galaxy-commits November 2016

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[galaxyproject/galaxy] 6fd58a: Merge pull request #3191 from dannon/version-16.10
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fd58afa6daf708f373513782ac907c154c266da https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- remove unused override this caused Help/Search to point at /root/tool_search Commit: 3f27777e76086ac94c95003882bb82003c277b4e https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: 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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Commit: d2c95b43fa33f9f4b14d274ffa60beb03a80fbb6 https://github.com/galaxyproject/galaxy/commit/d2c95b43fa33f9f4b14d274ffa60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tools.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.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3204 from galaxyproject/release_16.10 Merge release_16.10 into dev Compare: https://github.com/galaxyproject/galaxy/compare/78b533d1b544...d2c95b43fa33

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[galaxyproject/galaxy] 548d3e: Fixes for deleting histories broken in 1cc57b1eb2c...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: 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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Compare: https://github.com/galaxyproject/galaxy/compare/3f27777e7608...aadc14d967c3

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[galaxyproject/galaxy] c0a7fa: Don't load tools from paths that start with `.` or...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0a7fabc354598b1a40ea87291c28f70127db357 https://github.com/galaxyproject/galaxy/commit/c0a7fabc354598b1a40ea87291c2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load tools from paths that start with `.` or `_` Commit: 78b533d1b5445c843090ec42c134d2fa335134a3 https://github.com/galaxyproject/galaxy/commit/78b533d1b5445c843090ec42c134… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3201 from mvdbeek/do_not_load_tools_from_hidden_paths Don't load tools from paths that start with `.` or `_` Compare: https://github.com/galaxyproject/galaxy/compare/52c8e495dc17...78b533d1b544

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[galaxyproject/galaxy] 3ea730: Fix table
by GitHub 19 Nov '16

19 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ea730f734c71e5e3aa182c96f7be81850ee8527 https://github.com/galaxyproject/galaxy/commit/3ea730f734c71e5e3aa182c96f7b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Fix table Commit: 52c8e495dc1746e4280c7d6837dd590f9b98566e https://github.com/galaxyproject/galaxy/commit/52c8e495dc1746e4280c7d6837dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-19 (Sat, 19 Nov 2016) Changed paths: M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Merge pull request #3200 from erasche/user-info-page Fix table Compare: https://github.com/galaxyproject/galaxy/compare/33894ca744be...52c8e495dc17

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[galaxyproject/usegalaxy-playbook] 924a93: *sigh*
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 924a931311400fde319679c3f9901fa404cf6114 https://github.com/galaxyproject/usegalaxy-playbook/commit/924a931311400fde… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- *sigh*

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[galaxyproject/usegalaxy-playbook] 2b3d45: Mutable configs
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2b3d45fc7b0c1b55b35629eb39a003d68e350947 https://github.com/galaxyproject/usegalaxy-playbook/commit/2b3d45fc7b0c1b55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Mutable configs

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[galaxyproject/usegalaxy-playbook] 94ade5: Downtime message
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 94ade57d02e4430ef1173fcc42027d5e63752469 https://github.com/galaxyproject/usegalaxy-playbook/commit/94ade57d02e4430e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Downtime message

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[galaxyproject/galaxy] 5c4ac1: remove unused override
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- remove unused override this caused Help/Search to point at /root/tool_search Commit: 3f27777e76086ac94c95003882bb82003c277b4e https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override Compare: https://github.com/galaxyproject/galaxy/compare/6fd58afa6daf...3f27777e7608

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[galaxyproject/ansible-galaxy] 19535b: Drop support for "Galaxy pip"
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 19535b56292b72d38fcc1cf89580a1dd27c0f040 https://github.com/galaxyproject/ansible-galaxy/commit/19535b56292b72d38fcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Drop support for "Galaxy pip"

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[galaxyproject/galaxy] a20952: Large cleanup of unused methods from twilltestcase...
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a209523639a822dc546b9d2d946e6199df172368 https://github.com/galaxyproject/galaxy/commit/a209523639a822dc546b9d2d946e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_library_templates.py Log Message: ----------- Large cleanup of unused methods from twilltestcase. In addition to deleting unused methods, this also moves ones only used by test_library_templates into that file. Commit: 2bf1cf50a37d5295425798374959fbda0257b609 https://github.com/galaxyproject/galaxy/commit/2bf1cf50a37d5295425798374959… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_library_templates.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Reduce requirements for using get_filename in TwillTestCase. Do not use a self.tool_shed_test_file and make self.shed_tools_dict optional. Commit: b83cfe434ad875744d11d7516dc9cc11dfdec419 https://github.com/galaxyproject/galaxy/commit/b83cfe434ad875744d11d7516dc9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py Log Message: ----------- Refactor generic FunctionalTestCase from TwillTestCase. ApiTestCase uses this newer, smaller base class since these tests do not depend on Twill. Commit: 33894ca744be3fa2eebab6942832f2931d5f0bec https://github.com/galaxyproject/galaxy/commit/33894ca744be3fa2eebab6942832… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py M test/functional/test_library_templates.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #3190 from jmchilton/test_cleanup Various Test Cleanups and Refactorings Compare: https://github.com/galaxyproject/galaxy/compare/50f5c15f63a3...33894ca744be

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galaxy-commits November 2016