[galaxy-commits] [galaxyproject/galaxy] 0b8c98: Include database/jobs_directory in gitignore

3 Aug 2016

      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 0b8c984b76d696fcc36ee3bfc76ad8b91e3ea20c
      https://github.com/galaxyproject/galaxy/commit/0b8c984b76d696fcc36ee3bfc76ad...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Include database/jobs_directory in gitignore

  Commit: c6d2c8bf50fdb4d0b0685fabe1be47693cc99fe0
      https://github.com/galaxyproject/galaxy/commit/c6d2c8bf50fdb4d0b0685fabe1be4...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/hdcas.py
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/history_contents.py
    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:
  -----------
  Managers: implement a new view for history serialization to bypass state_counts, state, or state_ids; add create_time and update_time to both summaries of hdas and hdcas; serialize contents for histories using a contents serializer (avoiding hda and hdca serialization and just serializing the results of the union)

  Commit: 0a0edd9788357e3c9fd617f5f8ef64f589e0d9e1
      https://github.com/galaxyproject/galaxy/commit/0a0edd9788357e3c9fd617f5f8ef6...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/controllers/history.py

  Log Message:
  -----------
  History: have controller 'current history' faux-api methods return the 'current' view from the serializer

  Commit: 8d1cd494ce025d5b20c6e3087e3f1f44610254a8
      https://github.com/galaxyproject/galaxy/commit/8d1cd494ce025d5b20c6e3087e3f1...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-view.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/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: extract history preferences to it's own module

  Commit: f395793704015ed2dffafe2584259ef81aa20efd
      https://github.com/galaxyproject/galaxy/commit/f395793704015ed2dffafe2584259...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M static/maps/mvc/history/history-contents.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-contents.js

  Log Message:
  -----------
  UI, history: clean up history contents

  Commit: 0e4118cda67dc00ebb2fbc2ee6cd1fe674555210
      https://github.com/galaxyproject/galaxy/commit/0e4118cda67dc00ebb2fbc2ee6cd1...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M static/maps/mvc/history/history-model.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-model.js

  Log Message:
  -----------
  UI, history: clean up history model

  Commit: c030af5643ff01aa0bad0b6c6fa7bc4b3b47f6c5
      https://github.com/galaxyproject/galaxy/commit/c030af5643ff01aa0bad0b6c6fa7b...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: move to History.fetch for most ajax loading

  Commit: 9102096f4e80580239d46a726d3aa7066806564b
      https://github.com/galaxyproject/galaxy/commit/9102096f4e80580239d46a726d3aa...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-16 (Wed, 16 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: simplify set up of sessionStorage/HistoryPrefs

  Commit: 40a597dfda0474675f68ae391135ae059cc93082
      https://github.com/galaxyproject/galaxy/commit/40a597dfda0474675f68ae391135a...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-17 (Thu, 17 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.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/base-mvc.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js

  Log Message:
  -----------
  UI, history: first pass at paginating history-contents

  Commit: 1465a02790bd41dba9c573d943b9c9c0cd47ada6
      https://github.com/galaxyproject/galaxy/commit/1465a02790bd41dba9c573d943b9c...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-17 (Thu, 17 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M static/maps/mvc/history/history-contents.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-contents.js

  Log Message:
  -----------
  UI, history: fix history-contents comparator

  Commit: 5ed4f74c8deb8a6879d329f7de0a9ab898f98839
      https://github.com/galaxyproject/galaxy/commit/5ed4f74c8deb8a6879d329f7de0a9...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-17 (Thu, 17 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/history/history-contents.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/base-mvc.js
    M static/scripts/mvc/history/history-contents.js

  Log Message:
  -----------
  UI, history: rework fetch options building, have history-contents maintain includeHidden/Deleted

  Commit: 563096e302ded396766478152d71c2028a96cabe
      https://github.com/galaxyproject/galaxy/commit/563096e302ded396766478152d71c...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-17 (Thu, 17 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    A client/galaxy/scripts/mvc/history/history-preferences.js
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    A static/maps/mvc/history/history-preferences.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/base-mvc.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    A static/scripts/mvc/history/history-preferences.js

  Log Message:
  -----------
  UI, history: add missing history-preferences file, separate out controlled fetch collection

  Commit: 3102c4ca68aaacc646309517c2fd65cc14237d34
      https://github.com/galaxyproject/galaxy/commit/3102c4ca68aaacc646309517c2fd6...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-18 (Fri, 18 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/multi-panel.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/base-mvc.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/multi-panel.js
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, history: move order into ControlledFetchCollection

  Commit: fc5debdd3be9a46071762c093afbd2b655ca6ef9
      https://github.com/galaxyproject/galaxy/commit/fc5debdd3be9a46071762c093afbd...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-18 (Fri, 18 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-view.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: fix first search loading indicator on history-view

  Commit: 670484cebcebb49eea8b6fab445cce42d5292002
      https://github.com/galaxyproject/galaxy/commit/670484cebcebb49eea8b6fab445cc...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-18 (Fri, 18 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/list/list-view.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/list/list-view.js

  Log Message:
  -----------
  UI, history: fix current history panel loading indicator

  Commit: 61e4ed51eb275fa979a946d074bb71f51b1ac424
      https://github.com/galaxyproject/galaxy/commit/61e4ed51eb275fa979a946d074bb7...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-18 (Fri, 18 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/list/list-item.js
    M static/maps/mvc/list/list-item.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/list/list-item.js

  Log Message:
  -----------
  UI, history, lists: fix rendered event trigger from list-items

  Commit: 09567db13130bdbd0d7617cd4ff136d29cab1b90
      https://github.com/galaxyproject/galaxy/commit/09567db13130bdbd0d7617cd4ff13...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-21 (Mon, 21 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/list/list-view.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/base-mvc.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: minor cleanup

  Commit: 39f1d62cefede05be1518bd44488b41ee4f10b51
      https://github.com/galaxyproject/galaxy/commit/39f1d62cefede05be1518bd44488b...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-21 (Mon, 21 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.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/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view-edit.js

  Log Message:
  -----------
  UI, history: render counts from model data (instead of views), fix history-contents to filter properly

  Commit: ffbac21753dce1bec667539b3574dd4c3191b6d8
      https://github.com/galaxyproject/galaxy/commit/ffbac21753dce1bec667539b3574d...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-21 (Mon, 21 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/list/list-view.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: fix missing _attachView

  Commit: a0bbbaa918b51cf619303c33d2ad32e87fe3d784
      https://github.com/galaxyproject/galaxy/commit/a0bbbaa918b51cf619303c33d2ad3...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-22 (Tue, 22 Mar 2016)

  Changed paths:
    A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/history/hda-model.js
    M client/galaxy/scripts/mvc/history/hdca-model.js
    M client/galaxy/scripts/mvc/history/history-content-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-structure-view.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    A static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/history/hda-model.js.map
    M static/maps/mvc/history/hdca-model.js.map
    M static/maps/mvc/history/history-content-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-structure-view.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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
    A static/scripts/mvc/base/controlled-fetch-collection.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/history/hda-model.js
    M static/scripts/mvc/history/hdca-model.js
    M static/scripts/mvc/history/history-content-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-structure-view.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: add missing file (controlled-fetch-collection), fix fetchUpdated filters to bypass visible default filter for proper updating during workflows, fetch deleted and hidden via ajax when clicked, cleanup

  Commit: 9af60047f27f2da7f024eeb0a745d6f2bc99a7bc
      https://github.com/galaxyproject/galaxy/commit/9af60047f27f2da7f024eeb0a745d...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-23 (Wed, 23 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, histories: progressively load search details for history contents on first search

  Commit: daa7625542567caf23d4081b7e7c70d6958bed26
      https://github.com/galaxyproject/galaxy/commit/daa7625542567caf23d4081b7e7c7...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-28 (Mon, 28 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-item.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: implement infinite scrolling in all histories

  Commit: d2d066243e02cc3c612069e6015467e462212881
      https://github.com/galaxyproject/galaxy/commit/d2d066243e02cc3c612069e601546...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-28 (Mon, 28 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/hdca-model.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/hdca-model.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/hdca-model.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/list/list-view.js
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/history/view.mako

  Log Message:
  -----------
  UI, history: fix history/view.mako and history/display.mako to order their collections, load contents via ajax, and paginate correctly; Routes: correct history/view to allow history/view to view current history and history/view/{id} for cleaner urls

  Commit: 2a6694dda56ea909a5b3a1fc856c202de46d1750
      https://github.com/galaxyproject/galaxy/commit/2a6694dda56ea909a5b3a1fc856c2...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-29 (Tue, 29 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-view.js
    M templates/webapps/galaxy/history/view.mako
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, multi-history: update history collection to use PaginatedCollection, extract HistoryInnerView; Routes: re-add /history route, correct /history/view route for optional id

  Commit: 040f82a615489aea00040a1e232de5194c6e85d7
      https://github.com/galaxyproject/galaxy/commit/040f82a615489aea00040a1e232de...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-03-30 (Wed, 30 Mar 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  Corrections to search and order change in history/view_multiple

- Load initial histories using ajax instead of bootstrapping.
- Fix rendering after order change.
- Fix 'none found' message when searching datasets.
- Correct fetch filters when including deleted histories.

  Commit: 5dab37c155650e77a04769c04258151fbd22e08e
      https://github.com/galaxyproject/galaxy/commit/5dab37c155650e77a04769c042581...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-01 (Fri, 01 Apr 2016)

  Changed paths:
    M .gitignore
    M Makefile
    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/mvc/form/form-input.js
    M client/galaxy/scripts/mvc/form/form-parameters.js
    R client/galaxy/scripts/mvc/form/form-select-content.js
    M client/galaxy/scripts/mvc/library/library-dataset-view.js
    M client/galaxy/scripts/mvc/library/library-folder-view.js
    M client/galaxy/scripts/mvc/library/library-folderlist-view.js
    M client/galaxy/scripts/mvc/library/library-folderrow-view.js
    M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
    M client/galaxy/scripts/mvc/library/library-library-view.js
    M client/galaxy/scripts/mvc/library/library-librarylist-view.js
    M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
    M client/galaxy/scripts/mvc/library/library-model.js
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    A client/galaxy/scripts/mvc/ui/ui-select-content.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    M client/galaxy/style/less/base.less
    M client/galaxy/style/less/library.less
    M client/galaxy/style/less/ui.less
    M client/galaxy/style/less/upload.less
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/tool_data_table_conf.xml.sample
    M config/tool_shed.ini.sample
    A display_applications/iobio/bam.xml
    A display_applications/iobio/vcf.xml
    M doc/source/releases/index.rst
    M lib/galaxy/config.py
    A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
    A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
    A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
    A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
    A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
    A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
    A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
    A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
    A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
    A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
    A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
    A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
    A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
    A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
    A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
    A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
    A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
    A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
    A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
    A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
    A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
    A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
    A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
    A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
    A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
    A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
    A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
    A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
    M lib/galaxy/datatypes/display_applications/application.py
    A lib/galaxy/datatypes/molecules.py
    M lib/galaxy/datatypes/sniff.py
    A lib/galaxy/datatypes/test/5e5z.pdb
    A lib/galaxy/datatypes/test/drugbank_drugs.cml
    A lib/galaxy/datatypes/test/drugbank_drugs.inchi
    A lib/galaxy/datatypes/test/drugbank_drugs.mol2
    A lib/galaxy/datatypes/test/drugbank_drugs.sdf
    A lib/galaxy/datatypes/test/drugbank_drugs.smi
    A lib/galaxy/datatypes/test/q.fps
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/handler.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/custom_types.py
    A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
    R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py
    M lib/galaxy/model/util.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/evaluation.py
    M lib/galaxy/tools/execute.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/wrapped_json.py
    M lib/galaxy/tools/parser/interface.py
    M lib/galaxy/util/__init__.py
    R lib/galaxy/util/dictobj.py
    M lib/galaxy/util/jstree.py
    M lib/galaxy/util/log/fluent_log.py
    M lib/galaxy/util/object_wrapper.py
    M lib/galaxy/web/framework/base.py
    M lib/galaxy/web/framework/middleware/statsd.py
    M lib/galaxy/webapps/galaxy/api/datasets.py
    M lib/galaxy/webapps/galaxy/api/lda_datasets.py
    M lib/galaxy/webapps/galaxy/api/metrics.py
    M lib/galaxy/webapps/galaxy/api/remote_files.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy/workflow/run.py
    M lib/galaxy/workflow/scheduling_manager.py
    M lib/tool_shed/capsule/capsule_manager.py
    M lib/tool_shed/galaxy_install/dependency_display.py
    M lib/tool_shed/galaxy_install/install_manager.py
    M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
    M lib/tool_shed/galaxy_install/tool_migration_manager.py
    M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
    M lib/tool_shed/galaxy_install/update_repository_manager.py
    M lib/tool_shed/scripts/api/common.py
    M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
    M lib/tool_shed/tool_shed_registry.py
    M lib/tool_shed/util/common_util.py
    M lib/tool_shed/util/readme_util.py
    M lib/tool_shed/util/shed_util_common.py
    M run.sh
    M run_reports.sh
    M run_tests.sh
    M run_tool_shed.sh
    M scripts/bootstrap_history.py
    M scripts/functional_tests.py
    M scripts/summarize_timings.py
    M static/maps/layout/masthead.js.map
    M static/maps/layout/menu.js.map
    M static/maps/layout/page.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    R static/maps/mvc/form/form-select-content.js.map
    M static/maps/mvc/library/library-dataset-view.js.map
    M static/maps/mvc/library/library-folder-view.js.map
    M static/maps/mvc/library/library-folderlist-view.js.map
    M static/maps/mvc/library/library-folderrow-view.js.map
    M static/maps/mvc/library/library-foldertoolbar-view.js.map
    M static/maps/mvc/library/library-library-view.js.map
    M static/maps/mvc/library/library-librarylist-view.js.map
    M static/maps/mvc/library/library-librarytoolbar-view.js.map
    M static/maps/mvc/library/library-model.js.map
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/maps/mvc/tool/tool-form.js.map
    A static/maps/mvc/ui/ui-select-content.js.map
    M static/maps/mvc/ui/ui-select-default.js.map
    M static/maps/utils/utils.js.map
    M static/maps/viz/trackster/tracks.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/layout/masthead.js
    M static/scripts/layout/menu.js
    M static/scripts/layout/page.js
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    R static/scripts/mvc/form/form-select-content.js
    M static/scripts/mvc/library/library-dataset-view.js
    M static/scripts/mvc/library/library-folder-view.js
    M static/scripts/mvc/library/library-folderlist-view.js
    M static/scripts/mvc/library/library-folderrow-view.js
    M static/scripts/mvc/library/library-foldertoolbar-view.js
    M static/scripts/mvc/library/library-library-view.js
    M static/scripts/mvc/library/library-librarylist-view.js
    M static/scripts/mvc/library/library-librarytoolbar-view.js
    M static/scripts/mvc/library/library-model.js
    M static/scripts/mvc/tool/tool-form-base.js
    M static/scripts/mvc/tool/tool-form-workflow.js
    M static/scripts/mvc/tool/tool-form.js
    A static/scripts/mvc/ui/ui-select-content.js
    M static/scripts/mvc/ui/ui-select-default.js
    M static/scripts/utils/utils.js
    M static/scripts/viz/trackster/tracks.js
    M static/style/blue/base.css
    M static/style/blue/library.css
    A templates/admin/tool_shed_repository/browse_categories.mako
    A templates/admin/tool_shed_repository/browse_category.mako
    M templates/admin/tool_shed_repository/initiate_repository_installation.mako
    A templates/admin/tool_shed_repository/preview_repository.mako
    M templates/base/base_panels.mako
    M templates/webapps/galaxy/admin/index.mako
    A templates/webapps/galaxy/admin/toolsheds.mako
    M templates/webapps/galaxy/library/common/library_info.mako
    A test/base/driver_util.py
    M test/base/twilltestcase.py
    R test/functional/test_admin_features.py
    R test/functional/test_data_security.py
    R test/functional/test_dataset_features.py
    R test/functional/test_get_data.py
    R test/functional/test_library_features.py
    R test/functional/test_library_security.py
    R test/functional/test_metadata_editing.py
    R test/functional/test_sample_tracking.py
    R test/functional/test_tags.py
    M test/functional/test_toolbox.py
    R test/functional/test_ucsc_table_browser.py
    R test/functional/test_user_info.py
    M test/functional/tools/collection_creates_list.xml
    A test/functional/tools/for_workflows/create_input_collection.xml
    A test/functional/tools/for_workflows/split.xml
    M test/functional/tools/samples_tool_conf.xml
    A test/functional/tools/upload_tool_conf.xml
    M test/functional/workflow.py
    R test/install_and_test_tool_shed_repositories/__init__.py
    R test/install_and_test_tool_shed_repositories/base/__init__.py
    R test/install_and_test_tool_shed_repositories/base/test_db_util.py
    R test/install_and_test_tool_shed_repositories/base/twilltestcase.py
    R test/install_and_test_tool_shed_repositories/base/util.py
    R test/install_and_test_tool_shed_repositories/functional/__init__.py
    R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
    R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py
    R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
    R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py
    R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
    A test/manual/launch_and_run.sh
    A test/manual/workflow_job_conf.xml
    M test/manual/workflows_scaling.py
    M test/qunit/test-app.js
    A test/qunit/tests/form_tests.html
    A test/qunit/tests/form_tests.js
    A test/qunit/tests/page_tests.html
    A test/qunit/tests/page_tests.js
    M test/qunit/tests/ui_tests.js
    M test/tool_shed/base/twilltestcase.py
    A test/tool_shed/functional/test_0310_hg_api_features.py
    R test/tool_shed/functional/test_0310_hg_push_from_api.py
    M test/tool_shed/functional/test_0490_export_import_repositories.py
    M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
    M test/tool_shed/functional_tests.py
    M test/unit/jobs/test_runner_local.py
    M test/unit/managers/test_HistoryContentsManager.py
    M test/unit/test_lazy_process.py
    A tool-data/bam_iobio.loc.sample
    A tool-data/vcf_iobio.loc.sample

  Log Message:
  -----------
  (merge conflicted bundles)

  Commit: ea921d2d7a529242c25acbab787a9f6c0a280fbf
      https://github.com/galaxyproject/galaxy/commit/ea921d2d7a529242c25acbab787a9...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-01 (Fri, 01 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-contents.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/dataset/dataset-model.js
    M static/scripts/mvc/history/history-contents.js

  Log Message:
  -----------
  Add view/keys ability to history_contents.create

This allows the client to fetch the create_time for proper ordering
of history contents directly after a copy.

  Commit: c4f8a30bbddffbf8e514a8112f46ec8e340f62fe
      https://github.com/galaxyproject/galaxy/commit/c4f8a30bbddffbf8e514a8112f46e...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-04 (Mon, 04 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/layout/panel.js
    M client/galaxy/scripts/mvc/annotation.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M static/maps/layout/panel.js.map
    M static/maps/mvc/annotation.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.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/panel.js
    M static/scripts/mvc/annotation.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view-edit.js

  Log Message:
  -----------
  UI, history: correct current dataset, tags, annos

Correct the 'currently used dataset' indicator (the left, blue border)
making sure it clears when non-dataset related content loads in the
center panel.

Correct the toggling of tags and annotations in the current history
view forcing the subviews to show/hide based on the history view
and not by toggling them individually.

  Commit: 747d4755742d7e2e327f549b283e680068232dd9
      https://github.com/galaxyproject/galaxy/commit/747d4755742d7e2e327f549b283e6...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-04 (Mon, 04 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/dataset/dataset-li.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M static/maps/mvc/dataset/dataset-li.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit.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/dataset/dataset-li.js
    M static/scripts/mvc/history/history-model.js

  Log Message:
  -----------
  UI, history: fix visual update of setting_metadata

When a dataset moved from setting_metadata to some ready state, no
change (besides the state change) would be registered by the model
when the fetch returned. This would prevent an automatic re-render
of the view and the dataset would appear to be stuck in setting_
metadata.

  Commit: 5f88d5dac5cad5836e6ee8e5f0ef18cd31fb4ba9
      https://github.com/galaxyproject/galaxy/commit/5f88d5dac5cad5836e6ee8e5f0ef1...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-04 (Mon, 04 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.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/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, history: cleanup empty and loading messages

- Refactors renderEmptyMessage into base history view
- Fixes contents loading indicator selector
- Styles contents loading indicator (still oogly tho)

  Commit: 53163c3c6021e8b3d961a04ae6d7512543309587
      https://github.com/galaxyproject/galaxy/commit/53163c3c6021e8b3d961a04ae6d75...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-05 (Tue, 05 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/options-menu.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/options-menu.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/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/options-menu.js

  Log Message:
  -----------
  UI, history: revise options menu batch operations

- Have both 'Unhide hidden' and 'Delete hidden' fetch hidden datasets
(since we now can't rely on complete contents)
- Move both from options and into history-view-edit-current
- Some minor cleanup of options-menu

  Commit: b1d930494a8b7a4ccd181e61aa7038cdb4b49814
      https://github.com/galaxyproject/galaxy/commit/b1d930494a8b7a4ccd181e61aa703...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-07 (Thu, 07 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/copy-dialog.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/ui/error-modal.js
    M client/galaxy/scripts/mvc/ui/ui-modal.js
    M client/galaxy/style/less/base.less
    A client/galaxy/style/less/ui/error-modal.less
    M static/maps/mvc/history/copy-dialog.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/ui/error-modal.js.map
    M static/maps/mvc/ui/ui-modal.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/history/copy-dialog.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/ui/error-modal.js
    M static/scripts/mvc/ui/ui-modal.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI: extract error-modal from history

Extract the error handler and display used in history-view to it's own
module (mvc/ui/error-modal) and use it to remove alerts elsewhere.

This may be a start at standardizing error handling in some of the mvc
code.

  Commit: f9d61e4a4b8392554efcae89183b7fa2b75dfef9
      https://github.com/galaxyproject/galaxy/commit/f9d61e4a4b8392554efcae89183b7...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-07 (Thu, 07 Apr 2016)

  Changed paths:
    M .ci/flake8_wrapper.sh
    M .ci/py3_sources.txt
    M .gitignore
    M README.rst
    M client/galaxy/scripts/layout/menu.js
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/job_conf.xml.sample_advanced
    A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
    M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
    M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
    A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
    M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
    M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
    M config/tool_data_table_conf.xml.sample
    A contrib/galaxy_supervisor.conf
    A display_applications/biom/biom_simple.xml
    M doc/source/lib/modules.rst
    R doc/source/lib/pulsar.client.rst
    R doc/source/lib/pulsar.client.staging.rst
    R doc/source/lib/pulsar.client.transport.rst
    R doc/source/lib/pulsar.rst
    M lib/galaxy/config.py
    M lib/galaxy/datatypes/sniff.py
    M lib/galaxy/datatypes/tabular.py
    A lib/galaxy/datatypes/test/issue1818.tabular
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/pbs.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/security/__init__.py
    M lib/galaxy/tools/data/__init__.py
    M lib/galaxy/tools/deps/commands.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/parameters/output_collect.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/lineages/factory.py
    M lib/galaxy/tools/toolbox/parser.py
    M lib/galaxy/util/log/fluent_log.py
    M lib/galaxy/web/base/interactive_environments.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/visualization.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/workflow/modules.py
    R lib/pulsar/__init__.py
    R lib/pulsar/client/__init__.py
    R lib/pulsar/client/action_mapper.py
    R lib/pulsar/client/amqp_exchange.py
    R lib/pulsar/client/amqp_exchange_factory.py
    R lib/pulsar/client/client.py
    R lib/pulsar/client/config_util.py
    R lib/pulsar/client/decorators.py
    R lib/pulsar/client/destination.py
    R lib/pulsar/client/interface.py
    R lib/pulsar/client/job_directory.py
    R lib/pulsar/client/manager.py
    R lib/pulsar/client/object_client.py
    R lib/pulsar/client/path_mapper.py
    R lib/pulsar/client/setup_handler.py
    R lib/pulsar/client/staging/__init__.py
    R lib/pulsar/client/staging/down.py
    R lib/pulsar/client/staging/up.py
    R lib/pulsar/client/transport/__init__.py
    R lib/pulsar/client/transport/curl.py
    R lib/pulsar/client/transport/poster.py
    R lib/pulsar/client/transport/requests.py
    R lib/pulsar/client/transport/ssh.py
    R lib/pulsar/client/transport/standard.py
    R lib/pulsar/client/util.py
    M run_tests.sh
    M scripts/common_startup.sh
    M scripts/functional_tests.py
    M static/maps/layout/menu.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/layout/menu.js
    M templates/admin/tool_shed_repository/preview_repository.mako
    M templates/sharing_base.mako
    M templates/webapps/galaxy/admin/index.mako
    A templates/webapps/galaxy/visualization/gie.mako
    R templates/webapps/galaxy/workflow/export.mako
    M templates/webapps/galaxy/workflow/list.mako
    M templates/webapps/galaxy/workflow/run.mako
    M templates/webapps/galaxy/workflow/sharing.mako
    M test/base/driver_util.py
    A test/base/integration_util.py
    M test/functional/tools/samples_tool_conf.xml
    M test/functional/tools/upload_tool_conf.xml
    A test/integration/__init__.py
    A test/integration/embedded_pulsar_job_conf.xml
    A test/integration/test_pulsar_embedded.py
    A test/shed_functional/__init__.py
    A test/shed_functional/base/__init__.py
    A test/shed_functional/base/common.py
    A test/shed_functional/base/test_db_util.py
    A test/shed_functional/base/twilltestcase.py
    A test/shed_functional/functional/__init__.py
    A test/shed_functional/functional/test_0000_basic_repository_features.py
    A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
    A test/shed_functional/functional/test_0020_basic_repository_dependencies.py
    A test/shed_functional/functional/test_0030_repository_dependency_revisions.py
    A test/shed_functional/functional/test_0040_repository_circular_dependencies.py
    A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
    A test/shed_functional/functional/test_0060_workflows.py
    A test/shed_functional/functional/test_0070_invalid_tool.py
    A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
    A test/shed_functional/functional/test_0090_tool_search.py
    A test/shed_functional/functional/test_0100_complex_repository_dependencies.py
    A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
    A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
    A test/shed_functional/functional/test_0130_datatype_converters.py
    A test/shed_functional/functional/test_0140_tool_help_images.py
    A test/shed_functional/functional/test_0150_prior_installation_required.py
    A test/shed_functional/functional/test_0160_circular_prior_installation_required.py
    A test/shed_functional/functional/test_0170_complex_prior_installation_required.py
    A test/shed_functional/functional/test_0300_reset_all_metadata.py
    A test/shed_functional/functional/test_0310_hg_api_features.py
    A test/shed_functional/functional/test_0400_repository_component_reviews.py
    A test/shed_functional/functional/test_0410_repository_component_review_access_control.py
    A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
    A test/shed_functional/functional/test_0430_browse_utilities.py
    A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
    A test/shed_functional/functional/test_0450_skip_tool_tests.py
    A test/shed_functional/functional/test_0460_upload_to_repository.py
    A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
    A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
    A test/shed_functional/functional/test_0490_export_import_repositories.py
    A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
    A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
    A test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
    A test/shed_functional/functional/test_0530_repository_admin_feature.py
    A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
    A test/shed_functional/functional/test_1000_install_basic_repository.py
    A test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
    A test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
    A test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
    A test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
    A test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
    A test/shed_functional/functional/test_1060_install_repository_with_workflow.py
    A test/shed_functional/functional/test_1070_invalid_tool.py
    A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
    A test/shed_functional/functional/test_1090_repository_dependency_handling.py
    A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
    A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
    A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
    A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
    A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
    A test/shed_functional/functional/test_1150_datatype_converters.py
    A test/shed_functional/functional/test_1160_tool_help_images.py
    A test/shed_functional/functional/test_1170_prior_installation_required.py
    A test/shed_functional/functional/test_1180_circular_prior_installation_required.py
    A test/shed_functional/functional/test_1190_complex_prior_installation_required.py
    A test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
    A test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
    A test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
    A test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
    A test/shed_functional/functional/test_1300_reset_all_metadata.py
    A test/shed_functional/functional/test_1400_review_migration_stages.py
    A test/shed_functional/functional/test_1410_update_manager.py
    A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
    A test/shed_functional/functional/test_1430_repair_installed_repository.py
    A test/shed_functional/functional/test_1440_missing_env_sh_files.py
    A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
    A test/shed_functional/functional/test_1460_data_managers.py
    A test/shed_functional/functional/test_1470_updating_installed_repositories.py
    A test/shed_functional/functional_tests.py
    A test/shed_functional/test_data/0460_files/repository_dependencies.xml
    A test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar
    A test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar
    A test/shed_functional/test_data/0460_files/tool_dependencies.xml
    A test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar
    A test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar
    A test/shed_functional/test_data/0480_files/tool_dependencies.xml
    A test/shed_functional/test_data/0540_files/column_maker/column_maker.tar
    A test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml
    A test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar
    A test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml
    A test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml
    A test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar
    A test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar
    A test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar
    A test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar
    A test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar
    A test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar
    A test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
    A test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml
    A test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml
    A test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml
    A test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml
    A test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml
    A test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml
    A test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml
    A test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar
    A test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
    A test/shed_functional/test_data/bismark/bismark.tar
    A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml
    A test/shed_functional/test_data/blast/blast_datatypes.tar
    A test/shed_functional/test_data/blast/blastxml_to_top_descr.tar
    A test/shed_functional/test_data/bwa/bwa_base.tar
    A test/shed_functional/test_data/bwa/bwa_color.tar
    A test/shed_functional/test_data/bwa/complex/bwa_base.tar
    A test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml
    A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml
    A test/shed_functional/test_data/column_maker/column_maker.tar
    A test/shed_functional/test_data/convert_chars/convert_chars.tar
    A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar
    A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml
    A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
    A test/shed_functional/test_data/emboss/emboss.tar
    A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
    A test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml
    A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
    A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
    A test/shed_functional/test_data/filtering/README
    A test/shed_functional/test_data/filtering/filtering_0000.txt
    A test/shed_functional/test_data/filtering/filtering_1.1.0.tar
    A test/shed_functional/test_data/filtering/filtering_2.2.0.tar
    A test/shed_functional/test_data/filtering/filtering_test_data.tar
    A test/shed_functional/test_data/filtering/readme.txt
    A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
    A test/shed_functional/test_data/freebayes/freebayes.tar
    A test/shed_functional/test_data/freebayes/freebayes.xml
    A test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
    A test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
    A test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample
    A test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample
    A test/shed_functional/test_data/freebayes/tool_dependencies.xml
    A test/shed_functional/test_data/htseq_count/htseq_count.tar
    A test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar
    A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml
    A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar
    A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar
    A test/shed_functional/test_data/readme.txt
    A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz
    A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz
    A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
    A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz
    R test/tool_shed/__init__.py
    R test/tool_shed/base/__init__.py
    R test/tool_shed/base/common.py
    R test/tool_shed/base/test_db_util.py
    R test/tool_shed/base/twilltestcase.py
    R test/tool_shed/functional/__init__.py
    R test/tool_shed/functional/test_0000_basic_repository_features.py
    R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
    R test/tool_shed/functional/test_0020_basic_repository_dependencies.py
    R test/tool_shed/functional/test_0030_repository_dependency_revisions.py
    R test/tool_shed/functional/test_0040_repository_circular_dependencies.py
    R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
    R test/tool_shed/functional/test_0060_workflows.py
    R test/tool_shed/functional/test_0070_invalid_tool.py
    R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
    R test/tool_shed/functional/test_0090_tool_search.py
    R test/tool_shed/functional/test_0100_complex_repository_dependencies.py
    R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
    R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
    R test/tool_shed/functional/test_0130_datatype_converters.py
    R test/tool_shed/functional/test_0140_tool_help_images.py
    R test/tool_shed/functional/test_0150_prior_installation_required.py
    R test/tool_shed/functional/test_0160_circular_prior_installation_required.py
    R test/tool_shed/functional/test_0170_complex_prior_installation_required.py
    R test/tool_shed/functional/test_0300_reset_all_metadata.py
    R test/tool_shed/functional/test_0310_hg_api_features.py
    R test/tool_shed/functional/test_0400_repository_component_reviews.py
    R test/tool_shed/functional/test_0410_repository_component_review_access_control.py
    R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
    R test/tool_shed/functional/test_0430_browse_utilities.py
    R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
    R test/tool_shed/functional/test_0450_skip_tool_tests.py
    R test/tool_shed/functional/test_0460_upload_to_repository.py
    R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
    R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
    R test/tool_shed/functional/test_0490_export_import_repositories.py
    R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
    R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
    R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
    R test/tool_shed/functional/test_0530_repository_admin_feature.py
    R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
    R test/tool_shed/functional/test_1000_install_basic_repository.py
    R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
    R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
    R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
    R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
    R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
    R test/tool_shed/functional/test_1060_install_repository_with_workflow.py
    R test/tool_shed/functional/test_1070_invalid_tool.py
    R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
    R test/tool_shed/functional/test_1090_repository_dependency_handling.py
    R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
    R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
    R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
    R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
    R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
    R test/tool_shed/functional/test_1150_datatype_converters.py
    R test/tool_shed/functional/test_1160_tool_help_images.py
    R test/tool_shed/functional/test_1170_prior_installation_required.py
    R test/tool_shed/functional/test_1180_circular_prior_installation_required.py
    R test/tool_shed/functional/test_1190_complex_prior_installation_required.py
    R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
    R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
    R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
    R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
    R test/tool_shed/functional/test_1300_reset_all_metadata.py
    R test/tool_shed/functional/test_1400_review_migration_stages.py
    R test/tool_shed/functional/test_1410_update_manager.py
    R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
    R test/tool_shed/functional/test_1430_repair_installed_repository.py
    R test/tool_shed/functional/test_1440_missing_env_sh_files.py
    R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
    R test/tool_shed/functional/test_1460_data_managers.py
    R test/tool_shed/functional/test_1470_updating_installed_repositories.py
    R test/tool_shed/functional_tests.py
    R test/tool_shed/test_data/0460_files/repository_dependencies.xml
    R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar
    R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar
    R test/tool_shed/test_data/0460_files/tool_dependencies.xml
    R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar
    R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar
    R test/tool_shed/test_data/0480_files/tool_dependencies.xml
    R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
    R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
    R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
    R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
    R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
    R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar
    R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar
    R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar
    R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar
    R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar
    R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar
    R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
    R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml
    R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml
    R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml
    R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml
    R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml
    R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
    R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml
    R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar
    R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
    R test/tool_shed/test_data/bismark/bismark.tar
    R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml
    R test/tool_shed/test_data/blast/blast_datatypes.tar
    R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar
    R test/tool_shed/test_data/bwa/bwa_base.tar
    R test/tool_shed/test_data/bwa/bwa_color.tar
    R test/tool_shed/test_data/bwa/complex/bwa_base.tar
    R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml
    R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml
    R test/tool_shed/test_data/column_maker/column_maker.tar
    R test/tool_shed/test_data/convert_chars/convert_chars.tar
    R test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar
    R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml
    R test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml
    R test/tool_shed/test_data/emboss/emboss.tar
    R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
    R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml
    R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
    R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
    R test/tool_shed/test_data/filtering/README
    R test/tool_shed/test_data/filtering/filtering_0000.txt
    R test/tool_shed/test_data/filtering/filtering_1.1.0.tar
    R test/tool_shed/test_data/filtering/filtering_2.2.0.tar
    R test/tool_shed/test_data/filtering/filtering_test_data.tar
    R test/tool_shed/test_data/filtering/readme.txt
    R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
    R test/tool_shed/test_data/freebayes/freebayes.tar
    R test/tool_shed/test_data/freebayes/freebayes.xml
    R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
    R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
    R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample
    R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample
    R test/tool_shed/test_data/freebayes/tool_dependencies.xml
    R test/tool_shed/test_data/htseq_count/htseq_count.tar
    R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar
    R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml
    R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar
    R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
    R test/tool_shed/test_data/readme.txt
    R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz
    R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz
    R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
    R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz
    M test/unit/managers/test_HistoryContentsManager.py
    A test/unit/shed_unit/__init__.py
    A test/unit/shed_unit/test_fabric_util.py
    A test/unit/shed_unit/test_td_common_util.py
    A test/unit/shed_unit/test_tool_panel_manager.py
    R test/unit/tool_shed_unit_tests/__init__.py
    R test/unit/tool_shed_unit_tests/test_fabric_util.py
    R test/unit/tool_shed_unit_tests/test_td_common_util.py
    R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py
    M test/unit/tools/test_conda_resolution.py
    A tool-data/biom_simple_display.loc.sample

  Log Message:
  -----------
  (manual merge with dev)

  Commit: 434845fe464ba3f955b3dba349d65c35d19bdf6b
      https://github.com/galaxyproject/galaxy/commit/434845fe464ba3f955b3dba349d65...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-07 (Thu, 07 Apr 2016)

  Changed paths:
    M test/unit/managers/test_HistoryManager.py

  Log Message:
  -----------
  Tests: remove peek from history.contents serilaization

  Commit: 1fedef02fb634025fcf8d303cb4842b119cfbe1c
      https://github.com/galaxyproject/galaxy/commit/1fedef02fb634025fcf8d303cb484...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-07 (Thu, 07 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/hda-li-edit.js
    M client/galaxy/scripts/mvc/history/hda-li.js
    M client/galaxy/scripts/mvc/history/hdca-li.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-preferences.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/hda-li-edit.js.map
    M static/maps/mvc/history/hda-li.js.map
    M static/maps/mvc/history/hdca-li.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-preferences.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: doc and TODO cleanup

  Commit: 958a5e8d424a837a7e740dc9526455d2856608d4
      https://github.com/galaxyproject/galaxy/commit/958a5e8d424a837a7e740dc952645...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-08 (Fri, 08 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.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/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: fix subtitle counts and cleanup

- Move comma-sep into css
- Correct count calc in handlers
- Console stmts, templating, and method order

  Commit: 8a6f96f73400ef8d5749a51841cd073a273fe8b0
      https://github.com/galaxyproject/galaxy/commit/8a6f96f73400ef8d5749a51841cd0...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-08 (Fri, 08 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: simplify createHDCA and ajaxQueue

- use collection.create in createHDCA
- use ajax-queue module in history-contents.ajaxQueue
- Small fixes to DC.hasDetails, and item view rendering

  Commit: 81d36f903bc0e037cc6da67e101512aca542bad1
      https://github.com/galaxyproject/galaxy/commit/81d36f903bc0e037cc6da67e10151...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-08 (Fri, 08 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view.js
    M templates/webapps/galaxy/history/display.mako

  Log Message:
  -----------
  UI, histories: fix pagination for published

- Ensure all web controller history json is using view='current'
- Fix rendering of already fetched contents when
  searching and/or progressively fetching details
- minor doc cleanup

  Commit: ee240f46673e962a1c1df8ef20910b197b09df38
      https://github.com/galaxyproject/galaxy/commit/ee240f46673e962a1c1df8ef20910...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-08 (Fri, 08 Apr 2016)

  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:
  -----------
  (bundle scripts)

  Commit: c8512faf447c34dba6127e856e1dabb98248815e
      https://github.com/galaxyproject/galaxy/commit/c8512faf447c34dba6127e856e1da...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-08 (Fri, 08 Apr 2016)

  Changed paths:
    M .ci/py3_sources.txt
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M contrib/galaxy.debian-init
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/jobs/runners/cli.py
    M lib/galaxy/jobs/runners/drmaa.py
    M lib/galaxy/tools/cwl/parser.py
    M lib/galaxy/tools/cwl/runtime_actions.py
    M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/buildapp.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    R lib/tool_shed/scripts/api/add_repository_registry_entry.py
    R lib/tool_shed/scripts/api/common.py
    R lib/tool_shed/scripts/api/create_categories.py
    R lib/tool_shed/scripts/api/create_users.py
    R lib/tool_shed/scripts/api/export.py
    R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
    R lib/tool_shed/scripts/api/import_capsule.py
    R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
    R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
    R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
    R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
    R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
    R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
    R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
    R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
    R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
    R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
    R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
    R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
    R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
    R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
    R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
    M lib/tool_shed/util/shed_util_common.py
    A scripts/tool_shed/api/add_repository_registry_entry.py
    A scripts/tool_shed/api/common.py
    A scripts/tool_shed/api/create_categories.py
    A scripts/tool_shed/api/create_users.py
    A scripts/tool_shed/api/export.py
    A scripts/tool_shed/api/get_filtered_repository_revisions.py
    A scripts/tool_shed/api/import_capsule.py
    A scripts/tool_shed/api/remove_repository_registry_entry.py
    A scripts/tool_shed/api/reset_metadata_on_repositories.py
    A scripts/tool_shed/api/tool_shed_repository_revision_update.py
    A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
    A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
    A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
    A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh
    A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample
    A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
    A scripts/tool_shed/check_repositories_for_functional_tests.py
    A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
    A scripts/tool_shed/check_tool_dependency_definition_repositories.py
    A scripts/tool_shed/clean_up_tool_dependency_directory.py
    A scripts/tool_shed/deprecate_repositories_without_metadata.py
    A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/scripts/mvc/tool/tool-form-workflow.js

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: f3b8d5b0e308c5e9ef9b0a97d311d19f3f998794
      https://github.com/galaxyproject/galaxy/commit/f3b8d5b0e308c5e9ef9b0a97d311d...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-11 (Mon, 11 Apr 2016)

  Changed paths:
    M Makefile
    M lib/galaxy/version.py
    M run_tool_shed.sh
    M scripts/bootstrap_history.py

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: 7cb32818062b7f30647ec66608902029575a5454
      https://github.com/galaxyproject/galaxy/commit/7cb32818062b7f30647ec66608902...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-11 (Mon, 11 Apr 2016)

  Changed paths:
    M .gitignore
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-view.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/history/history-view.js

  Log Message:
  -----------
  Remove console and .gitignore duplication

  Commit: da5443161639217da86b5f54bf277c3021e67667
      https://github.com/galaxyproject/galaxy/commit/da5443161639217da86b5f54bf277...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-11 (Mon, 11 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view.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/history/history-model.js
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: remove scoping overrides

  Commit: 0a1d7982aa4b16b6111f92ccfc5814f49306b80a
      https://github.com/galaxyproject/galaxy/commit/0a1d7982aa4b16b6111f92ccfc581...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-11 (Mon, 11 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/history_contents.py
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.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/history/history-model.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js

  Log Message:
  -----------
  API, history: contents_shown to contents_active

Renames serialization attribute contents_shown to contents_active to
better match original terminology.

Adds both state_counts and active_counts to HistoryContentsManager and
then has serialize_contents_states and serialize_contents_active call
them from the HistorySerializer.

  Commit: fd3abf4104a58b7add3be22d89286356dbb4caee
      https://github.com/galaxyproject/galaxy/commit/fd3abf4104a58b7add3be22d89286...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-11 (Mon, 11 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M lib/galaxy/managers/histories.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/history/history-model.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/history/history-model.js

  Log Message:
  -----------
  API, history: rename current view 'dev-detailed'

Because current was a horrible and confusing name and dev-detailed may
highlight the volitility of the view more.

  Commit: 0484017e6832f418cd0f20b074d27a329cd0fc22
      https://github.com/galaxyproject/galaxy/commit/0484017e6832f418cd0f20b074d27...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-12 (Tue, 12 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/apps/history-panel.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/style/less/base.less
    A client/galaxy/style/less/flex.less
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-view-edit-current.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/history/history-view-edit-current.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: move history panel to flexbox

This allows us to avoid using absolutely positioned elements and
simplifies style rules a bit.

  Commit: 7722bf23ad4ccd60c114a3de1ceaa422924cfc7c
      https://github.com/galaxyproject/galaxy/commit/7722bf23ad4ccd60c114a3de1ceaa...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-12 (Tue, 12 Apr 2016)

  Changed paths:
    M client/bower.json
    M client/galaxy/scripts/libs/underscore.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/libs/underscore.js.map
    M static/maps/mvc/list/list-view.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/libs/underscore.js
    M static/scripts/mvc/list/list-view.js
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI: update underscorejs and fix findIndex

IE 11 does not have [].findIndex and the new scrolling causes an error
there. Underscore 1.8 has a cross-browser version and this commit
updates underscore and replaces the use of the native call.

  Commit: 1600d6c6e6f641c203d3f45787f19bda68d88d97
      https://github.com/galaxyproject/galaxy/commit/1600d6c6e6f641c203d3f45787f19...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-12 (Tue, 12 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js

  Log Message:
  -----------
  UI, history: shorten deleted/hidden load indicator

  Commit: 94f6f1e0049c962941b51d28ee0f0351423fbc52
      https://github.com/galaxyproject/galaxy/commit/94f6f1e0049c962941b51d28ee0f0...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-12 (Tue, 12 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/apps/history-panel.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/style/less/base.less
    M client/galaxy/style/less/flex.less
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-view-edit-current.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/history/history-view-edit-current.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: move towards a fixed header

  Commit: b5580c23f63f214fb465892b430c0d62d75fc3f9
      https://github.com/galaxyproject/galaxy/commit/b5580c23f63f214fb465892b430c0...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-12 (Tue, 12 Apr 2016)

  Changed paths:
    R buildbot_setup.sh
    M config/job_conf.xml.sample_advanced
    R install_and_test_tool_shed_repositories.sh
    M lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/jobs/command_factory.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/managers/configuration.py
    M lib/galaxy/web/framework/base.py
    M lib/galaxy/web/framework/helpers/__init__.py
    M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
    M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
    R scripts/tool_shed/check_repositories_for_functional_tests.py
    M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
    R scripts/tool_shed/check_tool_dependency_definition_repositories.py
    M scripts/tool_shed/deprecate_repositories_without_metadata.py
    M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
    M test/casperjs/casperjs_runner.py
    M test/unit/jobs/test_command_factory.py

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: 89cb03a037d770c4c895d4e8f872de04d385ada9
      https://github.com/galaxyproject/galaxy/commit/89cb03a037d770c4c895d4e8f872d...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-15 (Fri, 15 Apr 2016)

  Changed paths:
    M lib/galaxy/managers/annotatable.py
    M lib/galaxy/managers/history_contents.py

  Log Message:
  -----------
  History contents manager: improve contents query

Serializers in the index_v2 of history_contents were re-
querying the database for mapped model attributes.

- eagerload collection on hdcas
- undefer _metadata on hdas
- eaglerload tags and annotations for both
- rework annotatable manager mixin to cycle through annotations
bypassing the get_item_annotation_str call (which would bypass
item.annotations even if already loaded)

Anecdotally provides significant speed up.

  Commit: 32520078af5bf062344f9355894c3d83ebaf638d
      https://github.com/galaxyproject/galaxy/commit/32520078af5bf062344f9355894c3...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-15 (Fri, 15 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view.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/history/history-contents.js
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: raise pagination limits

- fetch more when scroll bar is at 512, not 128 px from bottom
- fetch 200 at first then 100 each fetch (from 100, 50)
- fetch 500 per fetch when searching (progressivelyFetchDetails)

  Commit: 4c7f367680898b16c395748c501bbca0c56e02ce
      https://github.com/galaxyproject/galaxy/commit/4c7f367680898b16c395748c501bb...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-15 (Fri, 15 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/layout/page.js
    M client/galaxy/scripts/mvc/citation/citation-model.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
    M client/galaxy/style/less/base.less
    M config/galaxy.ini.sample
    M lib/galaxy/config.py
    M lib/galaxy/dependencies/__init__.py
    M lib/galaxy/dependencies/conditional-requirements.txt
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
    M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
    M lib/galaxy/managers/context.py
    M lib/galaxy/tools/actions/upload_common.py
    M lib/galaxy/tools/errors.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/grouping.py
    M lib/galaxy/tools/wrappers.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/web/framework/helpers/grids.py
    M lib/galaxy/web/framework/middleware/remoteuser.py
    M lib/galaxy/web/framework/middleware/statsd.py
    M lib/galaxy/webapps/galaxy/api/remote_files.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/workflow/modules.py
    M static/maps/layout/page.js.map
    M static/maps/mvc/citation/citation-model.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/workflow/workflow-terminals.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/page.js
    M static/scripts/mvc/citation/citation-model.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/workflow/workflow-terminals.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/galaxy.panels.mako
    M templates/webapps/tool_shed/repository/view_changeset.mako
    M test/base/interactor.py
    M test/shed_functional/base/twilltestcase.py
    M tools/data_source/upload.py
    M tools/stats/grouping.py
    M tools/stats/grouping.xml

  Log Message:
  -----------
  (merge conflicts with dev)

  Commit: d9591127d89c61f5f172bc33d7532917facb3689
      https://github.com/galaxyproject/galaxy/commit/d9591127d89c61f5f172bc33d7532...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-22 (Fri, 22 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M client/galaxy/style/less/list-item.less
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-item.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, histories: move to a section based pagination

Breaks history contents into 500 element sections rendering each in
a accordian-style menu. Elements are sectioned according to their
hids and no more than 500 are rendered at any time.

  Commit: 9956eecb6ab25d71153ed2c877d7d4a9b4db5f07
      https://github.com/galaxyproject/galaxy/commit/9956eecb6ab25d71153ed2c877d7d...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-25 (Mon, 25 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js
    M templates/webapps/galaxy/history/display.mako

  Log Message:
  -----------
  UI, history: paginate by hid and show sections

- Order by hid or hid-asc (this loses the ability use others)
- Paginate by 'sections' of 500 hids showing only one expanded section
  at a time
  -- pro: this prevents large numbers of contents in the dom at once
  -- con: the visible contents can be very sparse (e.g. 2 of 500)
- Pagination only begins if more than 500 contents
- HistoryContents now has a parent reference (.history)

  Commit: 994300d3f65904b0532d383e5d6778520ea183ba
      https://github.com/galaxyproject/galaxy/commit/994300d3f65904b0532d383e5d677...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-29 (Fri, 29 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/mvc/history/hda-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/hda-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.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/history/hda-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-item.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: polish sectioning enough to show

(This is an extremely rough commit meant to have a working prototype
for others to test the UX abstraction of sectioning the histories)

- Reworks contents so that they're nested inside sections
- Fixes all a handful of the errors the previous change causes

  Commit: cf27a6ae28f6b2f02cee80ee4695275a0dd413c9
      https://github.com/galaxyproject/galaxy/commit/cf27a6ae28f6b2f02cee80ee46952...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-04-29 (Fri, 29 Apr 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: fetchHiddenInSection, clickSection

- add fetchHiddenInSection to load hidden contents in a particular
  section
- extract event handler from clickSection link to allow getting
  data-section from different part of the DOM in annotated history

  Commit: 3686ed55c39430d911e17a9e3821090c5de76a1f
      https://github.com/galaxyproject/galaxy/commit/3686ed55c39430d911e17a9e38210...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-02 (Mon, 02 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/utils/ajax-queue.js
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/utils/ajax-queue.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/utils/ajax-queue.js

  Log Message:
  -----------
  UI, history: use arrays when filtering contents

- Moves all history filtering to returning arrays and not new
HistoryContents (subset collections)
- Reworks contents.ajaxQueue
- Moves filterAndUpdate to contents from HistoryView

  Commit: a7c7af94af6564ab2bd7660b26f8bf81fc00ca4c
      https://github.com/galaxyproject/galaxy/commit/a7c7af94af6564ab2bd7660b26f8b...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-02 (Mon, 02 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M static/maps/mvc/history/history-contents.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-contents.js

  Log Message:
  -----------
  UI, history: fix create HDCA and return promise

  Commit: 7a6794e104fc978b279c61d15812791302d6fef2
      https://github.com/galaxyproject/galaxy/commit/7a6794e104fc978b279c61d158127...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-02 (Mon, 02 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-content-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-preferences.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/history/history-content-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-preferences.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-view.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/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-preferences.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: move show deleted/hidden into content

- Move d/h (deleted/hidden) control into history contents
- normalize names (show_deleted, showDeleted --> includeDeleted)
- add History.contentsShown that checks d/h flags to return num. shown
- move HistoryPreferences into HistoryContents.storage

Misc. fixes:
- fix collection.off to stopListening
- provide interface to HistoryPreferences so that consumers don't need
the model keys (easier to change them later on)
- (some) cleanup

  Commit: 2d9ec54fe2126ab21249c0f8918a27802b7b85bb
      https://github.com/galaxyproject/galaxy/commit/2d9ec54fe2126ab21249c0f8918a2...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-06 (Fri, 06 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.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/history/history-contents.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-item.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: auto-expand sections

- track scrolling and auto expand sections when scroll 'cursor' is over
  them for more than a certain time
- improve rendering speed by using previously existing renders

  Commit: f8e89ff3fc36eced72f568b8fa6cf6632b22ff06
      https://github.com/galaxyproject/galaxy/commit/f8e89ff3fc36eced72f568b8fa6cf...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-12 (Thu, 12 May 2016)

  Changed paths:
    M CONTRIBUTORS.md
    M Makefile
    M client/README.md
    M client/bower.json
    M client/galaxy/scripts/layout/page.js
    M client/galaxy/scripts/libs/backbone.js
    M client/galaxy/scripts/libs/bootstrap-tour.js
    M client/galaxy/scripts/libs/d3.js
    M client/galaxy/scripts/libs/jquery/jquery.js
    M client/galaxy/scripts/libs/jquery/jquery.migrate.js
    M client/galaxy/scripts/libs/raven.js
    M client/galaxy/scripts/libs/require.js
    M client/galaxy/scripts/libs/tracekit.js
    M client/galaxy/scripts/mvc/citation/citation-model.js
    M client/galaxy/scripts/mvc/collection/list-collection-creator.js
    M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M client/galaxy/scripts/mvc/form/form-input.js
    M client/galaxy/scripts/mvc/form/form-parameters.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/library/library-dataset-view.js
    M client/galaxy/scripts/mvc/library/library-folder-view.js
    M client/galaxy/scripts/mvc/library/library-library-view.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M client/galaxy/scripts/mvc/ui/popup-menu.js
    M client/galaxy/scripts/mvc/ui/ui-drilldown.js
    M client/galaxy/scripts/mvc/ui/ui-list.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-options.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.js
    M client/galaxy/scripts/ui/hoverhighlight.js
    M client/galaxy/scripts/ui/loading-indicator.js
    M client/galaxy/scripts/ui/mode-button.js
    M client/galaxy/scripts/ui/pagination.js
    M client/galaxy/scripts/ui/peek-column-selector.js
    M client/galaxy/scripts/utils/localization.js
    M client/galaxy/scripts/utils/metrics-logger.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/ui.less
    M client/grunt-tasks/scripts.js
    M client/grunt-tasks/style.js
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/plugins/tours/core.galaxy_ui.yaml
    M config/plugins/tours/core.scratchbook.yaml
    M config/plugins/visualizations/charts/static/views/group.js
    R config/plugins/visualizations/graphview/config/graphview.xml
    R config/plugins/visualizations/graphview/static/graphview.css
    R config/plugins/visualizations/graphview/static/graphview.js
    R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
    R config/plugins/visualizations/graphview/templates/graphview.mako
    M config/reports.ini.sample
    M config/tool_shed.ini.sample
    M lib/galaxy/config.py
    A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
    A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
    M lib/galaxy/datatypes/data.py
    A lib/galaxy/datatypes/mothur.py
    M lib/galaxy/datatypes/sniff.py
    M lib/galaxy/datatypes/tabular.py
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
    M lib/galaxy/dependencies/conda-environment.txt
    M lib/galaxy/dependencies/pinned-hashed-requirements.txt
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/command_factory.py
    M lib/galaxy/jobs/runners/drmaa.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/jobs/runners/slurm.py
    M lib/galaxy/jobs/runners/util/job_script/__init__.py
    M lib/galaxy/managers/context.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/cwl/cwltool_deps.py
    M lib/galaxy/tools/cwl/parser.py
    A lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/errors.py
    M lib/galaxy/tools/lint.py
    M lib/galaxy/tools/linters/__init__.py
    M lib/galaxy/tools/linters/citations.py
    M lib/galaxy/tools/linters/command.py
    A lib/galaxy/tools/linters/general.py
    M lib/galaxy/tools/linters/help.py
    M lib/galaxy/tools/linters/inputs.py
    M lib/galaxy/tools/linters/outputs.py
    M lib/galaxy/tools/linters/stdio.py
    M lib/galaxy/tools/linters/tests.py
    R lib/galaxy/tools/linters/top_level.py
    M lib/galaxy/tools/linters/xml_order.py
    M lib/galaxy/tools/loader_directory.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parser/factory.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/search/__init__.py
    M lib/galaxy/util/sanitize_html.py
    M lib/galaxy/util/validation.py
    M lib/galaxy/web/base/interactive_environments.py
    M lib/galaxy/web/framework/middleware/remoteuser.py
    M lib/galaxy/web/framework/webapp.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/web/proxy/js/package.json
    M lib/galaxy/webapps/galaxy/api/datatypes.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
    M lib/galaxy/webapps/tool_shed/api/users.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/galaxy/webapps/tool_shed/model/mapping.py
    M lib/galaxy/workflow/run.py
    M lib/tool_shed/capsule/capsule_manager.py
    M lib/tool_shed/dependencies/repository/relation_builder.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M lib/tool_shed/grids/repository_grids.py
    M lib/tool_shed/grids/util.py
    M lib/tool_shed/metadata/repository_metadata_manager.py
    M lib/tool_shed/repository_registry.py
    M lib/tool_shed/util/metadata_util.py
    M lib/tool_shed/util/repository_util.py
    M lib/tool_shed/util/shed_util_common.py
    M lib/tool_shed/utility_containers/__init__.py
    M lib/tool_shed/utility_containers/utility_container_manager.py
    M static/maps/layout/page.js.map
    M static/maps/libs/backbone.js.map
    M static/maps/libs/bootstrap-tour.js.map
    M static/maps/libs/d3.js.map
    M static/maps/libs/jquery/jquery.js.map
    M static/maps/libs/jquery/jquery.migrate.js.map
    M static/maps/libs/raven.js.map
    M static/maps/libs/require.js.map
    M static/maps/libs/tracekit.js.map
    M static/maps/mvc/citation/citation-model.js.map
    M static/maps/mvc/collection/list-collection-creator.js.map
    M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/library/library-dataset-view.js.map
    M static/maps/mvc/library/library-folder-view.js.map
    M static/maps/mvc/library/library-library-view.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tool-form.js.map
    M static/maps/mvc/ui/popup-menu.js.map
    M static/maps/mvc/ui/ui-drilldown.js.map
    M static/maps/mvc/ui/ui-list.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-options.js.map
    M static/maps/mvc/ui/ui-select-default.js.map
    M static/maps/ui/hoverhighlight.js.map
    M static/maps/ui/loading-indicator.js.map
    M static/maps/ui/mode-button.js.map
    M static/maps/ui/pagination.js.map
    M static/maps/ui/peek-column-selector.js.map
    M static/maps/utils/localization.js.map
    M static/maps/utils/metrics-logger.js.map
    M static/maps/utils/utils.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/layout/page.js
    M static/scripts/libs/backbone.js
    M static/scripts/libs/bootstrap-tour.js
    M static/scripts/libs/d3.js
    M static/scripts/libs/jquery/jquery.js
    M static/scripts/libs/jquery/jquery.migrate.js
    M static/scripts/libs/raven.js
    M static/scripts/libs/require.js
    M static/scripts/libs/tracekit.js
    M static/scripts/mvc/citation/citation-model.js
    M static/scripts/mvc/collection/list-collection-creator.js
    M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/library/library-dataset-view.js
    M static/scripts/mvc/library/library-folder-view.js
    M static/scripts/mvc/library/library-library-view.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tool-form.js
    M static/scripts/mvc/ui/popup-menu.js
    M static/scripts/mvc/ui/ui-drilldown.js
    M static/scripts/mvc/ui/ui-list.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-options.js
    M static/scripts/mvc/ui/ui-select-default.js
    M static/scripts/ui/hoverhighlight.js
    M static/scripts/ui/loading-indicator.js
    M static/scripts/ui/mode-button.js
    M static/scripts/ui/pagination.js
    M static/scripts/ui/peek-column-selector.js
    M static/scripts/utils/localization.js
    M static/scripts/utils/metrics-logger.js
    M static/scripts/utils/utils.js
    M static/style/blue/base.css
    M templates/base/base_panels.mako
    M templates/display_base.mako
    M templates/sharing_base.mako
    M templates/show_params.mako
    A templates/slug_editing_js.mako
    M templates/webapps/galaxy/data_manager/view_job.mako
    M templates/webapps/galaxy/galaxy.masthead.mako
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/library/common/browse_library.mako
    M templates/webapps/galaxy/library/common/ldda_info.mako
    M templates/webapps/galaxy/workflow/display.mako
    M templates/webapps/galaxy/workflow/run.mako
    M templates/webapps/galaxy/workflow/sharing.mako
    M templates/webapps/tool_shed/index.mako
    M templates/webapps/tool_shed/repository/common.mako
    M templates/webapps/tool_shed/repository/manage_repository.mako
    M test/api/test_tools.py
    M test/api/workflows_format_2/converter.py
    M test/api/workflows_format_2/interface.py
    M test/api/workflows_format_2/main.py
    A test/functional/tools/multi_data_repeat.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/integration/test_pulsar_embedded.py
    M test/qunit/test-common.js
    R test/qunit/test-libs/qunit-1.14.0.css
    R test/qunit/test-libs/qunit-1.14.0.js
    A test/qunit/test-libs/qunit-1.23.1.css
    A test/qunit/test-libs/qunit-1.23.1.js
    A test/qunit/test-libs/sinon-1.17.3.js
    R test/qunit/test-libs/sinon-1.9.1.js
    M test/qunit/tests/form_tests.js
    M test/qunit/tests/list-of-pairs-collection-creator.js
    M test/qunit/tests/metrics-logger.js
    M test/qunit/tests/page_tests.js
    M test/qunit/tests/ui_tests.html
    M test/qunit/tests/ui_tests.js
    A test/qunit/tests/utils_test.html
    A test/qunit/tests/utils_test.js
    M test/qunit/tests/workflow_editor_tests.js
    R test/shed_functional/functional/test_0450_skip_tool_tests.py
    M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
    A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
    A test/shed_functional/test_data/0550_files/filtering_1.0.tgz
    A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz
    A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz
    A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz
    A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz
    A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml
    M test/unit/test_objectstore.py
    M tools/data_source/biomart.xml
    M tools/filters/trimmer.xml

  Log Message:
  -----------
  (merge conflicts)

  Commit: 4423a381afa68e4ce3e47f44ed8c7973dee62a3e
      https://github.com/galaxyproject/galaxy/commit/4423a381afa68e4ce3e47f44ed8c7...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-16 (Mon, 16 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-view.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/history/history-contents.js
    M static/scripts/mvc/history/history-view.js

  Log Message:
  -----------
  UI, history: merge sectioned history layout

This merges with history-contents.pagination, adding sections of
history contents by hids but reverts the auto-expansion of those
sections when the scroll bar is moved 'over' them.

  Commit: 16830e8eb250f1ebd3db4afaee7dbddf03ebd60d
      https://github.com/galaxyproject/galaxy/commit/16830e8eb250f1ebd3db4afaee7db...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-16 (Mon, 16 May 2016)

  Changed paths:
    M CONTRIBUTORS.md
    M Makefile
    M client/README.md
    M client/bower.json
    M client/galaxy/scripts/layout/page.js
    M client/galaxy/scripts/libs/backbone.js
    M client/galaxy/scripts/libs/bootstrap-tour.js
    M client/galaxy/scripts/libs/d3.js
    M client/galaxy/scripts/libs/jquery/jquery.js
    M client/galaxy/scripts/libs/jquery/jquery.migrate.js
    M client/galaxy/scripts/libs/raven.js
    M client/galaxy/scripts/libs/require.js
    M client/galaxy/scripts/libs/tracekit.js
    M client/galaxy/scripts/libs/underscore.js
    M client/galaxy/scripts/mvc/citation/citation-model.js
    M client/galaxy/scripts/mvc/collection/collection-li.js
    M client/galaxy/scripts/mvc/collection/list-collection-creator.js
    M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/form/form-input.js
    M client/galaxy/scripts/mvc/form/form-parameters.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/library/library-dataset-view.js
    M client/galaxy/scripts/mvc/library/library-folder-view.js
    M client/galaxy/scripts/mvc/library/library-library-view.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M client/galaxy/scripts/mvc/ui/popup-menu.js
    M client/galaxy/scripts/mvc/ui/ui-drilldown.js
    M client/galaxy/scripts/mvc/ui/ui-list.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-options.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.js
    M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
    M client/galaxy/scripts/ui/hoverhighlight.js
    M client/galaxy/scripts/ui/loading-indicator.js
    M client/galaxy/scripts/ui/mode-button.js
    M client/galaxy/scripts/ui/pagination.js
    M client/galaxy/scripts/ui/peek-column-selector.js
    M client/galaxy/scripts/utils/localization.js
    M client/galaxy/scripts/utils/metrics-logger.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/base.less
    M client/galaxy/style/less/ui.less
    M client/grunt-tasks/scripts.js
    M client/grunt-tasks/style.js
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/job_conf.xml.sample_advanced
    M config/plugins/tours/core.galaxy_ui.yaml
    M config/plugins/tours/core.scratchbook.yaml
    M config/plugins/visualizations/charts/static/views/group.js
    R config/plugins/visualizations/graphview/config/graphview.xml
    R config/plugins/visualizations/graphview/static/graphview.css
    R config/plugins/visualizations/graphview/static/graphview.js
    R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
    R config/plugins/visualizations/graphview/templates/graphview.mako
    M config/reports.ini.sample
    M config/tool_shed.ini.sample
    R install_and_test_tool_shed_repositories.sh
    M lib/galaxy/config.py
    A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
    A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
    M lib/galaxy/datatypes/data.py
    A lib/galaxy/datatypes/mothur.py
    M lib/galaxy/datatypes/registry.py
    M lib/galaxy/datatypes/sniff.py
    M lib/galaxy/datatypes/tabular.py
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
    A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
    A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
    M lib/galaxy/dependencies/__init__.py
    M lib/galaxy/dependencies/conda-environment.txt
    M lib/galaxy/dependencies/conditional-requirements.txt
    M lib/galaxy/dependencies/pinned-hashed-requirements.txt
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/command_factory.py
    M lib/galaxy/jobs/runners/drmaa.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/jobs/runners/slurm.py
    M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
    M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
    M lib/galaxy/jobs/runners/util/job_script/__init__.py
    M lib/galaxy/managers/context.py
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/hdcas.py
    M lib/galaxy/managers/sharable.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/actions/upload_common.py
    M lib/galaxy/tools/cwl/cwltool_deps.py
    M lib/galaxy/tools/cwl/parser.py
    A lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/errors.py
    M lib/galaxy/tools/evaluation.py
    M lib/galaxy/tools/lint.py
    M lib/galaxy/tools/linters/__init__.py
    M lib/galaxy/tools/linters/citations.py
    M lib/galaxy/tools/linters/command.py
    A lib/galaxy/tools/linters/general.py
    M lib/galaxy/tools/linters/help.py
    M lib/galaxy/tools/linters/inputs.py
    M lib/galaxy/tools/linters/outputs.py
    M lib/galaxy/tools/linters/stdio.py
    M lib/galaxy/tools/linters/tests.py
    R lib/galaxy/tools/linters/top_level.py
    M lib/galaxy/tools/linters/xml_order.py
    M lib/galaxy/tools/loader_directory.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/grouping.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/parser/factory.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/search/__init__.py
    M lib/galaxy/tools/wrappers.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/sanitize_html.py
    M lib/galaxy/util/validation.py
    M lib/galaxy/web/base/interactive_environments.py
    M lib/galaxy/web/framework/helpers/grids.py
    M lib/galaxy/web/framework/middleware/remoteuser.py
    M lib/galaxy/web/framework/middleware/statsd.py
    M lib/galaxy/web/framework/webapp.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/web/proxy/js/package.json
    M lib/galaxy/webapps/galaxy/api/datatypes.py
    M lib/galaxy/webapps/galaxy/api/remote_files.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
    M lib/galaxy/webapps/tool_shed/api/users.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/galaxy/webapps/tool_shed/model/mapping.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy/workflow/run.py
    M lib/tool_shed/capsule/capsule_manager.py
    M lib/tool_shed/dependencies/repository/relation_builder.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M lib/tool_shed/grids/repository_grids.py
    M lib/tool_shed/grids/util.py
    M lib/tool_shed/metadata/repository_metadata_manager.py
    M lib/tool_shed/repository_registry.py
    M lib/tool_shed/util/metadata_util.py
    M lib/tool_shed/util/repository_util.py
    M lib/tool_shed/util/shed_util_common.py
    M lib/tool_shed/utility_containers/__init__.py
    M lib/tool_shed/utility_containers/utility_container_manager.py
    A scripts/api/filter_failed_datasets_from_collection.py
    M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
    R scripts/tool_shed/check_repositories_for_functional_tests.py
    M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
    R scripts/tool_shed/check_tool_dependency_definition_repositories.py
    M scripts/tool_shed/deprecate_repositories_without_metadata.py
    M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
    M static/maps/layout/page.js.map
    M static/maps/libs/backbone.js.map
    M static/maps/libs/bootstrap-tour.js.map
    M static/maps/libs/d3.js.map
    M static/maps/libs/jquery/jquery.js.map
    M static/maps/libs/jquery/jquery.migrate.js.map
    M static/maps/libs/raven.js.map
    M static/maps/libs/require.js.map
    M static/maps/libs/tracekit.js.map
    M static/maps/libs/underscore.js.map
    M static/maps/mvc/citation/citation-model.js.map
    M static/maps/mvc/collection/collection-li.js.map
    M static/maps/mvc/collection/list-collection-creator.js.map
    M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/library/library-dataset-view.js.map
    M static/maps/mvc/library/library-folder-view.js.map
    M static/maps/mvc/library/library-library-view.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tool-form.js.map
    M static/maps/mvc/ui/popup-menu.js.map
    M static/maps/mvc/ui/ui-drilldown.js.map
    M static/maps/mvc/ui/ui-list.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-options.js.map
    M static/maps/mvc/ui/ui-select-default.js.map
    M static/maps/mvc/workflow/workflow-terminals.js.map
    M static/maps/ui/hoverhighlight.js.map
    M static/maps/ui/loading-indicator.js.map
    M static/maps/ui/mode-button.js.map
    M static/maps/ui/pagination.js.map
    M static/maps/ui/peek-column-selector.js.map
    M static/maps/utils/localization.js.map
    M static/maps/utils/metrics-logger.js.map
    M static/maps/utils/utils.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/layout/page.js
    M static/scripts/libs/backbone.js
    M static/scripts/libs/bootstrap-tour.js
    M static/scripts/libs/d3.js
    M static/scripts/libs/jquery/jquery.js
    M static/scripts/libs/jquery/jquery.migrate.js
    M static/scripts/libs/raven.js
    M static/scripts/libs/require.js
    M static/scripts/libs/tracekit.js
    M static/scripts/libs/underscore.js
    M static/scripts/mvc/citation/citation-model.js
    M static/scripts/mvc/collection/collection-li.js
    M static/scripts/mvc/collection/list-collection-creator.js
    M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/library/library-dataset-view.js
    M static/scripts/mvc/library/library-folder-view.js
    M static/scripts/mvc/library/library-library-view.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tool-form.js
    M static/scripts/mvc/ui/popup-menu.js
    M static/scripts/mvc/ui/ui-drilldown.js
    M static/scripts/mvc/ui/ui-list.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-options.js
    M static/scripts/mvc/ui/ui-select-default.js
    M static/scripts/mvc/workflow/workflow-terminals.js
    M static/scripts/ui/hoverhighlight.js
    M static/scripts/ui/loading-indicator.js
    M static/scripts/ui/mode-button.js
    M static/scripts/ui/pagination.js
    M static/scripts/ui/peek-column-selector.js
    M static/scripts/utils/localization.js
    M static/scripts/utils/metrics-logger.js
    M static/scripts/utils/utils.js
    M static/style/blue/base.css
    M templates/base/base_panels.mako
    M templates/display_base.mako
    M templates/sharing_base.mako
    M templates/show_params.mako
    A templates/slug_editing_js.mako
    M templates/webapps/galaxy/data_manager/view_job.mako
    M templates/webapps/galaxy/galaxy.masthead.mako
    M templates/webapps/galaxy/galaxy.panels.mako
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/library/common/browse_library.mako
    M templates/webapps/galaxy/library/common/ldda_info.mako
    M templates/webapps/galaxy/workflow/display.mako
    M templates/webapps/galaxy/workflow/run.mako
    M templates/webapps/galaxy/workflow/sharing.mako
    M templates/webapps/tool_shed/index.mako
    M templates/webapps/tool_shed/repository/common.mako
    M templates/webapps/tool_shed/repository/manage_repository.mako
    M templates/webapps/tool_shed/repository/view_changeset.mako
    A test-data/composite_output_expected_log
    M test/api/test_tools.py
    M test/api/workflows_format_2/converter.py
    M test/api/workflows_format_2/interface.py
    M test/api/workflows_format_2/main.py
    M test/base/interactor.py
    M test/functional/tools/composite_output.xml
    A test/functional/tools/multi_data_repeat.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/integration/test_pulsar_embedded.py
    M test/qunit/test-common.js
    R test/qunit/test-libs/qunit-1.14.0.css
    R test/qunit/test-libs/qunit-1.14.0.js
    A test/qunit/test-libs/qunit-1.23.1.css
    A test/qunit/test-libs/qunit-1.23.1.js
    A test/qunit/test-libs/sinon-1.17.3.js
    R test/qunit/test-libs/sinon-1.9.1.js
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    M test/qunit/tests/list-of-pairs-collection-creator.js
    M test/qunit/tests/metrics-logger.js
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    M test/qunit/tests/ui_tests.html
    M test/qunit/tests/ui_tests.js
    A test/qunit/tests/utils_test.html
    A test/qunit/tests/utils_test.js
    M test/qunit/tests/workflow_editor_tests.js
    M test/shed_functional/base/twilltestcase.py
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    M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
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    M test/unit/managers/test_HDAManager.py
    M test/unit/managers/test_HistoryManager.py
    M test/unit/test_objectstore.py
    M test/unit/unittest_utils/galaxy_mock.py
    M tools/data_source/biomart.xml
    M tools/data_source/upload.py
    M tools/filters/trimmer.xml
    M tools/stats/grouping.py
    M tools/stats/grouping.xml

  Log Message:
  -----------
  (merge conflicts)

  Commit: 4db7940a5cad685b9a81bf0f2ccc9ecac7f6aa7a
      https://github.com/galaxyproject/galaxy/commit/4db7940a5cad685b9a81bf0f2ccc9...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-17 (Tue, 17 May 2016)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/apps/history-panel.js
    M client/galaxy/style/less/base.less
    A client/galaxy/style/less/dataset.less
    M client/galaxy/style/less/flex.less
    M client/galaxy/style/less/history.less
    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/style/blue/base.css

  Log Message:
  -----------
  History: move to a flex based layout

Change right-hand side of Analysis page and the history-panel within it
to use flexbox for layout. Allow scrolling withiin list-items not the
entire view itself. Provides a fixed header containing the history
controls.

  Commit: ca842c264664c6ba364e3645027858f6c1a88a8d
      https://github.com/galaxyproject/galaxy/commit/ca842c264664c6ba364e364502785...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-17 (Tue, 17 May 2016)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/apps/history-panel.js
    M client/galaxy/scripts/mvc/collection/collection-li.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M client/galaxy/style/less/base.less
    A client/galaxy/style/less/dataset.less
    A client/galaxy/style/less/flex.less
    M client/galaxy/style/less/history.less
    M lib/galaxy/datatypes/registry.py
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/hdcas.py
    M lib/galaxy/managers/sharable.py
    M lib/galaxy/tools/cwl/cwltool_deps.py
    M lib/galaxy/tools/cwl/parser.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/evaluation.py
    M lib/galaxy/tools/lint.py
    M lib/galaxy/tools/linters/general.py
    M lib/galaxy/tools/loader_directory.py
    M lib/galaxy/tools/parser/cwl.py
    A scripts/api/filter_failed_datasets_from_collection.py
    M static/maps/mvc/collection/collection-li.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/tool/tool-form.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/collection/collection-li.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/tool/tool-form.js
    M static/style/blue/base.css
    A test-data/composite_output_expected_log
    M test/functional/tools/composite_output.xml
    M test/unit/managers/test_HDAManager.py
    M test/unit/managers/test_HistoryManager.py
    M test/unit/unittest_utils/galaxy_mock.py

  Log Message:
  -----------
  Merge branch 'history.fixed-header'

...into history-contents.limiting

  Commit: 6e866335d207848e566926f13d255ba53b3cae3c
      https://github.com/galaxyproject/galaxy/commit/6e866335d207848e566926f13d255...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-23 (Mon, 23 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/style/less/flex.less
    M client/galaxy/style/less/history.less
    M client/galaxy/style/less/list-item.less
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/datasets.py
    M lib/galaxy/managers/history_contents.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view.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/history/history-contents.js
    M static/scripts/mvc/history/history-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: paginate w/ horizontal scrolling

- Render sections side by side and allow scrolling between sections

- Also: improve accesibility query by eagerloading dataset.actions
and using cache for user roles

  Commit: c6f8a9f00cc7722c2aa28a087227c6822b6dd667
      https://github.com/galaxyproject/galaxy/commit/c6f8a9f00cc7722c2aa28a087227c...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-23 (Mon, 23 May 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    A client/galaxy/scripts/ui/scrollable-pages.js
    M static/maps/mvc/history/history-view.js.map
    A static/maps/ui/scrollable-pages.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/history/history-view.js
    A static/scripts/ui/scrollable-pages.js

  Log Message:
  -----------
  (add missing files)

  Commit: 9a3fb8ab37237d9b7ad5c3aa0fd3b62a0468ebc4
      https://github.com/galaxyproject/galaxy/commit/9a3fb8ab37237d9b7ad5c3aa0fd3b...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-26 (Thu, 26 May 2016)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    R client/galaxy/scripts/ui/scrollable-pages.js
    M client/galaxy/style/less/base.less
    M client/galaxy/style/less/history.less
    M client/galaxy/style/less/list-item.less
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.js.map
    R static/maps/ui/scrollable-pages.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/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-item.js
    M static/scripts/mvc/list/list-view.js
    R static/scripts/ui/scrollable-pages.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/view.mako

  Log Message:
  -----------
  UI, history: rollback other pagination prototypes

Attempts to remove most of the sectioning/infinite scrolling
prototypes but leave the cleanup/refactoring in place for another
attempt.

  Commit: 5ff73677bbd06d6fb33e0ceb29e7af29a28adce5
      https://github.com/galaxyproject/galaxy/commit/5ff73677bbd06d6fb33e0ceb29e7a...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-05-31 (Tue, 31 May 2016)

  Changed paths:
    M Makefile
    M README.rst
    M client/galaxy/scripts/layout/scratchbook.js
    M client/galaxy/scripts/mvc/form/form-data.js
    M client/galaxy/scripts/mvc/form/form-input.js
    M client/galaxy/scripts/mvc/form/form-parameters.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/form/form-view.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    R client/galaxy/scripts/mvc/tool/tool-template.js
    M client/galaxy/scripts/mvc/ui/ui-frames.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-portlet.js
    M client/galaxy/scripts/mvc/ui/ui-select-content.js
    M client/galaxy/scripts/mvc/ui/ui-select.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/frame.less
    M client/galaxy/style/less/ui.less
    M config/job_conf.xml.sample_advanced
    M contrib/nagios/check_galaxy.py
    M cron/build_chrom_db.py
    M doc/source/releases/16.01.rst
    A doc/source/releases/16.04.rst
    M doc/source/releases/16.04_announce.rst
    A doc/source/releases/16.07_announce.rst
    M doc/source/releases/index.rst
    M lib/galaxy/auth/providers/ldap_ad.py
    M lib/galaxy/config.py
    M lib/galaxy/datatypes/assembly.py
    M lib/galaxy/datatypes/binary.py
    A lib/galaxy/datatypes/checkers.py
    M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
    M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
    M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
    M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
    M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
    M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
    M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
    M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/genetics.py
    M lib/galaxy/datatypes/images.py
    M lib/galaxy/datatypes/interval.py
    M lib/galaxy/datatypes/molecules.py
    M lib/galaxy/datatypes/mothur.py
    M lib/galaxy/datatypes/msa.py
    M lib/galaxy/datatypes/ngsindex.py
    M lib/galaxy/datatypes/proteomics.py
    M lib/galaxy/datatypes/qualityscore.py
    M lib/galaxy/datatypes/registry.py
    M lib/galaxy/datatypes/sequence.py
    M lib/galaxy/datatypes/sniff.py
    M lib/galaxy/datatypes/tabular.py
    M lib/galaxy/datatypes/text.py
    M lib/galaxy/datatypes/tracks.py
    M lib/galaxy/datatypes/triples.py
    M lib/galaxy/datatypes/xml.py
    M lib/galaxy/dependencies/__init__.py
    M lib/galaxy/dependencies/conditional-requirements.txt
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/actions/post.py
    M lib/galaxy/jobs/deferred/__init__.py
    M lib/galaxy/jobs/deferred/data_transfer.py
    M lib/galaxy/jobs/handler.py
    M lib/galaxy/jobs/mapper.py
    M lib/galaxy/jobs/metrics/collectl/processes.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/condor.py
    M lib/galaxy/jobs/runners/drmaa.py
    M lib/galaxy/jobs/runners/local.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/jobs/runners/slurm.py
    M lib/galaxy/jobs/splitters/multi.py
    M lib/galaxy/jobs/transfer_manager.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/citations.py
    M lib/galaxy/managers/folders.py
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/libraries.py
    M lib/galaxy/managers/roles.py
    M lib/galaxy/managers/tags.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/mapping.py
    M lib/galaxy/model/migrate/versions/0001_initial_tables.py
    M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
    M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
    M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
    M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
    M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
    M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
    M lib/galaxy/model/migrate/versions/0009_request_table.py
    M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
    M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0012_user_address.py
    M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
    M lib/galaxy/model/migrate/versions/0014_pages.py
    M lib/galaxy/model/migrate/versions/0015_tagging.py
    M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
    M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
    M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
    M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
    M lib/galaxy/model/migrate/versions/0021_user_prefs.py
    M lib/galaxy/model/migrate/versions/0025_user_info.py
    M lib/galaxy/model/migrate/versions/0027_request_events.py
    M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
    M lib/galaxy/model/migrate/versions/0029_user_actions.py
    M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
    M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
    M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
    M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
    M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
    M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0037_samples_library.py
    M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0040_page_annotations.py
    M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
    M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
    M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
    M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
    M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
    M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
    M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
    M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
    M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
    M lib/galaxy/model/migrate/versions/0053_item_ratings.py
    M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
    M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
    M lib/galaxy/model/migrate/versions/0057_request_notify.py
    M lib/galaxy/model/migrate/versions/0058_history_import_export.py
    M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
    M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
    M lib/galaxy/model/migrate/versions/0061_tasks.py
    M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
    M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
    M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
    M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
    M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
    M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
    M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
    M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
    M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
    M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
    M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
    M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
    M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
    M lib/galaxy/model/migrate/versions/0080_quota_tables.py
    M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
    M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
    M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
    M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0085_add_task_info.py
    M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
    M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
    M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
    M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
    M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
    M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
    M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
    M lib/galaxy/model/migrate/versions/0096_openid_provider.py
    M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
    M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
    M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
    M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
    M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
    M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
    M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
    M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
    M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
    M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
    M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
    M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
    M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
    M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
    M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
    M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
    M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
    M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
    M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
    M lib/galaxy/model/tool_shed_install/mapping.py
    M lib/galaxy/openid/providers.py
    M lib/galaxy/security/__init__.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/actions/upload_common.py
    M lib/galaxy/tools/data/__init__.py
    M lib/galaxy/tools/data_manager/manager.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/commands.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/docker_util.py
    M 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/evaluation.py
    M lib/galaxy/tools/execute.py
    M lib/galaxy/tools/imp_exp/__init__.py
    M lib/galaxy/tools/imp_exp/export_history.py
    M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
    M lib/galaxy/tools/loader_directory.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/dynamic_options.py
    M lib/galaxy/tools/parameters/grouping.py
    M lib/galaxy/tools/parameters/sanitize.py
    M lib/galaxy/tools/parser/output_objects.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/parser/yaml.py
    M lib/galaxy/tools/test.py
    M lib/galaxy/tools/toolbox/watcher.py
    M lib/galaxy/tools/util/maf_utilities.py
    A lib/galaxy/tools/verify/__init__.py
    A lib/galaxy/tools/verify/asserts/__init__.py
    A lib/galaxy/tools/verify/asserts/tabular.py
    A lib/galaxy/tools/verify/asserts/text.py
    A lib/galaxy/tools/verify/asserts/xml.py
    A lib/galaxy/tools/verify/test_data.py
    M lib/galaxy/util/__init__.py
    R lib/galaxy/util/backports/importlib/__init__.py
    M lib/galaxy/util/checkers.py
    M lib/galaxy/util/directory_hash.py
    M lib/galaxy/util/inflection.py
    M lib/galaxy/visualization/data_providers/genome.py
    M lib/galaxy/visualization/genomes.py
    M lib/galaxy/visualization/plugins/config_parser.py
    M lib/galaxy/visualization/plugins/registry.py
    M lib/galaxy/visualization/plugins/resource_parser.py
    M lib/galaxy/web/base/controller.py
    M lib/galaxy/web/base/controllers/admin.py
    M lib/galaxy/web/base/interactive_environments.py
    M lib/galaxy/web/base/pluginframework.py
    M lib/galaxy/web/framework/base.py
    M lib/galaxy/web/framework/webapp.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/webapps/galaxy/api/datatypes.py
    M lib/galaxy/webapps/galaxy/api/folder_contents.py
    M lib/galaxy/webapps/galaxy/api/group_roles.py
    M lib/galaxy/webapps/galaxy/api/group_users.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/api/library_contents.py
    M lib/galaxy/webapps/galaxy/api/quotas.py
    M lib/galaxy/webapps/galaxy/api/remote_files.py
    M lib/galaxy/webapps/galaxy/api/search.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/api/visualizations.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/async.py
    M lib/galaxy/webapps/galaxy/controllers/biostar.py
    M lib/galaxy/webapps/galaxy/controllers/data_manager.py
    M lib/galaxy/webapps/galaxy/controllers/dataset.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M lib/galaxy/webapps/galaxy/controllers/library_common.py
    M lib/galaxy/webapps/galaxy/controllers/page.py
    M lib/galaxy/webapps/galaxy/controllers/requests_common.py
    M lib/galaxy/webapps/galaxy/controllers/root.py
    M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
    M lib/galaxy/webapps/galaxy/controllers/user.py
    M lib/galaxy/webapps/galaxy/controllers/visualization.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/controllers/upload.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
    M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
    M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
    M lib/galaxy/workflow/extract.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy_ext/metadata/set_metadata.py
    M lib/galaxy_utils/sequence/fastq.py
    M lib/galaxy_utils/sequence/vcf.py
    M lib/tool_shed/capsule/capsule_manager.py
    M lib/tool_shed/galaxy_install/dependency_display.py
    M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
    M lib/tool_shed/galaxy_install/install_manager.py
    M lib/tool_shed/galaxy_install/installed_repository_manager.py
    M lib/tool_shed/galaxy_install/migrate/common.py
    M lib/tool_shed/galaxy_install/repair_repository_manager.py
    M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
    M lib/tool_shed/galaxy_install/tool_migration_manager.py
    M lib/tool_shed/galaxy_install/tools/data_manager.py
    M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
    M lib/tool_shed/galaxy_install/update_repository_manager.py
    M lib/tool_shed/galaxy_install/utility_containers/__init__.py
    M lib/tool_shed/metadata/metadata_generator.py
    M lib/tool_shed/repository_registry.py
    M lib/tool_shed/tool_shed_registry.py
    M lib/tool_shed/tools/data_table_manager.py
    M lib/tool_shed/tools/tool_validator.py
    M lib/tool_shed/util/basic_util.py
    M lib/tool_shed/util/commit_util.py
    M lib/tool_shed/util/common_util.py
    M lib/tool_shed/util/hg_util.py
    M lib/tool_shed/util/readme_util.py
    M lib/tool_shed/util/shed_util_common.py
    M lib/tool_shed/util/tool_dependency_util.py
    M lib/tool_shed/util/tool_util.py
    M lib/tool_shed/util/xml_util.py
    M lib/tool_shed/utility_containers/__init__.py
    M lib/tool_shed/utility_containers/utility_container_manager.py
    M scripts/api/data_manager_example_execute.py
    M scripts/api/search.py
    M scripts/api/upload_to_history.py
    M scripts/bootstrap_history.py
    M scripts/check_galaxy.py
    M scripts/cleanup_datasets/cleanup_datasets.py
    M scripts/cleanup_datasets/pgcleanup.py
    M scripts/cleanup_datasets/populate_uuid.py
    M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
    M scripts/cleanup_datasets/rename_purged_datasets.py
    M scripts/cleanup_datasets/update_dataset_size.py
    M scripts/cleanup_datasets/update_metadata.py
    M scripts/common_startup.sh
    M scripts/data_libraries/build_lucene_index.py
    M scripts/data_libraries/build_whoosh_index.py
    M scripts/drmaa_external_killer.py
    M scripts/drmaa_external_runner.py
    M scripts/extract_dataset_part.py
    M scripts/microbes/BeautifulSoup.py
    M scripts/microbes/harvest_bacteria.py
    M scripts/others/incorrect_gops_jobs.py
    M scripts/others/incorrect_gops_join_jobs.py
    M scripts/runtime_stats.py
    M scripts/tool_shed/api/common.py
    M scripts/tool_shed/api/create_categories.py
    M scripts/tool_shed/api/create_users.py
    M scripts/tool_shed/api/import_capsule.py
    M scripts/tool_shed/api/reset_metadata_on_repositories.py
    M scripts/tool_shed/build_ts_whoosh_index.py
    M scripts/tool_shed/check_download_urls.py
    M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
    M scripts/tool_shed/deprecate_repositories_without_metadata.py
    M scripts/tools/maf/check_loc_file.py
    M scripts/transfer.py
    M static/maps/layout/scratchbook.js.map
    M static/maps/mvc/form/form-data.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/form/form-view.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/maps/mvc/ui/ui-frames.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-portlet.js.map
    M static/maps/mvc/ui/ui-select-content.js.map
    M static/maps/mvc/ui/ui-select.js.map
    M static/maps/utils/utils.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/layout/scratchbook.js
    M static/scripts/mvc/form/form-data.js
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/form/form-view.js
    M static/scripts/mvc/tool/tool-form-base.js
    M static/scripts/mvc/ui/ui-frames.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-portlet.js
    M static/scripts/mvc/ui/ui-select-content.js
    M static/scripts/mvc/ui/ui-select.js
    M static/scripts/utils/utils.js
    M static/style/blue/base.css
    M templates/show_params.mako
    M templates/webapps/galaxy/workflow/editor_tool_form.mako
    M test/api/test_datasets.py
    M test/api/test_tools.py
    M test/api/test_workflows.py
    R test/base/asserts/__init__.py
    R test/base/asserts/tabular.py
    R test/base/asserts/text.py
    R test/base/asserts/xml.py
    M test/base/driver_util.py
    R test/base/test_data.py
    M test/base/twilltestcase.py
    M test/casperjs/casperjs_runner.py
    M test/casperjs/server_env.py
    M test/functional/test_data_managers.py
    M test/functional/test_toolbox.py
    A test/functional/tools/composite_output_tests.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/functional/tools/simple_constructs.yml
    M test/qunit/test-app.js
    M test/qunit/test-data/fakeserver.js
    M test/qunit/tests/form_tests.js
    M test/qunit/tests/modal_tests.js
    M test/qunit/tests/ui_tests.html
    M test/qunit/tests/ui_tests.js
    M test/shed_functional/base/twilltestcase.py
    M test/shed_functional/functional/test_0060_workflows.py
    M test/shed_functional/functional/test_0100_complex_repository_dependencies.py
    M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
    M test/shed_functional/functional/test_0300_reset_all_metadata.py
    M test/shed_functional/functional/test_0310_hg_api_features.py
    M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
    M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
    M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
    M test/shed_functional/functional/test_1300_reset_all_metadata.py
    M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
    M test/shed_functional/functional_tests.py
    M test/unit/managers/test_CollectionManager.py
    M test/unit/managers/test_DatasetManager.py
    M test/unit/managers/test_HistoryManager.py
    M test/unit/tools/test_execution.py
    M test/unit/tools/test_select_parameters.py
    M test/unit/visualizations/plugins/test_VisualizationPlugin.py
    M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
    M test/unit/web/base/test_HookPluginManager.py
    M test/unit/web/base/test_PageServingPluginManager.py
    M test/unit/web/base/test_PluginManager.py
    M test/unit/web/framework/test_webapp.py
    M tools/data_source/data_source.py
    M tools/data_source/fetch.py
    M tools/data_source/hbvar_filter.py
    M tools/data_source/microbial_import.py
    M tools/data_source/upload.py
    M tools/evolution/add_scores.py
    M tools/extract/extract_genomic_dna.py
    M tools/extract/liftOver_wrapper.py
    M tools/filters/axt_to_concat_fasta.xml
    M tools/filters/axt_to_fasta.xml
    M tools/filters/axt_to_lav.py
    M tools/filters/axt_to_lav.xml
    M tools/filters/bed2gff.xml
    M tools/filters/bed_to_bigbed.xml
    M tools/filters/bed_to_gff_converter.py
    M tools/filters/gff/extract_GFF_Features.py
    M tools/filters/gff/gff_filter_by_attribute.py
    M tools/filters/gff2bed.xml
    M tools/filters/gff_to_bed_converter.py
    M tools/filters/gtf2bedgraph.xml
    M tools/filters/gtf_to_bedgraph_converter.py
    M tools/filters/join.py
    M tools/filters/joinWrapper.py
    M tools/filters/lav_to_bed.py
    M tools/filters/mergeCols.py
    M tools/filters/sff_extract.py
    M tools/filters/sorter.py
    M tools/filters/wiggle_to_simple.py
    M tools/genomespace/genomespace_exporter.py
    M tools/genomespace/genomespace_file_browser.py
    M tools/maf/interval_maf_to_merged_fasta.py
    M tools/maf/maf_split_by_species.py
    M tools/maf/maf_thread_for_species.py
    M tools/maf/maf_to_fasta_concat.py
    M tools/maf/maf_to_fasta_multiple_sets.py
    M tools/metag_tools/blat_wrapper.py
    M tools/metag_tools/shrimp_color_wrapper.py
    M tools/metag_tools/shrimp_wrapper.py
    M tools/next_gen_conversion/fastq_conversions.py
    M tools/next_gen_conversion/fastq_gen_conv.py
    M tools/next_gen_conversion/solid_to_fastq.py
    M tools/ngs_simulation/ngs_simulation.py
    M tools/phenotype_association/pagetag.py
    M tools/phenotype_association/senatag.py
    M tools/solid_tools/maq_cs_wrapper.py
    M tools/solid_tools/solid_qual_stats.py
    M tools/sr_assembly/velveth_wrapper.py
    M tools/sr_mapping/bfast_wrapper.py
    M tools/stats/aggregate_scores_in_intervals.py
    M tools/stats/filtering.py
    M tools/stats/filtering.xml
    M tools/stats/grouping.py
    M tools/stats/gsummary.py
    M tools/stats/gsummary.xml

  Log Message:
  -----------
  (merge conflicts)

  Commit: 769a2e583bdbe1939d26c5e4e1e549b36b690d59
      https://github.com/galaxyproject/galaxy/commit/769a2e583bdbe1939d26c5e4e1e54...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-02 (Thu, 02 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-item.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/history/embed.mako

  Log Message:
  -----------
  UI, history: re-implement pagination

Hopefully in a simpler way. This version does not account for hid
sections, but uses limit offset - which leaves other (non-hid) sort
orders as an option.

This commit also fixes:

* issues with the fixed header in the published section
* ajax loading for histories embedded in pages

  Commit: 495c352cd90e603364f6737569f83a557d878423
      https://github.com/galaxyproject/galaxy/commit/495c352cd90e603364f6737569f83...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-03 (Fri, 03 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/history/history-view.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: add pagination load indicator

And fixes some styling issues.

  Commit: 2a38b11e87bf58872850c23af0185c98cab491e4
      https://github.com/galaxyproject/galaxy/commit/2a38b11e87bf58872850c23af0185...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-06 (Mon, 06 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/collection/collection-view.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M lib/galaxy/managers/base.py
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-view.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view-edit-current.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/collection/collection-view.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, history: fixes

- re-delegates events for collection views
- extends clicking for contents-container in annotated history view
- loads first 10 histories *and* current history for initial set in
multi-history page

  Commit: 8b2b289973f0ee87b14bb9688306a8dc23ac7e2f
      https://github.com/galaxyproject/galaxy/commit/8b2b289973f0ee87b14bb9688306a...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-06 (Mon, 06 Jun 2016)

  Changed paths:
    M client/galaxy/style/less/base.less
    A client/galaxy/style/less/collection.less
    R client/galaxy/style/less/collections.less
    M static/style/blue/bootstrap-tour.css
    M static/style/blue/jquery.rating.css

  Log Message:
  -----------
  Styles: minor fixes

- corrects plurality of collection.less
- chmod on bootstrap-tour.css and jquery.rating.css

  Commit: 1297ce261a43228cb3ed11f26fccd88aebcb93df
      https://github.com/galaxyproject/galaxy/commit/1297ce261a43228cb3ed11f26fccd...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-06 (Mon, 06 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/collection/collection-view.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/collection.less
    M client/galaxy/style/less/history.less
    M static/maps/mvc/collection/collection-view.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/list/list-view.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/collection/collection-view.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: fix flex for collection view

  Commit: 01a25ff64f82075f0de07700a2772e3f5ff40337
      https://github.com/galaxyproject/galaxy/commit/01a25ff64f82075f0de07700a2772...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-07 (Tue, 07 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
    M client/galaxy/scripts/mvc/dataset/dataset-li.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/dataset/dataset-li-edit.js.map
    M static/maps/mvc/dataset/dataset-li.js.map
    M static/maps/mvc/dataset/dataset-model.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.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/dataset/dataset-li.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-item.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: rendering fixes

- Tries to strike a balance between subview reuse using detach to
preserve event hash and subview re-creation when fully re-rendering
a history by removing views from the viewMap.
- Makes actions section a full height to make empty, anon histories
looking normal.
- Makes dataset models wait until the change is returned from the
server before triggering change on the model.

  Commit: d89843ead7176b90aef13b7b26cc3f73fedc4c3b
      https://github.com/galaxyproject/galaxy/commit/d89843ead7176b90aef13b7b26cc3...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-07 (Tue, 07 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/list/list-view.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/history/history-model.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/list/list-view.js
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, history: fix to delete_current most_recent

Fixes delete_current's call to most_recent, filtering out the deleted
and purged histories. Now, on delete_current the most recently *non-
deleted* history will be switched to.

  Commit: 86acee5a743e7afca530f9a194f82c0ed83c4b1a
      https://github.com/galaxyproject/galaxy/commit/86acee5a743e7afca530f9a194f82...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-08 (Wed, 08 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/embed.mako

  Log Message:
  -----------
  UI, history: fix search and misc.

- corrects search to work for individual history views
- refactors handleItem{Deletion,Visible}Change in history view edit
- reverts the experiment in the branch that recycled subviews between
renders - this simplifies many things
- corrects the rendering, signals, and timing of loading indicators
- small fixes, refactorings, and simplifications

  Commit: a41ff4265b4f54b832e40c0dc71707db5eb307e6
      https://github.com/galaxyproject/galaxy/commit/a41ff4265b4f54b832e40c0dc7170...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-13 (Mon, 13 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/apps/history-panel.js
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M lib/galaxy/managers/base.py
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/base/controlled-fetch-collection.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: more minor fixes

  Commit: ae6cb1bf88ba4293c6be4c5df3a717bccaca73fd
      https://github.com/galaxyproject/galaxy/commit/ae6cb1bf88ba4293c6be4c5df3a71...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-13 (Mon, 13 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-annotated.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/history/history-model.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/display.mako

  Log Message:
  -----------
  UI, history: fix annotations in published history

  Commit: f072ee7807591902b8ae605474aa089a33ead93d
      https://github.com/galaxyproject/galaxy/commit/f072ee7807591902b8ae605474aa0...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-14 (Tue, 14 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/dataset.less
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/history/history-model.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/history/embed.mako
    M templates/webapps/galaxy/history/view.mako
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, history: change to front page when adding

- Causes the contents to load the 'front' page before adding new
datasets. This allows them to be added in the proper place.
- Fixes annotation display on datasets.
- Adds annotation loading to histories embedded in Pages.

  Commit: 1b2c5dea990ed91325eb6a85b16184a1647d2e20
      https://github.com/galaxyproject/galaxy/commit/1b2c5dea990ed91325eb6a85b1618...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-15 (Wed, 15 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.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/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/history/embed.mako
    M templates/webapps/galaxy/history/view.mako

  Log Message:
  -----------
  UI, history: show search progress in subtitle

  Commit: 233d6d8d32e94671ce387efdb39f35bd3454eb8d
      https://github.com/galaxyproject/galaxy/commit/233d6d8d32e94671ce387efdb39f3...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-15 (Wed, 15 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/history-view.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/history/history-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: minor style/pagination fixes

  Commit: 6eb1cefe88b50eea7beb982bbfaf5674f13e7313
      https://github.com/galaxyproject/galaxy/commit/6eb1cefe88b50eea7beb982bbfaf5...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-15 (Wed, 15 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-view.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/history/history-view.js

  Log Message:
  -----------
  UI, history: get element count for all histories

- Moves the ajax call for hdca element counts to a listener of the
loading-done event. This allows (almost) all history views to be
decorated with hdca counts.

  Commit: fd78f99d61bcb141475875b85d3beb2945bc3a8e
      https://github.com/galaxyproject/galaxy/commit/fd78f99d61bcb141475875b85d3be...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-15 (Wed, 15 Jun 2016)

  Changed paths:
    M .ci/py3_sources.txt
    M client/bower.json
    R client/galaxy/scripts/libs/tracekit.js
    M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tools.js
    M client/galaxy/scripts/mvc/ui/ui-select-content.js
    M client/galaxy/style/less/library.less
    M client/grunt-tasks/install-libs.js
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/job_conf.xml.sample_advanced
    M config/tool_conf.xml.sample
    M contrib/galaxy_config_merger.py
    M contrib/nagios/check_galaxy.py
    M cron/build_chrom_db.py
    M cron/parse_builds.py
    M cron/parse_builds_3_sites.py
    M doc/source/dev/faq.rst
    M lib/galaxy/config.py
    M lib/galaxy/datatypes/binary.py
    M lib/galaxy/datatypes/molecules.py
    M lib/galaxy/datatypes/mothur.py
    M lib/galaxy/datatypes/sequence.py
    M lib/galaxy/datatypes/tabular.py
    A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/external_services/actions.py
    M lib/galaxy/external_services/parameters.py
    M lib/galaxy/external_services/service.py
    M lib/galaxy/forms/forms.py
    M lib/galaxy/jobs/actions/post.py
    M lib/galaxy/jobs/command_factory.py
    M lib/galaxy/jobs/metrics/instrumenters/collectl.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/drmaa.py
    A lib/galaxy/jobs/runners/kubernetes.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/jobs/runners/slurm.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
    M lib/galaxy/objectstore/__init__.py
    M lib/galaxy/objectstore/s3.py
    M lib/galaxy/security/__init__.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
    A lib/galaxy/tools/actions/model_operations.py
    M lib/galaxy/tools/cwl/parser.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/data_manager/manager.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/evaluation.py
    M lib/galaxy/tools/execute.py
    A lib/galaxy/tools/filter_failed_collection.xml
    A lib/galaxy/tools/flatten_collection.xml
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/dataset_matcher.py
    M lib/galaxy/tools/parameters/meta.py
    M lib/galaxy/tools/parameters/wrapped.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/filters/__init__.py
    A lib/galaxy/tools/unzip_collection.xml
    M lib/galaxy/tools/verify/__init__.py
    A lib/galaxy/tools/zip_collection.xml
    M lib/galaxy/util/__init__.py
    R lib/galaxy/util/directory_hash.py
    M lib/galaxy/visualization/data_providers/genome.py
    M lib/galaxy/web/base/controllers/admin.py
    M lib/galaxy/web/security/__init__.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/external_services.py
    M lib/galaxy/webapps/galaxy/controllers/user.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/tool_shed/api/categories.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
    M lib/galaxy/webapps/tool_shed/controllers/admin.py
    M lib/galaxy/webapps/tool_shed/controllers/hg.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
    M lib/galaxy/webapps/tool_shed/controllers/upload.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/galaxy/webapps/tool_shed/security/__init__.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy_utils/sequence/fastq.py
    M lib/tool_shed/capsule/capsule_manager.py
    M lib/tool_shed/dependencies/attribute_handlers.py
    M lib/tool_shed/dependencies/repository/relation_builder.py
    M lib/tool_shed/galaxy_install/dependency_display.py
    M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
    M lib/tool_shed/galaxy_install/install_manager.py
    M lib/tool_shed/galaxy_install/installed_repository_manager.py
    M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
    M lib/tool_shed/galaxy_install/repair_repository_manager.py
    M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
    M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
    M lib/tool_shed/galaxy_install/tool_migration_manager.py
    M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
    M lib/tool_shed/galaxy_install/update_repository_manager.py
    M lib/tool_shed/grids/repository_grids.py
    M lib/tool_shed/grids/util.py
    M lib/tool_shed/metadata/metadata_generator.py
    M lib/tool_shed/metadata/repository_metadata_manager.py
    M lib/tool_shed/repository_registry.py
    M lib/tool_shed/repository_types/metadata.py
    M lib/tool_shed/tools/tool_validator.py
    M lib/tool_shed/tools/tool_version_manager.py
    M lib/tool_shed/util/basic_util.py
    M lib/tool_shed/util/common_util.py
    M lib/tool_shed/util/container_util.py
    M lib/tool_shed/util/metadata_util.py
    M lib/tool_shed/util/readme_util.py
    M lib/tool_shed/util/repository_util.py
    M lib/tool_shed/util/shed_util_common.py
    M lib/tool_shed/util/workflow_util.py
    M lib/tool_shed/utility_containers/utility_container_manager.py
    M scripts/cleanup_datasets/admin_cleanup_datasets.py
    M scripts/cleanup_datasets/cleanup_datasets.py
    R static/maps/libs/tracekit.js.map
    M static/maps/mvc/library/library-foldertoolbar-view.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tools.js.map
    M static/maps/mvc/ui/ui-select-content.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
    R static/scripts/libs/tracekit.js
    M static/scripts/mvc/library/library-foldertoolbar-view.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tools.js
    M static/scripts/mvc/ui/ui-select-content.js
    M static/style/blue/base.css
    M static/style/blue/library.css
    M templates/admin/tool_shed_repository/repair_repository.mako
    M templates/base.mako
    M templates/base/base_panels.mako
    M templates/js-app.mako
    M templates/show_params.mako
    M templates/webapps/galaxy/galaxy.panels.mako
    M templates/webapps/galaxy/workflow/display.mako
    M templates/webapps/galaxy/workflow/run.mako
    M templates/webapps/galaxy/workflow/sharing.mako
    M templates/webapps/tool_shed/repository/common.mako
    A test-data/biom1_metadata_test.txt
    A test-data/input_taxonomy.biom1
    M test/api/helpers.py
    M test/api/test_tools.py
    M test/api/test_workflows.py
    M test/api/test_workflows_from_yaml.py
    M test/base/interactor.py
    M test/base/twilltestcase.py
    A test/functional/tools/checksum.xml
    A test/functional/tools/exit_code_from_file.xml
    A test/functional/tools/metadata_biom1.xml
    M test/functional/tools/sample_datatypes_conf.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/shed_functional/base/twilltestcase.py
    M test/shed_functional/functional/test_0000_basic_repository_features.py
    M test/shed_functional/functional/test_1000_install_basic_repository.py
    M test/unit/tools/test_actions.py
    M test/unit/tools/test_data_parameters.py
    M test/unit/tools/test_dataset_matcher.py
    M test/unit/tools/test_parameter_parsing.py
    M test/unit/tools/test_select_parameters.py
    M test/unit/workflows/test_run_parameters.py
    M tool_list.py
    M tools/data_source/data_source.py
    M tools/data_source/fetch.py
    M tools/data_source/genbank.py
    M tools/data_source/hbvar_filter.py
    M tools/data_source/import.py
    M tools/data_source/microbial_import.py
    M tools/data_source/microbial_import_code.py
    M tools/data_source/upload.py
    M tools/filters/axt_to_lav.py

  Log Message:
  -----------
  (merge conflicts)

  Commit: 48f48e9bd29430f58363eb47d95154ff4854ebe7
      https://github.com/galaxyproject/galaxy/commit/48f48e9bd29430f58363eb47d9515...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-23 (Thu, 23 Jun 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/style/less/history.less
    M client/galaxy/style/less/list-item.less
    M static/maps/mvc/history/history-view.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/history/history-view.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/history/view.mako

  Log Message:
  -----------
  UI, history: style cleanup, small tweaks

- Corrects history control sizing on Safari
- Corrects ul, li rendering of history in Chrome
- Lengthens fadeout of loading indicator to better transition when
rendering large numbers of contents
- Corrects page controls in history/view

  Commit: 6c6bfe5614f6fed3c88b19789369ee3f5aabc86b
      https://github.com/galaxyproject/galaxy/commit/6c6bfe5614f6fed3c88b19789369e...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-06-23 (Thu, 23 Jun 2016)

  Changed paths:
    M config/datatypes_conf.xml.sample
    M lib/galaxy/model/__init__.py
    M lib/galaxy/webapps/galaxy/api/visualizations.py
    M lib/galaxy/webapps/galaxy/controllers/dataset.py
    M lib/galaxy/webapps/galaxy/controllers/library_common.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M templates/webapps/galaxy/dataset/copy_view.mako
    M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
    M tools/filters/sff_extract.py

  Log Message:
  -----------
  (merge conflicts)

  Commit: cc8d421c570df3b3b8c53ba49ad1247729102ad1
      https://github.com/galaxyproject/galaxy/commit/cc8d421c570df3b3b8c53ba49ad12...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-05 (Tue, 05 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/scripts/ui/search-input.js
    M client/galaxy/style/less/ui/search-input.less
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.js.map
    M static/maps/ui/search-input.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/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js
    M static/scripts/ui/search-input.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: search and ui/search-input

- clarifies search progress in subtitle of edit/current histories
- corrects found display in subtitle when no results are found
- does not cause a search and render when entering the same terms
- does not clear search on full backspace or cut of input text
- does not cause clear and render if no previous terms existed
- removes onchange from search input (not needed yet)

  Commit: b1d652e59d6ccde1e73c90ffd483bbd600d110ff
      https://github.com/galaxyproject/galaxy/commit/b1d652e59d6ccde1e73c90ffd483b...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-05 (Tue, 05 Jul 2016)

  Changed paths:
    M .ci/py3_sources.txt
    M Makefile
    M client/galaxy/scripts/viz/trackster/painters.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/job_conf.xml.sample_advanced
    M config/plugins/interactive_environments/jupyter/config/jupyter.xml
    A display_applications/igv/bigwig.xml
    M lib/galaxy/config.py
    M lib/galaxy/dataset_collections/structure.py
    M lib/galaxy/datatypes/binary.py
    M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
    M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
    M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
    M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
    M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
    M lib/galaxy/datatypes/converters/interval_to_coverage.py
    M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
    M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
    M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
    M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
    M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
    M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
    M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
    M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
    M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
    M lib/galaxy/datatypes/dataproviders/column.py
    M lib/galaxy/datatypes/dataproviders/line.py
    M lib/galaxy/datatypes/sequence.py
    M lib/galaxy/datatypes/sniff.py
    M lib/galaxy/datatypes/tabular.py
    M lib/galaxy/datatypes/util/gff_util.py
    M lib/galaxy/jobs/runners/kubernetes.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/context.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/mapping.py
    M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
    M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
    M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
    M lib/galaxy/model/migrate/versions/0009_request_table.py
    M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
    M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0012_user_address.py
    M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
    M lib/galaxy/model/migrate/versions/0014_pages.py
    M lib/galaxy/model/migrate/versions/0015_tagging.py
    M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
    M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
    M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
    M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
    M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
    M lib/galaxy/model/migrate/versions/0021_user_prefs.py
    M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
    M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
    M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
    M lib/galaxy/model/migrate/versions/0025_user_info.py
    M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0027_request_events.py
    M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
    M lib/galaxy/model/migrate/versions/0029_user_actions.py
    M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
    M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
    M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
    M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
    M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
    M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
    M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0037_samples_library.py
    M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
    M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
    M lib/galaxy/model/migrate/versions/0040_page_annotations.py
    M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
    M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
    M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
    M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
    M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
    M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
    M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
    M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
    M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
    M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
    M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
    M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
    M lib/galaxy/model/migrate/versions/0053_item_ratings.py
    M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
    M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
    M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
    M lib/galaxy/model/migrate/versions/0057_request_notify.py
    M lib/galaxy/model/migrate/versions/0058_history_import_export.py
    M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
    M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
    M lib/galaxy/model/migrate/versions/0061_tasks.py
    M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
    M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
    M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
    M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
    M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
    M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
    M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
    M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
    M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
    M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
    M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
    M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
    M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
    M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
    M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
    M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
    M lib/galaxy/model/migrate/versions/0080_quota_tables.py
    M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
    M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
    M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
    M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
    M lib/galaxy/model/migrate/versions/0085_add_task_info.py
    M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
    M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
    M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
    M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
    M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
    M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
    M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
    M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
    M lib/galaxy/model/migrate/versions/0096_openid_provider.py
    M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
    M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
    M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
    M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
    M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
    M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
    M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
    M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
    M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
    M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
    M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
    M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
    M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
    M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
    M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
    M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
    M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
    M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
    M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
    M lib/galaxy/model/migrate/versions/0119_job_metrics.py
    M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
    M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
    M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
    M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
    M lib/galaxy/model/migrate/versions/0124_job_state_history.py
    M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
    M lib/galaxy/model/migrate/versions/0126_password_reset.py
    M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
    M lib/galaxy/model/migrate/versions/0128_session_timeout.py
    M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
    M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
    M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
    A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
    M lib/galaxy/security/__init__.py
    M lib/galaxy/security/passwords.py
    M lib/galaxy/tools/parameters/dataset_matcher.py
    M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
    M lib/galaxy/visualization/genomes.py
    M lib/galaxy/web/base/interactive_environments.py
    M lib/galaxy/web/proxy/js/lib/proxy.js
    M lib/galaxy/webapps/galaxy/controllers/user.py
    M lib/galaxy/webapps/tool_shed/config.py
    M run_tests.sh
    M scripts/api/data_manager_example_execute.py
    M scripts/api/example_watch_folder.py
    M scripts/api/form_create_from_xml.py
    M scripts/api/history_create_history.py
    M scripts/api/history_delete_history.py
    M scripts/api/import_library_dataset_to_history.py
    M scripts/api/import_workflows_from_installed_tool_shed_repository.py
    M scripts/api/library_create_folder.py
    M scripts/api/library_create_library.py
    M scripts/api/library_upload_from_import_dir.py
    M scripts/api/load_data_with_metadata.py
    M scripts/api/repair_tool_shed_repository.py
    M scripts/api/request_type_create_from_xml.py
    M scripts/api/requests_update_state.py
    M scripts/api/sample_dataset_update_status.py
    M scripts/api/sample_update_state.py
    M scripts/api/search.py
    M scripts/api/sequencer_configuration_create.py
    M scripts/api/upload_to_history.py
    M scripts/api/workflow_delete.py
    M scripts/api/workflow_execute.py
    M scripts/api/workflow_import.py
    M scripts/api/workflow_import_from_file_rpark.py
    M scripts/bootstrap_history.py
    M scripts/build_toolbox.py
    M scripts/check_galaxy.py
    M scripts/check_python.py
    M scripts/cleanup_datasets/pgcleanup.py
    M scripts/cleanup_datasets/populate_uuid.py
    M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
    M scripts/cleanup_datasets/rename_purged_datasets.py
    M scripts/cleanup_datasets/update_dataset_size.py
    M scripts/cleanup_datasets/update_metadata.py
    M scripts/data_libraries/build_whoosh_index.py
    M scripts/db_shell.py
    M scripts/drmaa_external_runner.py
    M scripts/fetch_eggs.py
    M scripts/set_dataset_sizes.py
    M static/maps/viz/trackster/painters.js.map
    M static/maps/viz/trackster/tracks.js.map
    M static/scripts/viz/trackster/painters.js
    M static/scripts/viz/trackster/tracks.js
    M templates/user/change_password.mako
    M test/api/helpers.py
    M test/api/test_datasets.py
    M test/api/test_tool_data.py
    M test/api/test_workflow_extraction.py
    M test/api/test_workflows.py
    M test/shed_functional/base/twilltestcase.py
    M test/shed_functional/functional_tests.py
    M test/unit/datatypes/dataproviders/test_base_dataproviders.py
    M test/unit/datatypes/dataproviders/test_line_dataproviders.py
    M test/unit/managers/base.py
    M test/unit/managers/test_DatasetManager.py
    M test/unit/managers/test_HDAManager.py
    M test/unit/managers/test_HDCAManager.py
    M test/unit/managers/test_HistoryContentsManager.py
    M test/unit/managers/test_HistoryManager.py
    M test/unit/managers/test_UserManager.py
    M test/unit/test_galaxy_mapping.py
    M test/unit/tools/test_toolbox.py
    M test/unit/visualizations/plugins/test_VisualizationPlugin.py
    M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
    M test/unit/web/base/test_HookPluginManager.py
    M test/unit/web/base/test_PageServingPluginManager.py
    M test/unit/web/base/test_PluginManager.py
    M tools/stats/aggregate_scores_in_intervals.py
    M tox.ini

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: dd37dedc2a1e570053b8be9b0f8896cca8bc4cd0
      https://github.com/galaxyproject/galaxy/commit/dd37dedc2a1e570053b8be9b0f889...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-06 (Wed, 06 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/collection/collection-li.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/collection/collection-li.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/history/history-view.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: scroll to new items, clean up

  Commit: 8a159ade93040ea1cb6a0657c7089eebc5a92366
      https://github.com/galaxyproject/galaxy/commit/8a159ade93040ea1cb6a0657c7089...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-06 (Wed, 06 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/collection/collection-li-edit.js
    M client/galaxy/scripts/mvc/collection/collection-view.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/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/hda-li-edit.js
    M client/galaxy/scripts/mvc/history/hda-li.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-li-edit.js.map
    M static/maps/mvc/collection/collection-view.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/dataset/dataset-model.js.map
    M static/maps/mvc/history/hda-li-edit.js.map
    M static/maps/mvc/history/hda-li.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.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/dataset/dataset-li-edit.js
    M static/scripts/mvc/dataset/dataset-li.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/list/list-view.js
    M static/style/blue/base.css

  Log Message:
  -----------
  UI, history: clean up

  Commit: aee39774121ef2610387431b6024ddd12c997834
      https://github.com/galaxyproject/galaxy/commit/aee39774121ef2610387431b6024d...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-11 (Mon, 11 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/multi-panel.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/history/history-view-edit.js
    M static/scripts/mvc/history/multi-panel.js

  Log Message:
  -----------
  UI, history: switch to front when dropping content

When a history with a drop target accepts data to be copied, this
has the view's current page switch to the top/front before the copy
happens.

  Commit: e842e0b2ba5c77674e11f8a1a0eceb4765db2621
      https://github.com/galaxyproject/galaxy/commit/e842e0b2ba5c77674e11f8a1a0ece...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-11 (Mon, 11 Jul 2016)

  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
    M test/qunit/tests/history_contents_model_tests.js

  Log Message:
  -----------
  Tests, history: hda delete happens after return

- Change qunit test history_contents_model_tests to account for the
use of the '{ wait: true }' backbone flag being used when 'save'd.
This causes the attribute to be set when the ajax call returns
successfully.

  Commit: a33203b3b5d5ad9b74ff00a693dcb85efff746e3
      https://github.com/galaxyproject/galaxy/commit/a33203b3b5d5ad9b74ff00a693dcb...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-12 (Tue, 12 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.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/history/history-view.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: increase page select affordance

  Commit: 817c63eeea3d13604f7e9faa817d973f18ab52c6
      https://github.com/galaxyproject/galaxy/commit/817c63eeea3d13604f7e9faa817d9...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-12 (Tue, 12 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/dataset/data.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M lib/galaxy/datatypes/binary.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/molecules.py
    M lib/galaxy/datatypes/tabular.py
    M lib/galaxy/datatypes/text.py
    M lib/galaxy/jobs/runners/kubernetes.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/wrappers.py
    M lib/galaxy/webapps/galaxy/api/datasets.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/dataset.py
    M lib/galaxy/webapps/galaxy/controllers/tag.py
    M lib/galaxy/workflow/modules.py
    M scripts/common_startup.sh
    M setup.cfg
    M static/maps/mvc/dataset/data.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    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/dataset/data.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tool-template.js
    M test/api/test_tools.py
    A test/functional/tools/identifier_collection.xml
    M test/functional/tools/samples_tool_conf.xml

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: 709ae896ea40a60127d814087c6f56327f79bf3e
      https://github.com/galaxyproject/galaxy/commit/709ae896ea40a60127d814087c6f5...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-12 (Tue, 12 Jul 2016)

  Changed paths:
    M lib/galaxy/managers/history_contents.py

  Log Message:
  -----------
  Serializer: better name & doc

  Commit: 87fbdc4ad6345ebe56d652358e34e9de57981535
      https://github.com/galaxyproject/galaxy/commit/87fbdc4ad6345ebe56d652358e34e...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-12 (Tue, 12 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M static/maps/mvc/history/history-view.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/history/history-view.js

  Log Message:
  -----------
  UI, history: create tooltip on each render

  Commit: 53f34b8c9e2105972e82f22a5f802399b6656f0a
      https://github.com/galaxyproject/galaxy/commit/53f34b8c9e2105972e82f22a5f802...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-28 (Thu, 28 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-view-edit-current.js

  Log Message:
  -----------
  UI, history: rerender contents on unhiding hidden

- Waits till all hidden datasets are saved as unhidden and then, if the
history is not showing hidden datasets, rerenders the entire contents

  Commit: 97b171632d9b16e54fad4b46b0f419bf31866882
      https://github.com/galaxyproject/galaxy/commit/97b171632d9b16e54fad4b46b0f41...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-28 (Thu, 28 Jul 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/list/list-view.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/list/list-view.js

  Log Message:
  -----------
  UI, history: render on deleted/hidden toggle

- Fixes lack of render when only one hidden/deleted dataset is shown
by sending a `renderAll` flag then caught by the update listener

  Commit: 62de9bf76a6e5a6d7857ad031f8499d7453e12ea
      https://github.com/galaxyproject/galaxy/commit/62de9bf76a6e5a6d7857ad031f849...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-07-28 (Thu, 28 Jul 2016)

  Changed paths:
    M .ci/flake8_blacklist.txt
    A .ci/flake8_lint_include_list.txt
    A .ci/flake8_wrapper_imports.sh
    M .ci/py3_sources.txt
    M .gitignore
    M .travis.yml
    A client/galaxy/scripts/layout/generic-nav-view.js
    M client/galaxy/scripts/layout/menu.js
    M client/galaxy/scripts/layout/page.js
    M client/galaxy/scripts/mvc/collection/collection-li.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/collection/collection-view-edit.js
    M client/galaxy/scripts/mvc/collection/collection-view.js
    M client/galaxy/scripts/mvc/form/form-data.js
    M client/galaxy/scripts/mvc/form/form-parameters.js
    M client/galaxy/scripts/mvc/form/form-repeat.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/form/form-view.js
    M client/galaxy/scripts/mvc/history/hdca-li-edit.js
    M client/galaxy/scripts/mvc/history/hdca-li.js
    M client/galaxy/scripts/mvc/history/hdca-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M client/galaxy/scripts/mvc/ui/ui-buttons.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-select-content.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.js
    M client/galaxy/scripts/mvc/ui/ui-tabs.js
    M client/galaxy/scripts/mvc/upload/default/default-view.js
    M client/galaxy/scripts/mvc/upload/upload-button.js
    M client/galaxy/scripts/mvc/upload/upload-view.js
    M client/galaxy/style/less/base.less
    M client/galaxy/style/less/ui.less
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M config/job_conf.xml.sample_advanced
    M config/object_store_conf.xml.sample
    A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
    A config/plugins/interactive_environments/neo/config/neo.ini.sample
    A config/plugins/interactive_environments/neo/config/neo.xml
    A config/plugins/interactive_environments/neo/static/js/neo.js
    A config/plugins/interactive_environments/neo/templates/neo.mako
    M config/plugins/visualizations/charts/static/app.css
    M config/plugins/visualizations/charts/static/app.js
    M config/plugins/visualizations/charts/static/charts/forms/default.js
    M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
    M config/plugins/visualizations/charts/static/library/datasets.js
    M config/plugins/visualizations/charts/static/library/jobs.js
    M config/plugins/visualizations/charts/static/library/storage.js
    R config/plugins/visualizations/charts/static/library/ui-table-form.js
    M config/plugins/visualizations/charts/static/models/chart.js
    M config/plugins/visualizations/charts/static/models/config.js
    R config/plugins/visualizations/charts/static/models/group.js
    R config/plugins/visualizations/charts/static/models/groups.js
    M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
    M config/plugins/visualizations/charts/static/views/editor.js
    R config/plugins/visualizations/charts/static/views/group.js
    A config/plugins/visualizations/charts/static/views/groups.js
    M config/plugins/visualizations/charts/static/views/settings.js
    M config/plugins/visualizations/charts/static/views/types.js
    M config/plugins/visualizations/charts/static/views/viewer.js
    M config/plugins/visualizations/charts/static/views/viewport.js
    M config/plugins/visualizations/graphviz/config/graphviz.xml
    M config/plugins/visualizations/graphviz/static/js/graphVis.js
    M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
    M config/plugins/visualizations/graphviz/templates/graphviz.mako
    M config/tool_data_table_conf.xml.sample
    A config/tool_destinations.yml.sample
    A display_applications/ucsc/trackhub.xml
    A doc/source/admin/grt.rst
    M doc/source/admin/index.rst
    M doc/source/admin/interactive_environments.rst
    M doc/source/dev/index.rst
    A doc/source/dev/interactive_environments.rst
    M doc/source/lib/galaxy.objectstore.rst
    M lib/galaxy/config.py
    M lib/galaxy/datatypes/data.py
    A lib/galaxy/datatypes/neo4j.py
    M lib/galaxy/datatypes/set_metadata_tool.xml
    M lib/galaxy/datatypes/tracks.py
    M lib/galaxy/dependencies/__init__.py
    M lib/galaxy/dependencies/conditional-requirements.txt
    M lib/galaxy/dependencies/pinned-requirements.txt
    M lib/galaxy/jobs/actions/post.py
    A lib/galaxy/jobs/dynamic_tool_destination.py
    M lib/galaxy/jobs/mapper.py
    M lib/galaxy/jobs/runners/kubernetes.py
    M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/configuration.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/mapping.py
    M lib/galaxy/objectstore/__init__.py
    A lib/galaxy/objectstore/azure_blob.py
    M lib/galaxy/security/validate_user_input.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/resolvers/__init__.py
    M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
    M lib/galaxy/tools/deps/resolvers/homebrew.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
    M lib/galaxy/tools/deps/views.py
    M lib/galaxy/tools/execute.py
    M lib/galaxy/tools/parameters/basic.py
    A lib/galaxy/tools/toolbox/requirements.py
    M lib/galaxy/tools/wrappers.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/web/__init__.py
    M lib/galaxy/web/base/controller.py
    M lib/galaxy/web/buildapp.py
    M lib/galaxy/web/framework/base.py
    M lib/galaxy/web/framework/decorators.py
    M lib/galaxy/web/framework/helpers/__init__.py
    M lib/galaxy/web/framework/middleware/remoteuser.py
    M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/api/users.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/dataset.py
    M lib/galaxy/webapps/galaxy/controllers/forms.py
    M lib/galaxy/webapps/galaxy/controllers/library_common.py
    M lib/galaxy/webapps/galaxy/controllers/root.py
    M lib/galaxy/webapps/galaxy/controllers/user.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    A lib/galaxy/webapps/reports/controllers/history.py
    A lib/galaxy/webapps/reports/controllers/tools.py
    M lib/galaxy/webapps/reports/controllers/users.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/workflow/extract.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy/workflow/render.py
    M lib/tool_shed/galaxy_install/install_manager.py
    M lib/tool_shed/galaxy_install/repair_repository_manager.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
    M lib/tool_shed/util/shed_util_common.py
    A scripts/communication/communication_server.py
    A scripts/communication/template/communication.css
    A scripts/communication/template/communication.html
    A scripts/communication/template/communication.js
    A scripts/grt.py
    A scripts/grt.yml.sample
    M setup.cfg
    A static/maps/layout/generic-nav-view.js.map
    M static/maps/layout/menu.js.map
    M static/maps/layout/page.js.map
    M static/maps/mvc/collection/collection-li.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/collection/collection-view-edit.js.map
    M static/maps/mvc/collection/collection-view.js.map
    M static/maps/mvc/form/form-data.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-repeat.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/form/form-view.js.map
    M static/maps/mvc/history/hdca-li-edit.js.map
    M static/maps/mvc/history/hdca-li.js.map
    M static/maps/mvc/history/hdca-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tool-form.js.map
    M static/maps/mvc/ui/ui-buttons.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-select-content.js.map
    M static/maps/mvc/ui/ui-select-default.js.map
    M static/maps/mvc/ui/ui-tabs.js.map
    M static/maps/mvc/upload/default/default-view.js.map
    M static/maps/mvc/upload/upload-button.js.map
    M static/maps/mvc/upload/upload-view.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/layout/generic-nav-view.js
    M static/scripts/layout/menu.js
    M static/scripts/layout/page.js
    M static/scripts/mvc/collection/collection-li.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/collection/collection-view-edit.js
    M static/scripts/mvc/collection/collection-view.js
    M static/scripts/mvc/form/form-data.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-repeat.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/form/form-view.js
    M static/scripts/mvc/history/hdca-li-edit.js
    M static/scripts/mvc/history/hdca-li.js
    M static/scripts/mvc/history/hdca-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/tool/tool-form-base.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tool-form.js
    M static/scripts/mvc/ui/ui-buttons.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-select-content.js
    M static/scripts/mvc/ui/ui-select-default.js
    M static/scripts/mvc/ui/ui-tabs.js
    M static/scripts/mvc/upload/default/default-view.js
    M static/scripts/mvc/upload/upload-button.js
    M static/scripts/mvc/upload/upload-view.js
    A static/style/base.css
    M static/style/blue/base.css
    M templates/admin/impersonate.mako
    M templates/admin/tool_shed_repository/common.mako
    M templates/admin/tool_shed_repository/manage_repository.mako
    M templates/admin/tool_shed_repository/preview_repository.mako
    M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
    M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
    M templates/admin/tool_shed_repository/select_tool_panel_section.mako
    M templates/base.mako
    M templates/base/base_panels.mako
    M templates/ind_share_base.mako
    M templates/js-app.mako
    A templates/user/communication_settings.mako
    M templates/user/index.mako
    M templates/webapps/galaxy/history/grid.mako
    A templates/webapps/reports/history_and_dataset_per_user.mako
    A templates/webapps/reports/history_and_dataset_type.mako
    A templates/webapps/reports/history_per_user.mako
    M templates/webapps/reports/index.mako
    A templates/webapps/reports/tool_error_messages.mako
    A templates/webapps/reports/tool_execution_time.mako
    A templates/webapps/reports/tool_execution_time_per_month.mako
    A templates/webapps/reports/tools_and_job_state.mako
    A templates/webapps/reports/tools_and_job_state_per_month.mako
    M templates/webapps/tool_shed/repository/common.mako
    M templates/webapps/tool_shed/repository/export_repository.mako
    A test-data/neostore.zip
    M test/api/test_users.py
    M test/api/test_workflows.py
    M test/base/driver_util.py
    M test/base/twilltestcase.py
    A test/functional/tools/output_filter_exception_1.xml
    M test/functional/tools/samples_tool_conf.xml
    A test/integration/test_resolvers.py
    M test/qunit/tests/ui_tests.js
    M test/qunit/tests/upload_dialog_tests.js
    M test/shed_functional/base/twilltestcase.py
    M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
    M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
    A test/unit/datatypes/test_data.py
    A test/unit/jobs/dynamic_tool_destination/__init__.py
    A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
    A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
    A test/unit/jobs/dynamic_tool_destination/data/test.empty
    A test/unit/jobs/dynamic_tool_destination/data/test.fasta
    A test/unit/jobs/dynamic_tool_destination/data/test1.full
    A test/unit/jobs/dynamic_tool_destination/data/test3.full
    A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
    A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
    A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
    A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
    A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
    A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
    A test/unit/jobs/dynamic_tool_destination/ymltests.py
    M test/unit/managers/test_UserManager.py
    M test/unit/tools/test_conda_resolution.py
    M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
    M tools/stats/gsummary.xml
    M tox.ini

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: 21b93be1104ac2175ba128ee604425ee44ea17cf
      https://github.com/galaxyproject/galaxy/commit/21b93be1104ac2175ba128ee60442...
  Author: carlfeberhard <carlfeberhard@gmail.com>
  Date:   2016-08-02 (Tue, 02 Aug 2016)

  Changed paths:
    M .ci/flake8_lint_include_list.txt
    M .ci/py3_sources.txt
    M Makefile
    M client/bower.json
    A client/galaxy/scripts/libs/jquery.complexify.js
    M client/galaxy/scripts/libs/jquery/jquery.js
    M client/galaxy/scripts/libs/raven.js
    M client/galaxy/scripts/mvc/history/options-menu.js
    M client/galaxy/style/less/base.less
    M client/grunt-tasks/install-libs.js
    M client/webpack.config.js
    M config/datatypes_conf.xml.sample
    M lib/galaxy/datatypes/assembly.py
    M lib/galaxy/datatypes/constructive_solid_geometry.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/dataproviders/base.py
    M lib/galaxy/datatypes/images.py
    M lib/galaxy/datatypes/msa.py
    M lib/galaxy/datatypes/ngsindex.py
    M lib/galaxy/datatypes/proteomics.py
    M lib/galaxy/datatypes/tabular.py
    M lib/galaxy/objectstore/azure_blob.py
    M lib/galaxy/version.py
    M lib/galaxy/web/framework/webapp.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M run_tests.sh
    M scripts/bootstrap_history.py
    M scripts/nosetests.py
    A static/maps/libs/jquery.complexify.js.map
    M static/maps/libs/jquery/jquery.js.map
    M static/maps/libs/raven.js.map
    M static/maps/mvc/history/options-menu.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/libs/jquery.complexify.js
    M static/scripts/libs/jquery/jquery.js
    M static/scripts/libs/raven.js
    M static/scripts/mvc/history/options-menu.js
    M static/style/blue/base.css
    M templates/user/change_password.mako
    M templates/user/register.mako
    M test/unit/tools/test_tool_deps.py
    M tox.ini

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/dev' into history-contents.limiting

  Commit: 2d15e50d0f5c65d0dc9d896d1e47ba546d5a7e42
      https://github.com/galaxyproject/galaxy/commit/2d15e50d0f5c65d0dc9d896d1e47b...
  Author: Dannon Baker <dannon.baker@gmail.com>
  Date:   2016-08-03 (Wed, 03 Aug 2016)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/apps/history-panel.js
    M client/galaxy/scripts/layout/panel.js
    M client/galaxy/scripts/mvc/annotation.js
    M client/galaxy/scripts/mvc/base-mvc.js
    A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
    M client/galaxy/scripts/mvc/collection/collection-li-edit.js
    M client/galaxy/scripts/mvc/collection/collection-li.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    M client/galaxy/scripts/mvc/collection/collection-view.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/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/history/copy-dialog.js
    M client/galaxy/scripts/mvc/history/hda-li-edit.js
    M client/galaxy/scripts/mvc/history/hda-li.js
    M client/galaxy/scripts/mvc/history/hda-model.js
    M client/galaxy/scripts/mvc/history/hdca-li.js
    M client/galaxy/scripts/mvc/history/hdca-model.js
    M client/galaxy/scripts/mvc/history/history-content-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    A client/galaxy/scripts/mvc/history/history-preferences.js
    M client/galaxy/scripts/mvc/history/history-structure-view.js
    M client/galaxy/scripts/mvc/history/history-view-annotated.js
    M client/galaxy/scripts/mvc/history/history-view-edit-current.js
    M client/galaxy/scripts/mvc/history/history-view-edit.js
    M client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/history/options-menu.js
    M client/galaxy/scripts/mvc/list/list-item.js
    M client/galaxy/scripts/mvc/list/list-view.js
    M client/galaxy/scripts/mvc/ui/error-modal.js
    M client/galaxy/scripts/mvc/ui/ui-modal.js
    M client/galaxy/scripts/ui/search-input.js
    M client/galaxy/scripts/utils/ajax-queue.js
    M client/galaxy/style/less/base.less
    A client/galaxy/style/less/collection.less
    R client/galaxy/style/less/collections.less
    A client/galaxy/style/less/dataset.less
    A client/galaxy/style/less/flex.less
    M client/galaxy/style/less/history.less
    M client/galaxy/style/less/list-item.less
    A client/galaxy/style/less/ui/error-modal.less
    M client/galaxy/style/less/ui/search-input.less
    M lib/galaxy/managers/annotatable.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/datasets.py
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/hdcas.py
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/history_contents.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/layout/panel.js.map
    M static/maps/mvc/annotation.js.map
    M static/maps/mvc/base-mvc.js.map
    A static/maps/mvc/base/controlled-fetch-collection.js.map
    M static/maps/mvc/collection/collection-li-edit.js.map
    M static/maps/mvc/collection/collection-li.js.map
    M static/maps/mvc/collection/collection-model.js.map
    M static/maps/mvc/collection/collection-view.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/dataset/dataset-model.js.map
    M static/maps/mvc/history/copy-dialog.js.map
    M static/maps/mvc/history/hda-li-edit.js.map
    M static/maps/mvc/history/hda-li.js.map
    M static/maps/mvc/history/hda-model.js.map
    M static/maps/mvc/history/hdca-li.js.map
    M static/maps/mvc/history/hdca-model.js.map
    M static/maps/mvc/history/history-content-model.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/history-model.js.map
    A static/maps/mvc/history/history-preferences.js.map
    M static/maps/mvc/history/history-structure-view.js.map
    M static/maps/mvc/history/history-view-annotated.js.map
    M static/maps/mvc/history/history-view-edit-current.js.map
    M static/maps/mvc/history/history-view-edit.js.map
    M static/maps/mvc/history/history-view.js.map
    M static/maps/mvc/history/multi-panel.js.map
    M static/maps/mvc/history/options-menu.js.map
    M static/maps/mvc/list/list-item.js.map
    M static/maps/mvc/list/list-view.js.map
    M static/maps/mvc/ui/error-modal.js.map
    M static/maps/mvc/ui/ui-modal.js.map
    M static/maps/ui/search-input.js.map
    M static/maps/utils/ajax-queue.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/layout/panel.js
    M static/scripts/mvc/annotation.js
    M static/scripts/mvc/base-mvc.js
    A static/scripts/mvc/base/controlled-fetch-collection.js
    M static/scripts/mvc/collection/collection-model.js
    M static/scripts/mvc/collection/collection-view.js
    M static/scripts/mvc/dataset/dataset-li-edit.js
    M static/scripts/mvc/dataset/dataset-li.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/history/copy-dialog.js
    M static/scripts/mvc/history/hda-model.js
    M static/scripts/mvc/history/hdca-model.js
    M static/scripts/mvc/history/history-content-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    A static/scripts/mvc/history/history-preferences.js
    M static/scripts/mvc/history/history-structure-view.js
    M static/scripts/mvc/history/history-view-annotated.js
    M static/scripts/mvc/history/history-view-edit-current.js
    M static/scripts/mvc/history/history-view-edit.js
    M static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/history/options-menu.js
    M static/scripts/mvc/list/list-item.js
    M static/scripts/mvc/list/list-view.js
    M static/scripts/mvc/ui/error-modal.js
    M static/scripts/mvc/ui/ui-modal.js
    M static/scripts/ui/search-input.js
    M static/scripts/utils/ajax-queue.js
    M static/style/blue/base.css
    M static/style/blue/bootstrap-tour.css
    M static/style/blue/jquery.rating.css
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/history/embed.mako
    M templates/webapps/galaxy/history/view.mako
    M templates/webapps/galaxy/history/view_multiple.mako
    M test/qunit/tests/history_contents_model_tests.js
    M test/unit/managers/test_HistoryManager.py

  Log Message:
  -----------
  Merge branch 'history-contents.limiting' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/7389b93bd613...2d15e50d0f5c

[galaxy-commits] [galaxyproject/galaxy] 0b8c98: Include database/jobs_directory in gitignore

GitHub