Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 237ecc77898f90d8d2d5d95741ff6fbaecc9e936
https://github.com/galaxyproject/galaxy/commit/237ecc77898f90d8d2d5d95741ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-template.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-template.js
M static/style/blue/base.css
Log Message:
-----------
Add form help class
Commit: ddc2a12eb18e036e2e5cad072eb4ea99328ec7b2
https://github.com/galaxyproject/galaxy/commit/ddc2a12eb18e036e2e5cad072eb4…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-template.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-template.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #1428 from guerler/add_pseudo_class_000
Add form help class
Compare: https://github.com/galaxyproject/galaxy/compare/8bd293683bd2...ddc2a12eb18e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c416426522c7cf8f684f12937a42354abd4ce875
https://github.com/galaxyproject/galaxy/commit/c416426522c7cf8f684f12937a42…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
Log Message:
-----------
Remove dup NiceConfigParser from loadwsgi.py.
We are really adopting pastescript as our own.
Commit: 39f5c5d207f091f214b87d391a5aefb47402b9fc
https://github.com/galaxyproject/galaxy/commit/39f5c5d207f091f214b87d391a5a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Make docutils an optional dependency of galaxy-lib.
Commit: 951b95e07964885e2fac88b685f498aca2f3e7fc
https://github.com/galaxyproject/galaxy/commit/951b95e07964885e2fac88b685f4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/util/multi_byte.py
Log Message:
-----------
Make wchartype an optional dependency of galaxy-lib.
Commit: 8bd293683bd2144a877ec7206c003d52892c5796
https://github.com/galaxyproject/galaxy/commit/8bd293683bd2144a877ec7206c00…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/multi_byte.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
Log Message:
-----------
Merge pull request #1427 from jmchilton/lib-deps
Revise galaxy-lib dependencies.
Compare: https://github.com/galaxyproject/galaxy/compare/0bad80ebdf2a...8bd293683bd2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0203a69d88c854c1fe3a210c83ff3ee0d943f4df
https://github.com/galaxyproject/galaxy/commit/0203a69d88c854c1fe3a210c83ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/bower.json
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
A client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/grunt-tasks/install-libs.js
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/tours/__init__.py
A lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/buildapp.py
A static/maps/galaxy.menu.js.map
M static/maps/layout/menu.js.map
A static/maps/libs/bootstrap-tour.js.map
A static/maps/mvc/tours.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/galaxy.menu.js
M static/scripts/layout/menu.js
A static/scripts/libs/bootstrap-tour.js
A static/scripts/mvc/tours.js
M static/scripts/mvc/upload/upload-button.js
M static/style/blue/base.css
A static/style/blue/bootstrap-tour.css
M templates/base.mako
M templates/base/base_panels.mako
Log Message:
-----------
Tours.
Commit: 40382fb0c1d7ec38252413aa50b3cb24418d158e
https://github.com/galaxyproject/galaxy/commit/40382fb0c1d7ec38252413aa50b3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
A config/plugins/tours/galaxy_ui.yaml
Log Message:
-----------
Add slightly modified intro tour from bjoern, mostly compatible.
Commit: f107b17928bddbe4f87e757f2301d56b807253cf
https://github.com/galaxyproject/galaxy/commit/f107b17928bddbe4f87e757f2301…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/tours.js
M client/webpack.config.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Refactor a bit, adjust textinsert action to trigger 'change' on the element.
Commit: 1e5640163a36c12e5f9e719358a1653a0fb18401
https://github.com/galaxyproject/galaxy/commit/1e5640163a36c12e5f9e719358a1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M static/maps/mvc/tours.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Tour shim in onload, check sessionStorage (or would local be more appropriate?)
Commit: 7110a0cc5e411062b8c6e5857e04ce10f121ffdd
https://github.com/galaxyproject/galaxy/commit/7110a0cc5e411062b8c6e5857e04…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Document necessary tweak.
Commit: 9e7eaaa7aaf9c9a6928edc08abecbc26a3a76004
https://github.com/galaxyproject/galaxy/commit/9e7eaaa7aaf9c9a6928edc08abec…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M static/maps/mvc/tours.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Finish sessionStorage and restart of tours across multiple pages.
Commit: 5a3524245b41f2978b81ee01176dcf1caa382d50
https://github.com/galaxyproject/galaxy/commit/5a3524245b41f2978b81ee01176d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M static/maps/mvc/tours.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Actually let people end a tour.
Commit: ffede653023a49aabcfcc958816b20e0e183a4ba
https://github.com/galaxyproject/galaxy/commit/ffede653023a49aabcfcc958816b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Debugging cruft.
Commit: 8c1beb2af5633660efc8ec7caaa871416f2508ea
https://github.com/galaxyproject/galaxy/commit/8c1beb2af5633660efc8ec7caaa8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M config/plugins/tours/galaxy_ui.yaml
M lib/galaxy/tours/__init__.py
M static/maps/mvc/tours.js.map
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
title override, working on fixing style.
Commit: 4efa8e73b3479f3914b6b54d6a8bc4651aec7ef4
https://github.com/galaxyproject/galaxy/commit/4efa8e73b3479f3914b6b54d6a8b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M config/plugins/tours/galaxy_ui.yaml
M lib/galaxy/tours/__init__.py
M static/maps/mvc/tours.js.map
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Consolidate to standard options dict, minor refactorings.
Commit: 38b3c6e97aa0d6fe595be0f6e9021109ddd17226
https://github.com/galaxyproject/galaxy/commit/38b3c6e97aa0d6fe595be0f6e902…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Build client, bundle.
Commit: 9b14d515db16d3a769532740a9b807b37a1177bd
https://github.com/galaxyproject/galaxy/commit/9b14d515db16d3a769532740a9b8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M static/style/blue/bootstrap-tour.css
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Stylize!
Commit: e8116b8bbf22373ae8e784e83cf55426fd5b60bc
https://github.com/galaxyproject/galaxy/commit/e8116b8bbf22373ae8e784e83cf5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M static/style/blue/base.css
Log Message:
-----------
Flip global vars back, now that bootstrap-tours.css is included and will override.
Commit: aecc5d864f8e211c6f60ea8717f726c5807a1a76
https://github.com/galaxyproject/galaxy/commit/aecc5d864f8e211c6f60ea8717f7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M config/plugins/tours/galaxy_ui.yaml
M static/maps/mvc/tours.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Make tours.js safe (but possibly not functional wrt/ listing) to use on pages without Galaxy object.
Commit: 2c5241dc3bba2114b43fe7f7e6e2efb17b705a28
https://github.com/galaxyproject/galaxy/commit/2c5241dc3bba2114b43fe7f7e6e2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Full client rebuild.
Commit: e325eba37c159e78a20895edbd6d521657f9b650
https://github.com/galaxyproject/galaxy/commit/e325eba37c159e78a20895edbd6d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-21 (Mon, 21 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M config/plugins/tours/galaxy_ui.yaml
M lib/galaxy/tours/__init__.py
M lib/galaxy/webapps/galaxy/api/tours.py
M static/maps/mvc/tours.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Some tweaks care of @bgruening. This adds (slightly tweaked) functionality to support a series of clicks, still needs a delay between clicks, and since it's the most common case that pre/postclick will be a single item, a list shouldn't be required here.
Commit: 578e201d64aa33224a586fe7928a8be5b476d332
https://github.com/galaxyproject/galaxy/commit/578e201d64aa33224a586fe7928a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-28 (Mon, 28 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M static/maps/mvc/tours.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Launch tour on GET arg (?tour_id=core.galaxy_ui).
Commit: 4322f5e9b9e152aec75339925228b90ef759b47b
https://github.com/galaxyproject/galaxy/commit/4322f5e9b9e152aec75339925228…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-29 (Tue, 29 Dec 2015)
Changed paths:
A config/plugins/tours/core.galaxy_ui.yaml
R config/plugins/tours/galaxy_ui.yaml
M lib/galaxy/tours/__init__.py
Log Message:
-----------
Force tour_id to be locked to filename, instead of allowing these to be out of sync.
Commit: 401583d730a6d5d1e57c82bb08c3216b40856d8f
https://github.com/galaxyproject/galaxy/commit/401583d730a6d5d1e57c82bb08c3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-12-29 (Tue, 29 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Move TOURS.giveTour at the top level of the namespace instead of a method of the view.
Commit: 603cb2f18dfc1f4518066e514f660f7db91eb45d
https://github.com/galaxyproject/galaxy/commit/603cb2f18dfc1f4518066e514f66…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
A config/plugins/tours/core.history.yaml
Log Message:
-----------
Add history tour from @bgruening
Commit: d23541092070b3dff9ef18a56620fc93837d9233
https://github.com/galaxyproject/galaxy/commit/d23541092070b3dff9ef18a56620…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Remove tour id from tour; unique and namespaced by filename and not a separate identifier.
Commit: e243fe3bc1e66dfcb9de778e66ff99028c56f358
https://github.com/galaxyproject/galaxy/commit/e243fe3bc1e66dfcb9de778e66ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/tours/__init__.py
Log Message:
-----------
Slight refactoring, fix .yaml stripping bug.
Commit: 0ef88e1e5397bc094a4a0f9f9683fdaffab35f48
https://github.com/galaxyproject/galaxy/commit/0ef88e1e5397bc094a4a0f9f9683…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add tour reloading API endpoint.
Commit: b9faf84b245a39780373545f778586bcc9ace916
https://github.com/galaxyproject/galaxy/commit/b9faf84b245a39780373545f7785…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
A test/api/test_tours.py
Log Message:
-----------
Stub an API test for tours so I can refactor a little.
Commit: 01fed4b6d4d473d81fe2e89ee8199b00d0815a00
https://github.com/galaxyproject/galaxy/commit/01fed4b6d4d473d81fe2e89ee819…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/tours/__init__.py
Log Message:
-----------
Allow .yml extensions.
Though not the "official" extension for YAML files, it is actually seen much more common in the wild.
Commit: b35a39bd55d088fa25d2b3999fa482b83055f38a
https://github.com/galaxyproject/galaxy/commit/b35a39bd55d088fa25d2b3999fa4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tours.py
Log Message:
-----------
Prefer self.app to trans.app.
See comments here https://github.com/galaxyproject/galaxy/pull/1392#commitcomment-15141262 for instance for argument why this is superior.
Commit: da8b943f538d55c2d8290870eb19210c831cb627
https://github.com/galaxyproject/galaxy/commit/da8b943f538d55c2d8290870eb19…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/frame.less
R client/galaxy/style/less/masthead.less
M client/galaxy/style/less/ui.less
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
A config/plugins/interactive_environments/jupyter/config/jupyter.xml
A config/plugins/interactive_environments/jupyter/static/js/jupyter.js
A config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/visualizations/charts/templates/charts.mako
M config/tool_conf.xml.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/managers/workflows.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/cwl/__init__.py
A lib/galaxy/tools/cwl/cwltool_deps.py
A lib/galaxy/tools/cwl/parser.py
A lib/galaxy/tools/cwl/representation.py
A lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/__init__.py
A lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
A lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/history_query.py
A lib/galaxy/tools/parameters/wrapped_json.py
A lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
A lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/directory_hash.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/configuration.py
A lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/tool_util.py
M run.sh
M run_tests.sh
M scripts/common_startup.sh
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/onload.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/onload.js
M static/scripts/utils/uploadbox.js
M static/style/blue/base.css
M static/style/blue/masthead.css
M templates/admin/reload_tool.mako
M templates/webapps/galaxy/galaxy.masthead.mako
A test/api/test_workflow_missing_tool.ga
M test/api/test_workflows.py
A test/functional/tools/inputs_as_json.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/test-app.js
A test/qunit/tests/masthead_tests.html
A test/qunit/tests/masthead_tests.js
A test/qunit/tests/modal_tests.html
A test/qunit/tests/modal_tests.js
A test/qunit/tests/popover_tests.html
A test/qunit/tests/popover_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/twilltestcase.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
A test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M tox.ini
Log Message:
-----------
Merge.
Commit: 7587809bb6f08a1ff4754b8d13b8ebfafaabc259
https://github.com/galaxyproject/galaxy/commit/7587809bb6f08a1ff4754b8d13b8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/pluginframework.py
Log Message:
-----------
Improve tour directory logic.
- Refactor plugin framework logic for finding configuration directories out into util.
- Rework tours to use the plugin framework logic to parse configuration directories.
- Rework tour logic to allow multiple tour configuration directories.
- Fix up config.ini.sample comments on interactive environments and tours to reflect these changes and include more information like the viz directory does.
Commit: c28d4d01eef483a2c8255f1ac14d636ab60351a7
https://github.com/galaxyproject/galaxy/commit/c28d4d01eef483a2c8255f1ac14d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
Correctly specify default tour location.
Commit: 4ef3e21c954a8bfe5b12758252ffcb5b303445f8
https://github.com/galaxyproject/galaxy/commit/4ef3e21c954a8bfe5b12758252ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Fix onclick handling broken w/ #1407
Commit: 5c765c08715c17c07c1916c8c7a484d8ef71a954
https://github.com/galaxyproject/galaxy/commit/5c765c08715c17c07c1916c8c7a4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Merge branch 'dev' into interactive_tours
Commit: 1d97e4271ef40969bb117e424691418ccecec7a2
https://github.com/galaxyproject/galaxy/commit/1d97e4271ef40969bb117e424691…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Merge dev to include menu/onclick fix.
Commit: 1876ea6bb2565ccaf7f6475f9387e43f91e34bb5
https://github.com/galaxyproject/galaxy/commit/1876ea6bb2565ccaf7f6475f9387…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/webapps/galaxy/api/tours.py
A test/api/test_tours.py
Log Message:
-----------
Merge pull request #8 from jmchilton/interactive_tours
Minor tweaks to interactive tours backend.
Commit: 5924857c2c7e012875b9840811ab22b9d4935cfa
https://github.com/galaxyproject/galaxy/commit/5924857c2c7e012875b9840811ab…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
Fix pre/postclick that got broken somewhere along the way w/ patches&merges.
Commit: 9416e6f3f75513f8e86f741d5c2f322708abdb0b
https://github.com/galaxyproject/galaxy/commit/9416e6f3f75513f8e86f741d5c2f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-frames.js
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-frames.js
Log Message:
-----------
Merge and resolve conflicts, rebuilding.
Commit: 3d1b3f9806007e456ea5f409df5be96b69aabdb7
https://github.com/galaxyproject/galaxy/commit/3d1b3f9806007e456ea5f409df5b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
Log Message:
-----------
How'd that get there?
Commit: a1a549ea67b28679b079f4150cf6ce18bc87dd56
https://github.com/galaxyproject/galaxy/commit/a1a549ea67b28679b079f4150cf6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Re-add identifiers to masthead, new ones for scratchbook (thanks @guerler)
Commit: 6bd854ebe428a69f2e5664448330b8a4b2aafe77
https://github.com/galaxyproject/galaxy/commit/6bd854ebe428a69f2e5664448330…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/bower.json
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
A client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/onload.js
M client/grunt-tasks/install-libs.js
M client/webpack.config.js
M config/galaxy.ini.sample
A config/plugins/tours/core.galaxy_ui.yaml
A config/plugins/tours/core.history.yaml
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/pluginframework.py
A lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/buildapp.py
A static/maps/galaxy.menu.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
A static/maps/libs/bootstrap-tour.js.map
A static/maps/mvc/tours.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/galaxy.menu.js
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bootstrap-tour.js
A static/scripts/mvc/tours.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/onload.js
A static/style/blue/bootstrap-tour.css
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
A test/api/test_tours.py
Log Message:
-----------
Merge pull request #1422 from dannon/interactive_tours
Interactive Tours
Compare: https://github.com/galaxyproject/galaxy/compare/1730c12f8d3b...6bd854ebe428
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 884b1d42db8ca46dc5613e398cc22015a5384935
https://github.com/galaxyproject/galaxy/commit/884b1d42db8ca46dc5613e398cc2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-frames.js
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-frames.js
Log Message:
-----------
Change scratchbook close icon
Commit: 1730c12f8d3ba9d7e32bfbd1625835ab0d7dae53
https://github.com/galaxyproject/galaxy/commit/1730c12f8d3ba9d7e32bfbd16258…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-frames.js
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-frames.js
Log Message:
-----------
Merge pull request #1425 from guerler/fix_close_icon_000
Change scratchbook close icon
Compare: https://github.com/galaxyproject/galaxy/compare/099f1447a666...1730c12f8d3b