November 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 426140: Fixes for WorkflowContentsManager requiring app du...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4261403fad1c5fd1346b0cfe9fd25e97459cd028 https://github.com/galaxyproject/galaxy/commit/4261403fad1c5fd1346b0cfe9fd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fixes for WorkflowContentsManager requiring app during init. Commit: dc41856812f9064c518a8e45c4559b2f32fe9db2 https://github.com/galaxyproject/galaxy/commit/dc41856812f9064c518a8e45c455… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #1173 from jmchilton/wfcfix Fixes for WorkflowContentsManager requiring app during init. Compare: https://github.com/galaxyproject/galaxy/compare/1b06e8d674ed...dc41856812f9

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[galaxyproject/galaxy] bd476c: Readd jquery.migrate to galaxy.panels template bec...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd476ce146d47e12b25e4faacc6ae7eeed09fbe2 https://github.com/galaxyproject/galaxy/commit/bd476ce146d47e12b25e4faacc6a… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Readd jquery.migrate to galaxy.panels template because it is needed for farbtastic, which is used in visualizations. Commit: 1b06e8d674edd7f1a1f9397429b319670891a8bd https://github.com/galaxyproject/galaxy/commit/1b06e8d674edd7f1a1f9397429b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1126 from jgoecks/farbtastic-fix Readd jquery.migrate to galaxy.panels template because it is needed f… Compare: https://github.com/galaxyproject/galaxy/compare/f4dab5523b68...1b06e8d674ed

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[galaxyproject/galaxy] 624741: add onbeforeunload to IE
by GitHub 26 Nov '15

26 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62474100f8f075ce519d008336060dfa952da725 https://github.com/galaxyproject/galaxy/commit/62474100f8f075ce519d00833606… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- add onbeforeunload to IE Commit: f4dab5523b687c079df68d4d2988dc830429bd93 https://github.com/galaxyproject/galaxy/commit/f4dab5523b687c079df68d4d2988… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #1178 from bgruening/obbeforechange_ie Prevent GIEs from being closed without user confirmation Compare: https://github.com/galaxyproject/galaxy/compare/2a54ff08292d...f4dab5523b68

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[galaxyproject/galaxy] c408b0: Do not check for tool migrations when running test...
by GitHub 26 Nov '15

26 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c408b0ec6515deccd92a264edd4ab78061a06b87 https://github.com/galaxyproject/galaxy/commit/c408b0ec6515deccd92a264edd4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. Commit: 2a54ff08292d85b3ecdab79e307b4b5d0aba4cc3 https://github.com/galaxyproject/galaxy/commit/2a54ff08292d85b3ecdab79e307b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Merge pull request #1176 from jmchilton/auto_migrate Do not check for tool migrations when running tests. Compare: https://github.com/galaxyproject/galaxy/compare/0c75af7192b7...2a54ff08292d

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[galaxyproject/galaxy] 368da1: Call onbeforeunload before hiding iframe through d...
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 368da171f5f4490029fb6e80b888e5b091051901 https://github.com/galaxyproject/galaxy/commit/368da171f5f4490029fb6e80b888… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Call onbeforeunload before hiding iframe through display() Validated message Commit: 0c75af7192b7f34260098a21ff30d98492ba738e https://github.com/galaxyproject/galaxy/commit/0c75af7192b7f34260098a21ff30… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #1157 from guerler/revise_iframe_unload_001 Call onbeforeunload before hiding iframe through display() Compare: https://github.com/galaxyproject/galaxy/compare/6fda0e0aac54...0c75af7192b7

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[galaxyproject/galaxy] be7b00: try running 15.10 on older docker image
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be7b003c771b0b1169e1336e17e2b12b0acbea37 https://github.com/galaxyproject/galaxy/commit/be7b003c771b0b1169e1336e17e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- try running 15.10 on older docker image Commit: a5200a4d5f970be6f7d47eb25b4e4050ab32d6da https://github.com/galaxyproject/galaxy/commit/a5200a4d5f970be6f7d47eb25b4e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1172 from martenson/fix-dockerimage-version [15.10] run 15.10 tests on older docker image Commit: 6fda0e0aac54c1c9e758110b4868b4a3fece16aa https://github.com/galaxyproject/galaxy/commit/6fda0e0aac54c1c9e758110b4868… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-25 (Wed, 25 Nov 2015) Log Message: ----------- Merge branch 'master' into dev Conflicts: run_tests.sh Compare: https://github.com/galaxyproject/galaxy/compare/4f6aad473d99...6fda0e0aac54

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[galaxyproject/galaxy] be7b00: try running 15.10 on older docker image
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: be7b003c771b0b1169e1336e17e2b12b0acbea37 https://github.com/galaxyproject/galaxy/commit/be7b003c771b0b1169e1336e17e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- try running 15.10 on older docker image Commit: a5200a4d5f970be6f7d47eb25b4e4050ab32d6da https://github.com/galaxyproject/galaxy/commit/a5200a4d5f970be6f7d47eb25b4e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1172 from martenson/fix-dockerimage-version [15.10] run 15.10 tests on older docker image Compare: https://github.com/galaxyproject/galaxy/compare/d89670e939d8...a5200a4d5f97

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[galaxyproject/galaxy] be7b00: try running 15.10 on older docker image
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: be7b003c771b0b1169e1336e17e2b12b0acbea37 https://github.com/galaxyproject/galaxy/commit/be7b003c771b0b1169e1336e17e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- try running 15.10 on older docker image Commit: a5200a4d5f970be6f7d47eb25b4e4050ab32d6da https://github.com/galaxyproject/galaxy/commit/a5200a4d5f970be6f7d47eb25b4e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1172 from martenson/fix-dockerimage-version [15.10] run 15.10 tests on older docker image Compare: https://github.com/galaxyproject/galaxy/compare/d89670e939d8...a5200a4d5f97

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[galaxyproject/galaxy] bbef5e: Improvements to release notes generation.
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bbef5ed7373b33eaa30f2e493311413e0cea018b https://github.com/galaxyproject/galaxy/commit/bbef5ed7373b33eaa30f2e493311… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Improvements to release notes generation. - Add last commit for 15.10 (need to automate finding that). - Generate next release annoucement. - Generate annoucement for this release. - Respect the minor tag. Commit: b7bf42e1b4fae9e4c2e3b246868518992dbcce10 https://github.com/galaxyproject/galaxy/commit/b7bf42e1b4fae9e4c2e3b2468685… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst Log Message: ----------- Fill in release notes for 15.10. Commit: 4f4526bc303eeb40dae9d71d5dc161bb8b398ae6 https://github.com/galaxyproject/galaxy/commit/4f4526bc303eeb40dae9d71d5dc1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate old Data Libraries Commit: 8e8b5d445d28d459dc75cbe3ed35d6c9dd8bbd40 https://github.com/galaxyproject/galaxy/commit/8e8b5d445d28d459dc75cbe3ed35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove inbound flag Commit: cbf5c68ad76d47f74b95df20604b1ae1f787d9d1 https://github.com/galaxyproject/galaxy/commit/cbf5c68ad76d47f74b95df20604b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Don't override search url -- this currently affects main where Help->Search ends up at root.com... Commit: adcf513390e05039acc0ebe761b833686ff7fe13 https://github.com/galaxyproject/galaxy/commit/adcf513390e05039acc0ebe761b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Simply remove tool_search_url -- it isn't used and it's totally composable. Commit: 743603b4b72078ad251ecd66e37f17f323a71d51 https://github.com/galaxyproject/galaxy/commit/743603b4b72078ad251ecd66e37f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #1140 from dannon/menufix_2 [15.10] Don't override search url Commit: cf16e2c7d39657a13d48615841c192a667428b93 https://github.com/galaxyproject/galaxy/commit/cf16e2c7d39657a13d48615841c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add bitbucker deprecation notice Commit: 76fc6becd65f829db924e3726ade11dc0735e2ca https://github.com/galaxyproject/galaxy/commit/76fc6becd65f829db924e3726ade… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add text highlights Commit: a98e56c9ee53a29f89db9740ad418bad12f32259 https://github.com/galaxyproject/galaxy/commit/a98e56c9ee53a29f89db9740ad41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #868 from jmchilton/release_notes [15.10] Release notes Commit: e9ed5bfa626765754629af20f1567d7102bac231 https://github.com/galaxyproject/galaxy/commit/e9ed5bfa626765754629af20f156… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- clarify the bitbucket support Commit: a5aeea0685d5e7d1f4406f9abf69ca3da3add160 https://github.com/galaxyproject/galaxy/commit/a5aeea0685d5e7d1f4406f9abf69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Slight wording tweak Commit: ceb8ee127af9390a2cbd3b6046dc360d98992060 https://github.com/galaxyproject/galaxy/commit/ceb8ee127af9390a2cbd3b6046dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #11 from dannon/tweak-notes Slight wording tweak Commit: 09db120ad84dcaa851a6ae3dbc351a7a958ce736 https://github.com/galaxyproject/galaxy/commit/09db120ad84dcaa851a6ae3dbc35… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1141 from martenson/tweak-notes [15.10] release notes tweaks Commit: 286f7142871db5cb7b5ec8873cae8cb41fa335e3 https://github.com/galaxyproject/galaxy/commit/286f7142871db5cb7b5ec8873cae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1085 from guerler/fix_grids_000 [15.10] Fix dataset grid history change Commit: 82ce6244653fe96f01f4b01bb4ecd366a1b45db0 https://github.com/galaxyproject/galaxy/commit/82ce6244653fe96f01f4b01bb4ec… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled. Commit: 7a4be88693d8541827cf47f8d7dd3989eef84ef7 https://github.com/galaxyproject/galaxy/commit/7a4be88693d8541827cf47f8d7dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- fix missing configuration; broke TS password reset Commit: aa52b6cff1d4b694a96a1b37da263a72cbd3a726 https://github.com/galaxyproject/galaxy/commit/aa52b6cff1d4b694a96a1b37da26… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M config/tool_shed.ini.sample Log Message: ----------- add pretty_datetime_format to TS config sample Commit: d89670e939d86e6b57988fe14c5695f457b751e2 https://github.com/galaxyproject/galaxy/commit/d89670e939d86e6b57988fe14c56… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #1170 from martenson/fix-password-reset [15.10] fix missing configuration which broke TS password reset Commit: 4f6aad473d99d7327b3c2aa395f1b546a443fc02 https://github.com/galaxyproject/galaxy/commit/4f6aad473d99d7327b3c2aa395f1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M config/tool_shed.ini.sample A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/config.py M scripts/bootstrap_history.py M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/11edf3559d70...4f6aad473d99

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[galaxyproject/galaxy] bbef5e: Improvements to release notes generation.
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: bbef5ed7373b33eaa30f2e493311413e0cea018b https://github.com/galaxyproject/galaxy/commit/bbef5ed7373b33eaa30f2e493311… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Improvements to release notes generation. - Add last commit for 15.10 (need to automate finding that). - Generate next release annoucement. - Generate annoucement for this release. - Respect the minor tag. Commit: b7bf42e1b4fae9e4c2e3b246868518992dbcce10 https://github.com/galaxyproject/galaxy/commit/b7bf42e1b4fae9e4c2e3b2468685… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst Log Message: ----------- Fill in release notes for 15.10. Commit: 4f4526bc303eeb40dae9d71d5dc161bb8b398ae6 https://github.com/galaxyproject/galaxy/commit/4f4526bc303eeb40dae9d71d5dc1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate old Data Libraries Commit: 8e8b5d445d28d459dc75cbe3ed35d6c9dd8bbd40 https://github.com/galaxyproject/galaxy/commit/8e8b5d445d28d459dc75cbe3ed35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove inbound flag Commit: 05f3da308d6a58dc8528f317fa6ea4ffa1fb7610 https://github.com/galaxyproject/galaxy/commit/05f3da308d6a58dc8528f317fa6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Fix macro bug with empty CDATA being None instead of ''. Fixes galaxyproject/planemo#362 thanks for the report @erasche. Test using the following command: ``` nosetests test/unit/tools/test_tool_loader.py ``` Commit: eb16ba3743a7e42cc9ad43f0d7a3eb926ba60cd8 https://github.com/galaxyproject/galaxy/commit/eb16ba3743a7e42cc9ad43f0d7a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #1122 from jmchilton/empty_cdata_macro [15.10] Fix macro bug with empty CDATA being None instead of ''. Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7 https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: 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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.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/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.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/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: cbf5c68ad76d47f74b95df20604b1ae1f787d9d1 https://github.com/galaxyproject/galaxy/commit/cbf5c68ad76d47f74b95df20604b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Don't override search url -- this currently affects main where Help->Search ends up at root.com... Commit: adcf513390e05039acc0ebe761b833686ff7fe13 https://github.com/galaxyproject/galaxy/commit/adcf513390e05039acc0ebe761b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Simply remove tool_search_url -- it isn't used and it's totally composable. Commit: 743603b4b72078ad251ecd66e37f17f323a71d51 https://github.com/galaxyproject/galaxy/commit/743603b4b72078ad251ecd66e37f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #1140 from dannon/menufix_2 [15.10] Don't override search url Commit: cf16e2c7d39657a13d48615841c192a667428b93 https://github.com/galaxyproject/galaxy/commit/cf16e2c7d39657a13d48615841c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add bitbucker deprecation notice Commit: 76fc6becd65f829db924e3726ade11dc0735e2ca https://github.com/galaxyproject/galaxy/commit/76fc6becd65f829db924e3726ade… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add text highlights Commit: a98e56c9ee53a29f89db9740ad418bad12f32259 https://github.com/galaxyproject/galaxy/commit/a98e56c9ee53a29f89db9740ad41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #868 from jmchilton/release_notes [15.10] Release notes Commit: e9ed5bfa626765754629af20f1567d7102bac231 https://github.com/galaxyproject/galaxy/commit/e9ed5bfa626765754629af20f156… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- clarify the bitbucket support Commit: a5aeea0685d5e7d1f4406f9abf69ca3da3add160 https://github.com/galaxyproject/galaxy/commit/a5aeea0685d5e7d1f4406f9abf69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Slight wording tweak Commit: ceb8ee127af9390a2cbd3b6046dc360d98992060 https://github.com/galaxyproject/galaxy/commit/ceb8ee127af9390a2cbd3b6046dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #11 from dannon/tweak-notes Slight wording tweak Commit: 09db120ad84dcaa851a6ae3dbc351a7a958ce736 https://github.com/galaxyproject/galaxy/commit/09db120ad84dcaa851a6ae3dbc35… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1141 from martenson/tweak-notes [15.10] release notes tweaks Commit: 286f7142871db5cb7b5ec8873cae8cb41fa335e3 https://github.com/galaxyproject/galaxy/commit/286f7142871db5cb7b5ec8873cae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1085 from guerler/fix_grids_000 [15.10] Fix dataset grid history change Commit: 82ce6244653fe96f01f4b01bb4ecd366a1b45db0 https://github.com/galaxyproject/galaxy/commit/82ce6244653fe96f01f4b01bb4ec… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled. Commit: 7a4be88693d8541827cf47f8d7dd3989eef84ef7 https://github.com/galaxyproject/galaxy/commit/7a4be88693d8541827cf47f8d7dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- fix missing configuration; broke TS password reset Commit: aa52b6cff1d4b694a96a1b37da263a72cbd3a726 https://github.com/galaxyproject/galaxy/commit/aa52b6cff1d4b694a96a1b37da26… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M config/tool_shed.ini.sample Log Message: ----------- add pretty_datetime_format to TS config sample Commit: d89670e939d86e6b57988fe14c5695f457b751e2 https://github.com/galaxyproject/galaxy/commit/d89670e939d86e6b57988fe14c56… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #1170 from martenson/fix-password-reset [15.10] fix missing configuration which broke TS password reset Compare: https://github.com/galaxyproject/galaxy/compare/73f46f4e0814...d89670e939d8

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