- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] e9ed5b: clarify the bitbucket support
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/a98e56c9ee53...09db120ad84d

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[galaxyproject/galaxy] bbef5e: Improvements to release notes generation.
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/743603b4b720...a98e56c9ee53

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[galaxyproject/infrastructure-playbook] 4f7e0a: Fix missing library/ directory
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4f7e0ac5bb70e0624470f7f56c3c687dacfd51eb https://github.com/galaxyproject/infrastructure-playbook/commit/4f7e0ac5bb7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A galaxyenv/library/README A galaxyenv/library/cron.py R library/README R library/cron.py A play-galaxy Log Message: ----------- Fix missing library/ directory Commit: 8a9299e280e58cf92c80943def2ecb0c44dcbc5d https://github.com/galaxyproject/infrastructure-playbook/commit/8a9299e280e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M galaxyenv/host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/1654f593b3…

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[galaxyproject/galaxy] cbf5c6: Don't override search url -- this currently affect...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/0fdca7d40a22...743603b4b720

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[galaxyproject/galaxy] ed992b: A large assortment of escaping fixes to primarily ...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… 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/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/multi-panel.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/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).

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