying up to date with galaxy dev

.ci/flake8_wrapper.sh

@@ -5,4 +5,4 @@ set -e
 flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` .
 
 # Apply stricter rules for the directories shared with Pulsar
-flake8 --ignore= --max-line-length=150 lib/galaxy/jobs/runners/util/ lib/pulsar/
+flake8 --ignore= --max-line-length=150 lib/galaxy/jobs/runners/util/

.ci/py3_sources.txt

@@ -1,6 +1,6 @@
 lib/galaxy/util/
 lib/galaxy/jobs/runners/util/
-lib/pulsar/
+lib/galaxy/tools/cwl/
 lib/galaxy/tools/parser/
 lib/galaxy/tools/lint.py
 lib/galaxy/tools/lint_util.py

.gitignore

@@ -14,6 +14,7 @@ database/citations
 database/community_files
 database/compiled_templates
 database/files
+database/jobs_directory
 database/job_working_directory
 database/pbs
 database/tmp
@@ -64,6 +65,8 @@ object_store_conf.xml
 job_metrics_conf.xml
 workflow_schedulers_conf.xml
 config/*
+config/plugins/interactive_environments/**/*.ini
+!config/plugins
 static/welcome.html.*
 static/welcome.html
 

CONTRIBUTORS.md

@@ -11,6 +11,7 @@ The following individuals have contributed code to Galaxy:
 * Finn Bacall <finn.bacall@cs.man.ac.uk>
 * Dannon Baker <dannon.baker@gmail.com>
 * Christopher Bare <christopherbare@gmail.com>
+* Marius van den Beek <m.vandenbeek@gmail.com>
 * Dan Blanchard <dan.blanchard@gmail.com>
 * Daniel Blankenberg <dan.blankenberg@gmail.com> <dan@bx.psu.edu>
 * James Boocock <sfk2001@gmail.com>
@@ -19,6 +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>
+* Freek de Bruijn <freek.de.bruijn@nbic.nl>
 * Richard Burhans <burhans@bx.psu.edu>
 * Jennifer Cabral <jencabral@gmail.com>
 * Martin Čech <marten@bx.psu.edu>
@@ -42,14 +44,16 @@ The following individuals have contributed code to Galaxy:
 * Eric Enns <eric.enns@gmail.com>
 * Dorine Francheteau <dorine@bx.psu.edu>
 * Jaime Frey <jfrey@cs.wisc.edu>
-* Carie Genote <cganote@iu.edu>
+* Carrie Ganote <cganote@iu.edu>
 * Jeremy Goecks <jeremy.goecks@emory.edu> <jgoecks@gwu.edu>
 * Nuwan Goonasekera <nuwan.goonasekera@gmail.com>
 * Björn Grüning <bjoern.gruening@gmail.com> <bjoern@gruenings.eu>
 * Aysam Guerler <aysam.guerler@gmail.com>
 * Simon Guest <simon.guest@agresearch.co.nz>
 * Jianbin He <jbhe@bx.psu.edu>
+* Peter van Heusden <pvh@sanbi.ac.za>
 * Morita Hideyuki <h-morita@esm.co.jp>
+* Saskia Hiltemann <zazkia@gmail.com>
 * Rob Hooft <rob.hooft@nbic.nl>
 * Y. Hoogstrate <y.hoogstrate@erasmusmc.nl>
 * Jian-Long Huang <jlh@pyhub.org>
@@ -101,9 +105,6 @@ The following individuals have contributed code to Galaxy:
 * Andrew Warren <anwarren@vbi.vt.edu>
 * Trevor Wennblom <trevor@well.com>
 * Yi Zhang <yizhang@bx.psu.edu>
-* Freek de Bruijn <freek.de.bruijn@nbic.nl>
-* Peter van Heusden <pvh@sanbi.ac.za>
-* Marius van den Beek <m.vandenbeek@gmail.com>
 
 # Institutional sponsors
 

Makefile

@@ -5,12 +5,56 @@ 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-ensure-upstream: ## Ensure upstream branch for release commands setup
+	if [ ! `git remote -v | grep -q $(RELEASE_UPSTREAM)` ]; then git remote add $(RELEASE_UPSTREAM) git@github.com:galaxyproject/galaxy.git; fi
+
+release-merge-stable-to-next: release-ensure-upstream ## Merge last release into dev
+	git fetch $(RELEASE_UPSTREAM) && git checkout dev && git merge --ff-only $(RELEASE_UPSTREAM)/dev && git merge $(RELEASE_UPSTREAM)/$(RELEASE_PREVIOUS)
+
+release-push-dev: release-ensure-upstream # Push local dev branch upstream
+	git push $(RELEASE_UPSTREAM) dev
+
+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 +66,7 @@ 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
@@ -35,13 +79,13 @@ clean-grunt-docker-image: ## Remove grunt docker image
 
 
 # Release Targets
-create_release_rc: ## 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 pull --ff-only $(RELEASE_UPSTREAM) dev
 	git push origin dev
 	git checkout -b release_$(RELEASE_CURR)
 	git push origin release_$(RELEASE_CURR)
-	git push ${RELEASE_UPSTREAM} release_$(RELEASE_CURR)
+	git 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
@@ -62,8 +106,11 @@ create_release_rc: ## Create a release-candidate branch
 	git push origin 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: ## Create a release branch
+create_release: release-ensure-upstream ## Create a release branch
 	git pull --ff-only $(RELEASE_UPSTREAM) master
 	git push origin master
 	git checkout release_$(RELEASE_CURR)

README.rst

@@ -56,3 +56,8 @@ Issues and Galaxy Development
 =============================
 
 Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .
+
+Roadmap
+=============================
+
+Interested in the next steps for Galaxy? Take a look here: https://github.com/galaxyproject/galaxy/issues/1928

client/README.md

@@ -91,13 +91,15 @@ Grunt can also do an automatic, partial rebuild of any files you change *as you
 
 1. opening a new terminal session
 2. `cd client`
-3. `grunt watch`
+3. Watch with:
+    1. `grunt watch` to watch the *scripts/* folder
+    2. `grunt watch-style` to watch the *style/* folder
 
-This starts a new grunt watch process that will monitor the files in `client/galaxy/scripts` for changes and copy and
-pack them when they change.
+This starts a new grunt watch process that will monitor the files, in the corresponding folder, for changes and copy and
+rebuild them when they change.
 
-You can stop the `grunt watch` task by pressing `Ctrl+C`. Note: you should also be able to background that task if you
-prefer.
+You can stop the watch task by pressing `Ctrl+C`. Note: you should also be able to background that task
+if you prefer.
 
 
 Using a Locally Installed Version of Grunt

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'
             }]
         });
@@ -97,7 +93,12 @@ var Collection = Backbone.Collection.extend({
                     title   : 'Saved Visualizations',
                     url     : 'visualization/list',
                     target  : '_frame'
-            }]
+                },{
+                    title   : 'Interactive Environments',
+                    url     : 'visualization/gie_list',
+                    target  : 'galaxy_main'
+                }
+            ]
         });
 
         //
@@ -274,7 +275,7 @@ var Tab = Backbone.View.extend({
         this.$toggle.html( this.model.get( 'title' ) || '' )
                     .removeClass().addClass( 'dropdown-toggle' )
                     .addClass( this.model.get( 'cls' ) )
-                    .addClass( this.model.get( 'icon' ) && 'fa fa-2x ' + this.model.get( 'icon' ) )
+                    .addClass( this.model.get( 'icon' ) && 'dropdown-icon fa ' + this.model.get( 'icon' ) )
                     .addClass( this.model.get( 'toggle' ) && 'toggle' )
                     .attr( 'target', this.model.get( 'target' ) )
                     .attr( 'href', this.model.get( 'url' ) )