Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 417d1d251e7e7c735a8d4aefd53edcec941db1f4 https://github.com/galaxyproject/galaxy/commit/417d1d251e7e7c735a8d4aefd53ed... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- Initial commit to get this rolling, library-security does not exist and needs to be created, among others. Commit: bc870cdf66ecaaf218cd20debdbcc68b20e7f959 https://github.com/galaxyproject/galaxy/commit/bc870cdf66ecaaf218cd20debdbcc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Update galaxy.ini.sample and config. Commit: 11829c4f9df12cf8e8e3e7a14dc11e9a02afe6a4 https://github.com/galaxyproject/galaxy/commit/11829c4f9df12cf8e8e3e7a14dc11... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/managers/configuration.py M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- More defaults, these should be consolidated. Commit: e12c07cacd12fbf4a2fb148242be5bea7c13221e https://github.com/galaxyproject/galaxy/commit/e12c07cacd12fbf4a2fb148242be5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako Log Message: ----------- Use config.py for defaults used in managers/configuration. Commit: ed1d19a967989416caebd3588fe6b8b6460764e2 https://github.com/galaxyproject/galaxy/commit/ed1d19a967989416caebd3588fe6b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Update reports and toolshed app configs as well. Commit: 72cd0ba00ad05793751105dccf434c9868791b2a https://github.com/galaxyproject/galaxy/commit/72cd0ba00ad05793751105dccf434... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Adjust link to the new Galaxy HUB site Commit: b4fda2ccd49fd7b406a5521bce3243ff6ffb7950 https://github.com/galaxyproject/galaxy/commit/b4fda2ccd49fd7b406a5521bce324... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #16 from bgruening/wf_link /learn/advanced-workflow/variables-edit Commit: ea3796152a01aad87f0585bf83ceb661392ba4d4 https://github.com/galaxyproject/galaxy/commit/ea3796152a01aad87f0585bf83ceb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Replace wiki.galaxyproject.org links in /lib Commit: 04a32064f1d553c01828092b445175a9c7d8a53d https://github.com/galaxyproject/galaxy/commit/04a32064f1d553c01828092b44517... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/viz/phyloviz.js M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js Log Message: ----------- Update wiki.galaxyproject.org links in client Commit: a5143ce7a86cb64c81b0ffa36a90742b872cec15 https://github.com/galaxyproject/galaxy/commit/a5143ce7a86cb64c81b0ffa36a907... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako Log Message: ----------- Convert wiki.galaxyproject.org links in templates Commit: 29aa00e42129bec564a9f1009547e3b740b29709 https://github.com/galaxyproject/galaxy/commit/29aa00e42129bec564a9f1009547e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/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-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/grid/grid-template.js M 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M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/layout/menu.js A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.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-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/style/blue/base.css R templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/show_params.mako R templates/user/dbkeys.mako M templates/webapps/galaxy/admin/manage_dependencies.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/display.mako A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api_asserts.py M test/base/data/test_workflow_pause.ga M test/base/driver_util.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py A test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/qunit/package.json M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/ui_tests.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/filters/trimmer.py M tools/filters/trimmer.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into wiki-to-hub Commit: 0dd75e6cdd985ec3711987ef8adb3fe6365b8501 https://github.com/galaxyproject/galaxy/commit/0dd75e6cdd985ec3711987ef8adb3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako A templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Attempt to rectify bad merge. Commit: 05e81192bd91559876da1a82b734c7e49e15f43e https://github.com/galaxyproject/galaxy/commit/05e81192bd91559876da1a82b734c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M test/qunit/tests/form_tests.js Log Message: ----------- Update tool form qunit test text. Commit: 89e692d980965f5a1963818180ccaf62ae2c207f https://github.com/galaxyproject/galaxy/commit/89e692d980965f5a1963818180cca... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M config/galaxy.ini.sample M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/workflow/workflow-forms.js M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Tweaks for @nsoranzo. Commit: 5fe7b7208c8668b7d4dd9dc31568c77a0a8c2562 https://github.com/galaxyproject/galaxy/commit/5fe7b7208c8668b7d4dd9dc31568c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Fix support link Commit: f0740136831623adf8b2c1fe9ed17dbf4327ebc4 https://github.com/galaxyproject/galaxy/commit/f0740136831623adf8b2c1fe9ed17... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M config/galaxy.ini.sample Log Message: ----------- Small tweaks for data-libraries URLS Commit: dab18fb2387d737f859637bbd37d9b0ce3ec658c https://github.com/galaxyproject/galaxy/commit/dab18fb2387d737f859637bbd37d9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/qunit/tests/form_tests.js Log Message: ----------- Merge branch 'wiki-to-hub' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/760160a02cd9...dab18fb2387d