- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 7a4be8: fix missing configuration; broke TS password reset
by GitHub 25 Nov '15

25 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy 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/82ce6244653f...d89670e939d8

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[galaxyproject/usegalaxy-playbook] e1ce91: update mutable confs on Test
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e1ce9175fd23fa3af6f6389f17a31d66f5ddbae2 https://github.com/galaxyproject/usegalaxy-playbook/commit/e1ce9175fd23fa3a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update mutable confs on Test

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[galaxyproject/usegalaxy-playbook] 3ccada: update Test for a change...
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ccada13afe38f35d861cd88a38a019b8395da56 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ccada13afe38f35… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test for a change...

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[galaxyproject/usegalaxy-playbook] 292816: Revert "update TTS"
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 292816b71a8244991500f52b87128067e73bb48c https://github.com/galaxyproject/usegalaxy-playbook/commit/292816b71a824499… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- Revert "update TTS" This reverts commit 7fb048393b5682c1139be2c3e927788659966d80.

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[galaxyproject/galaxy] 1ea68f: Save a query per output during tool execution.
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ea68f938408b72f8f0f4ebe2545550baea85037 https://github.com/galaxyproject/galaxy/commit/1ea68f938408b72f8f0f4ebe2545… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Save a query per output during tool execution. Commit: 42d006162c095669a2c7afe1ab0f1fb67b000798 https://github.com/galaxyproject/galaxy/commit/42d006162c095669a2c7afe1ab0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Another tool dataset creation optimization... Rather than using three transactions to create an HDA, a dataset, and its roles - do this all in one transaction. Commit: 01c57908eaf8bd589ce8738fdab14d415543d072 https://github.com/galaxyproject/galaxy/commit/01c57908eaf8bd589ce8738fdab1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Another tool execution optimization... Prefetch all groups, roles, and associations when using User.all_users(). This reduces three queries down to one if the user has no groups or group roles and only belongs to the private user role, obviously the number of queries saved would increase more and more if the user belonged to multiple roles or groups. Commit: 11edf3559d7092c9e3fada3f04d9291bea64f2f0 https://github.com/galaxyproject/galaxy/commit/11edf3559d7092c9e3fada3f04d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1166 from jmchilton/tool_opts_2 Another set of tool execution optimizations Compare: https://github.com/galaxyproject/galaxy/compare/853efcea14d1...11edf3559d70

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[galaxyproject/usegalaxy-playbook] 7fb048: update TTS
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7fb048393b5682c1139be2c3e927788659966d80 https://github.com/galaxyproject/usegalaxy-playbook/commit/7fb048393b5682c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] 32728e: Small optimizations to running tools.
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32728e23921553c75fda61acadb4f5dc82a4f915 https://github.com/galaxyproject/galaxy/commit/32728e23921553c75fda61acadb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Small optimizations to running tools. Commit: 853efcea14d1ce11961d171324dbce03e6694117 https://github.com/galaxyproject/galaxy/commit/853efcea14d1ce11961d171324db… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1163 from jmchilton/tool_opts_1 Small optimizations to running tools. Compare: https://github.com/galaxyproject/galaxy/compare/77166a7295b1...853efcea14d1

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[galaxyproject/galaxy] 9cc8e0: add local grunt-cli dependency for qunit tests
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9cc8e08537291a85885ee3ad52daeb36b95b4f8e https://github.com/galaxyproject/galaxy/commit/9cc8e08537291a85885ee3ad52da… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M test/qunit/package.json Log Message: ----------- add local grunt-cli dependency for qunit tests Commit: 77166a7295b1fe13f366414361b1752e6c0dd953 https://github.com/galaxyproject/galaxy/commit/77166a7295b1fe13f366414361b1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M test/qunit/package.json Log Message: ----------- Merge pull request #1159 from martenson/local-grunt-cli-dep add local grunt-cli dependency for qunit tests Compare: https://github.com/galaxyproject/galaxy/compare/3cadcdffb51f...77166a7295b1

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[galaxyproject/galaxy] b6451d: Fix bugs in test and code introduced in PR #1113.
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6451d0be60a3bf2ca7c65c7700cb7361cb50754 https://github.com/galaxyproject/galaxy/commit/b6451d0be60a3bf2ca7c65c7700c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/functional/tools/output_format_collection.xml M test/unit/tools/test_actions.py Log Message: ----------- Fix bugs in test and code introduced in PR #1113. Commit: 3cadcdffb51f3994ed6ca0f4a9508f31fba1c4a6 https://github.com/galaxyproject/galaxy/commit/3cadcdffb51f3994ed6ca0f4a950… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/functional/tools/output_format_collection.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1155 from nsoranzo/fix_for_1113 Fix bugs in test and code introduced in PR #1113. Compare: https://github.com/galaxyproject/galaxy/compare/11f9fed4acb3...3cadcdffb51f

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[galaxyproject/galaxy] 82ce62: Fix for re-installing an uninstalled TS repository...
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy 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.

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[galaxyproject/galaxy] a16cb0: Fix for re-installing an uninstalled TS repository...
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a16cb06705676aa49e725c8ab58521c239dfea4d https://github.com/galaxyproject/galaxy/commit/a16cb06705676aa49e725c8ab585… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-22 (Sun, 22 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: 11f9fed4acb3fb912bc0e0e5c0232fb85c974f2f https://github.com/galaxyproject/galaxy/commit/11f9fed4acb3fb912bc0e0e5c023… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1154 from gregvonkuster/dev Fix for re-installing an uninstalled TS repository with a dependency Compare: https://github.com/galaxyproject/galaxy/compare/2e510bd5e12a...11f9fed4acb3

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[galaxyproject/galaxy] 312746: Allow accessing collection elements in format_sour...
by GitHub 22 Nov '15

22 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 312746d1698e99e13b9a60db881d0093da6cc4c0 https://github.com/galaxyproject/galaxy/commit/312746d1698e99e13b9a60db881d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Allow accessing collection elements in format_source. Can do it by numeric index or element name, e.g. input[0] or input["forward"]. Only works for 1-D collections. Implements #699. Run new and most relevant existing tests with the following commands: ``` nosetests test/unit/tools/test_actions.py ./run_tests.sh -framework -id output_format_collection ./run_tests.sh -framework -id output_format ``` Commit: 2e510bd5e12ab5e2c401e835e0f84f29376766db https://github.com/galaxyproject/galaxy/commit/2e510bd5e12ab5e2c401e835e0f8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-21 (Sat, 21 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1113 from jmchilton/format_source_collection Allow accessing collection elements in format_source. Compare: https://github.com/galaxyproject/galaxy/compare/ab0829f2e8df...2e510bd5e12a

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[galaxyproject/galaxy] b4c77b: Introduce "Format 2" workflow definitions.
by GitHub 21 Nov '15

21 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4c77b761799b3a8752a6fec500717b1a6f3818b https://github.com/galaxyproject/galaxy/commit/b4c77b761799b3a8752a6fec5007… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Introduce "Format 2" workflow definitions. This is a slight tightening up of the ad-hoc, experimental workflow YAML definition used by the test framework (and by Kyle, but lets just admit Kyle is part of Galaxy's test framework). This format is still defined entirely client side by transcoding the YAML or python object description into real (or format 1) Galaxy workflows - so these cannot realisticaly be declared part of Galaxy's public interface and can remain experimental and subject to change. In addition to refactoring the code implementing these workflows for upstream modifications to explore new features, the format itself has been made slightly more stringent in two ways: - 'steps' must now be explicit (previously converted auto-convert list to dict). - Ensure the workflow declared a 'class' is defined and the class is 'GalaxyWorkflow'. This will help with discovery of workflow objects with downstream tooling (planemo for workflows?) and brings the Galaxy definition slightly more inline with the CWL definition for workflows (very slightly). Commit: ab0829f2e8df480d467f3b575c18a1ace38543cd https://github.com/galaxyproject/galaxy/commit/ab0829f2e8df480d467f3b575c18… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #1096 from jmchilton/format_2 Outline "Format 2" workflow definitions. Compare: https://github.com/galaxyproject/galaxy/compare/a664deeee76b...ab0829f2e8df

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[galaxyproject/galaxy] 40e3e7: Rebuild style with lessc > 2.5 (which everyone nee...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 40e3e7926aec154fa5f761cf5a7e84fad98b785c https://github.com/galaxyproject/galaxy/commit/40e3e7926aec154fa5f761cf5a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Rebuild style with lessc > 2.5 (which everyone needs to update to now, or we'll have battling commits of packed css Commit: 5c285eaee751a9257e01b6ae4fcff70305e34d56 https://github.com/galaxyproject/galaxy/commit/5c285eaee751a9257e01b6ae4fcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M static/maps/galaxy-app-base.js.map Log Message: ----------- Add grunt check task to verify npm modules are up to date Commit: d4a380b49d0c84fd1765aa5f6e6ad0f85f1b5585 https://github.com/galaxyproject/galaxy/commit/d4a380b49d0c84fd1765aa5f6e6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/package.json Log Message: ----------- Swap devDependencies for flat dependencies -- this allows npm ls (and thereby grunt-check-modules) to enforce dep versions. Commit: a664deeee76bcde33c725f37d61d8b41ea220b3d https://github.com/galaxyproject/galaxy/commit/a664deeee76bcde33c725f37d61d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1130 from dannon/repack_dev Enforce client build deps are up-to-date. Rebuild style with lessc > 2.5 Compare: https://github.com/galaxyproject/galaxy/compare/119e26f4e5f9...a664deeee76b

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[galaxyproject/galaxy] b8b0e4: Strip whitespace
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b8b0e4412247bd0f7611710ce69e0b4e9a76b4d7 https://github.com/galaxyproject/galaxy/commit/b8b0e4412247bd0f7611710ce69e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js Log Message: ----------- Strip whitespace Commit: f0e28555af8129eae424c3e677b6bb22a4c68154 https://github.com/galaxyproject/galaxy/commit/f0e28555af8129eae424c3e677b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Support onclick for menu items. Commit: 81f1b7f8e0ce0febe18460e67a97651aa1fd72a3 https://github.com/galaxyproject/galaxy/commit/81f1b7f8e0ce0febe18460e67a97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Remove debugging logic and shortcut. Commit: 119e26f4e5f91a2091ff1cacffb3f2f99c4c79f4 https://github.com/galaxyproject/galaxy/commit/119e26f4e5f91a2091ff1cacffb3… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Merge pull request #1142 from dannon/menu_onclick_addition Menu onclick addition Compare: https://github.com/galaxyproject/galaxy/compare/303af68c3369...119e26f4e5f9

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[galaxyproject/galaxy] 844fac: UI, Lists: throttle selector animation when number...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 844facd1f1ea3d669cf7e61463c8ca8966c69006 https://github.com/galaxyproject/galaxy/commit/844facd1f1ea3d669cf7e61463c8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- UI, Lists: throttle selector animation when number of list items > 20 Commit: 303af68c33699bada56ddbc95a5f8272401b2f0e https://github.com/galaxyproject/galaxy/commit/303af68c33699bada56ddbc95a5f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge pull request #1149 from carlfeberhard/history.selector-anim UI, Lists: throttle selector animation when number of list items > 20 Compare: https://github.com/galaxyproject/galaxy/compare/7bb88b3f44a5...303af68c3369

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[galaxyproject/galaxy] 8e8b5d: Remove inbound flag
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/09db120ad84d...286f7142871d

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[galaxyproject/galaxy] f629cb: Refactor tool parsing, parse id first.
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f629cbdb6aa34a349e088382a51054a946e0185e https://github.com/galaxyproject/galaxy/commit/f629cbdb6aa34a349e088382a510… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Refactor tool parsing, parse id first. Small refactoring cleans up downstream diff for dynamic tool branch. Commit: 8189fb450bdb90f3ff7af220c573c128ed776085 https://github.com/galaxyproject/galaxy/commit/8189fb450bdb90f3ff7af220c573… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Add tool version to workflow extract. Commit: 0b070f406c650e664c413dc60897fafd6e3611a8 https://github.com/galaxyproject/galaxy/commit/0b070f406c650e664c413dc60897… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add app property to workflow contents manager. Most other managers already have this. Commit: 0030f4c5499b0121e2c7e25388ac402272728ba7 https://github.com/galaxyproject/galaxy/commit/0030f4c5499b0121e2c7e25388ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- API test fix from @nsoranzo. Commit: 7bb88b3f44a53fcd881d69f01d84d88624157ff5 https://github.com/galaxyproject/galaxy/commit/7bb88b3f44a53fcd881d69f01d84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1097 from jmchilton/cwl_refactoring Small Tool and Workflow Cleanups from CWL Work. Compare: https://github.com/galaxyproject/galaxy/compare/05ed24535333...7bb88b3f44a5

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