- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ac82e7: Add backrefs to mapped objects pointing at Dataset
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac82e7561c70b7492b03150da849058af1131837 https://github.com/galaxyproject/galaxy/commit/ac82e7561c70b7492b03150da849… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Add backrefs to mapped objects pointing at Dataset Commit: a70e9ad2ce5691fa6dcda7b4871645c2d4607616 https://github.com/galaxyproject/galaxy/commit/a70e9ad2ce5691fa6dcda7b48716… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #6754 from natefoo/dataset-backrefs Add backrefs to mapped objects pointing at Dataset Compare: https://github.com/galaxyproject/galaxy/compare/f6d3059f7e1b...a70e9ad2ce56 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 827e08: Initial work on updating styles
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 827e082bc521cfb287fc5572cdf386c6dc415d7e https://github.com/galaxyproject/galaxy/commit/827e082bc521cfb287fc5572cdf3… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss A client/galaxy/style/source_material/error_icon.svg M client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/info_icon.svg A client/galaxy/style/source_material/ok_icon.svg A client/galaxy/style/source_material/wait_icon.svg A client/galaxy/style/source_material/warn_icon.svg M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Initial work on updating styles Commit: 546eb18ca1e1a3f22fd162b5bcf674705c173601 https://github.com/galaxyproject/galaxy/commit/546eb18ca1e1a3f22fd162b5bcf6… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Improving spacing and forms. Commit: 7ddac47efaa9fa8435e4cb4c207bf557429dcd2d https://github.com/galaxyproject/galaxy/commit/7ddac47efaa9fa8435e4cb4c207b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom margin classes Commit: b5c8adb713806d2ad9a48a6f202ed57d584099cc https://github.com/galaxyproject/galaxy/commit/b5c8adb713806d2ad9a48a6f202e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom form error highlighting Commit: c25fcbdff9bbf05c102efea6fcc8e3144c5ad002 https://github.com/galaxyproject/galaxy/commit/c25fcbdff9bbf05c102efea6fcc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unused no-padding style Commit: 487c1199c9cdc603c7874750784c8f2323d3f8e6 https://github.com/galaxyproject/galaxy/commit/487c1199c9cdc603c7874750784c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom label wrapper Commit: 52b1e03419102821d6bfe7eb8bc77585d0162943 https://github.com/galaxyproject/galaxy/commit/52b1e03419102821d6bfe7eb8bc7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Remove unused generic icon size handler, move to upload styles Commit: 36aa8594e2126ea1b30c62f1e0511a5558708a4e https://github.com/galaxyproject/galaxy/commit/36aa8594e2126ea1b30c62f1e051… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Add comments for style helpers, remove unused styles Commit: f8d974d92d98edc43a35b0cc060b1ac249ee7a0c https://github.com/galaxyproject/galaxy/commit/f8d974d92d98edc43a35b0cc060b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom styles for admin side panel Commit: 40277c46aef2f7507026acd8c8f2c1d711800fad https://github.com/galaxyproject/galaxy/commit/40277c46aef2f7507026acd8c8f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Properly extend tab styles, remove unused specifications Commit: a5f22f60156be5e6228da32b5e48dbf00dc75408 https://github.com/galaxyproject/galaxy/commit/a5f22f60156be5e6228da32b5e48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Build user preferences without custom styles Commit: a5d4eba337632740dd640e5389d3683429b06557 https://github.com/galaxyproject/galaxy/commit/a5d4eba337632740dd640e5389d3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Revise list selectors, remove custom styles Commit: 1de8006e788fb74a9336231025c3adb1fa6ac6eb https://github.com/galaxyproject/galaxy/commit/1de8006e788fb74a9336231025c3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Use es6 string for library selection template Commit: fc4254bc1b0e75e52156c4b9a5453b73d7dd8e35 https://github.com/galaxyproject/galaxy/commit/fc4254bc1b0e75e52156c4b9a545… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom styles for ui-slider, fix code convention for if-statements Remove label test Commit: 5311c6d78260188e95d3a84f23d9521a0e075088 https://github.com/galaxyproject/galaxy/commit/5311c6d78260188e95d3a84f23d9… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #7 from guerler/styles-refresh-2018-adds Styles refresh 2018 additions and custom style removals Commit: de45a0037918ad9ba69b58d39ea8eac75b19fa3c https://github.com/galaxyproject/galaxy/commit/de45a0037918ad9ba69b58d39ea8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Reduce portlet style customization, fix appearance Commit: 87bc585302a13e2a40227a0fce0667d572685625 https://github.com/galaxyproject/galaxy/commit/87bc585302a13e2a40227a0fce06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Consolidate portlet sub section styles Commit: 0e5bff875ad423d49f443be8f5b1f2f58c044b74 https://github.com/galaxyproject/galaxy/commit/0e5bff875ad423d49f443be8f5b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove narrow portlet, reuse section portlet instead Commit: 3210ec0d0dec1aa64ffef813ee4483ee258f10ed https://github.com/galaxyproject/galaxy/commit/3210ec0d0dec1aa64ffef813ee44… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix collapsible handling, improve contrast Commit: 413272237ef9c1e0558c0319b0855e782af88194 https://github.com/galaxyproject/galaxy/commit/413272237ef9c1e0558c0319b085… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix portlet margins Commit: 6af59d2e2c50a843f6fb83266c6372408d15afea https://github.com/galaxyproject/galaxy/commit/6af59d2e2c50a843f6fb83266c63… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #8 from guerler/styles-refresh-2018-adds-2 Consolidate portlet classes, fix tool form views Commit: ff633a0ab3c26cc2fb285bdb3ae98f8d849d94dc https://github.com/galaxyproject/galaxy/commit/ff633a0ab3c26cc2fb285bdb3ae9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove ui-form-section style Commit: ccb5962750a5cdefb23a961a7953e693c8c93fe8 https://github.com/galaxyproject/galaxy/commit/ccb5962750a5cdefb23a961a7953… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove portlet plain class Commit: dcab17c08a8a236531c17d7316bcb821b1b0543f https://github.com/galaxyproject/galaxy/commit/dcab17c08a8a236531c17d7316bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove button-menu class Commit: 699324936f8589ed169214d4a9820d1e51a90e48 https://github.com/galaxyproject/galaxy/commit/699324936f8589ed169214d4a982… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove more button style customizations Commit: a4f9d3f346fd3a08525e9765ece6026fae21a740 https://github.com/galaxyproject/galaxy/commit/a4f9d3f346fd3a08525e9765ece6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove customizations from plain button icons Commit: 1f3bf401c8ee7d6b8a82ec7df35d41a22e8a47f9 https://github.com/galaxyproject/galaxy/commit/1f3bf401c8ee7d6b8a82ec7df35d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M .ci/flake8_blacklist.txt A .ci/jenkins/api-py3/run_tests.sh A .ci/jenkins/framework-py3/run_tests.sh A .ci/jenkins/integration-py3/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M .gitignore M .travis.yml M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M 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lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/steps.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py R openid/aol.xml A pytest.ini M run_tests.sh M scripts/common_startup_functions.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M 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tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge branch 'dev' into styles-refresh-2018-3 Commit: 2e77d5f7fb80b11cdba33ae130195e29fe83e830 https://github.com/galaxyproject/galaxy/commit/2e77d5f7fb80b11cdba33ae13019… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Remove message size customization Commit: 5d33cf16326723e54e64b44f6eacd2f8f348cc79 https://github.com/galaxyproject/galaxy/commit/5d33cf16326723e54e64b44f6eac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Reduce and move table 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lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/steps.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py R openid/aol.xml A pytest.ini M run_tests.sh M scripts/common_startup_functions.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/plugin_staging.py M scripts/secret_decoder_ring.py M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_common.mako M templates/legacy/grid_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/11.tabular A test-data/configfile.json M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py A test/api/test_roles.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga M test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py M test/base/populators.py M test/base/rules_test_data.py M test/base/workflows_format_2/converter.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/conftest.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml A test/functional/tools/column_param_configfile.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/metadata_biom1.xml M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/unicode_stream.xml R test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/objectstore_selection_job_conf.xml A test/integration/objectstore_selection_job_resource_parameters_conf.xml A test/integration/objectstore_selection_rules/__init__.py A test/integration/objectstore_selection_rules/rules.py M test/integration/test_data_manager_table_reload.py M test/integration/test_mules_as_job_handlers.py A test/integration/test_objectstore_jobs.py A test/integration/test_objectstore_selection.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py M test/selenium_tests/framework.py M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py A test/unit/test_model_copy.py M test/unit/test_objectstore.py M test/unit/test_remote_shell.py M test/unit/test_rule_utils.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py A tool-data/intermine_simple_display.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample A tools/data_source/intermine.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge branch 'styles-refresh-2018-3' into styles-refresh-2018 Commit: a5311b490356bb1b4d7543a4ddd2007bc3bc14a7 https://github.com/galaxyproject/galaxy/commit/a5311b490356bb1b4d7543a4ddd2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Use default alert style, remove ui-message customizations Commit: 889d5154931b64d04c9439646749ad05b5c650e7 https://github.com/galaxyproject/galaxy/commit/889d5154931b64d04c9439646749… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove use form text styles Commit: 4fd94ceb5feb1a2c46e7647887aa3c27fb6f9fa1 https://github.com/galaxyproject/galaxy/commit/4fd94ceb5feb1a2c46e7647887aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unnecessary form styles Commit: a1ef7601e416bcbc67454bb254dae101ff14d2c6 https://github.com/galaxyproject/galaxy/commit/a1ef7601e416bcbc67454bb254da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove limit loader text style customization, not needed Commit: 34b94e3ff5d5ec494ea8fc99454f646deeb656e3 https://github.com/galaxyproject/galaxy/commit/34b94e3ff5d5ec494ea8fc99454f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Reduce customization of select2 fields Commit: 6e4dbb78dd00bf20a517759ebcd4bf28a0fa2409 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styles Commit: 570bc975f0bf40ec32fd24862b4bddac65e76159 https://github.com/galaxyproject/galaxy/commit/570bc975f0bf40ec32fd24862b4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Consolidate backbone wrapper for default buttons Commit: 069b97d8ddea1305a316ae073b09f8457574767d 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Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Reduce input element customization, remove gs browser customization Commit: 398e30c471b662f14a20fcd8bd4569927c870b49 https://github.com/galaxyproject/galaxy/commit/398e30c471b662f14a20fcd8bd45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix search bar icons, fix ui tests Commit: 87c9ffa4d8c4db3bf233405e1e8b324cdd36675c https://github.com/galaxyproject/galaxy/commit/87c9ffa4d8c4db3bf233405e1e8b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M 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client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Improve visibility of upload settings in popover Commit: 085ed55ac6f1b59d3d7a55fdf561b564a60ac66c https://github.com/galaxyproject/galaxy/commit/085ed55ac6f1b59d3d7a55fdf561… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/scripts/qunit/test.js R client/galaxy/scripts/qunit/tests/popover_tests.js Log Message: ----------- Remove legacy test case Fix Commit: b1b3959be47b1c5027096cc064a72e5a7899d78a https://github.com/galaxyproject/galaxy/commit/b1b3959be47b1c5027096cc064a7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix input element default value style Commit: 12b6594c86f3c43701c02e8307fd35bd5a229c82 https://github.com/galaxyproject/galaxy/commit/12b6594c86f3c43701c02e8307fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js Log Message: ----------- Remove legacy test case Commit: 31e5a217e3596afab44fcd0033bcf8f6ed75fb08 https://github.com/galaxyproject/galaxy/commit/31e5a217e3596afab44fcd0033bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Adjust dropdown toggle handling, and other minor fixes Commit: f5cbfdab6f7d4031bf89633f30dd397d2f3cd842 https://github.com/galaxyproject/galaxy/commit/f5cbfdab6f7d4031bf89633f30dd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom float clearing class Commit: b10b8c4fa267c0283b066463e013a291ef33786a https://github.com/galaxyproject/galaxy/commit/b10b8c4fa267c0283b066463e013… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M client/galaxy/style/scss/charts.scss M static/style/blue/base.css Log Message: ----------- Fix header buttons Commit: 28476dfab4d1763a81576300b391be3bb8ad80d5 https://github.com/galaxyproject/galaxy/commit/28476dfab4d1763a81576300b391… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Reduce spacing in history panel Commit: 217862ed22dae3380c49c60f8e80b8a91e08ae0c 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client/galaxy/style/scss/theme/blue.scss R client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Remove outdated plain theme, consolidate blue theme Commit: 787b19a481bb90bc40197e485b17ba641d39ffea https://github.com/galaxyproject/galaxy/commit/787b19a481bb90bc40197e485b17… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Restore default gray-600 color used for text-muted Commit: 47429b486d53717caae84f8704898e584a66ea37 https://github.com/galaxyproject/galaxy/commit/47429b486d53717caae84f870489… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Additional variable cleanup and theme separation Commit: b3a79e7d7e65fe5e3f4c7765879b8c27898ef212 https://github.com/galaxyproject/galaxy/commit/b3a79e7d7e65fe5e3f4c7765879b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Improve visibility of links by relying in default link color Commit: 570366b39c79b34b10715a6b7dd788f1eb0ebd0e https://github.com/galaxyproject/galaxy/commit/570366b39c79b34b10715a6b7dd7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/style/scss/base.scss R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss R client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/library.scss A client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/theme/blue.scss M static/style/blue/base.css Log Message: ----------- Consolidate color and variable declarations as theme Commit: 5e6e26f8fb647a558d0eded3b8365f287a8e7aca https://github.com/galaxyproject/galaxy/commit/5e6e26f8fb647a558d0eded3b836… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/style/scss/overrides.scss M static/style/blue/base.css Log Message: ----------- Fix alert word wrapping Commit: 12497d51cd668d7d58f5ab83968cb52bd4a073ed https://github.com/galaxyproject/galaxy/commit/12497d51cd668d7d58f5ab83968c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed 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paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix selector checkbox in history panel Commit: 4054ffc31165b533cb292c58edafac49b59de9de https://github.com/galaxyproject/galaxy/commit/4054ffc31165b533cb292c58edaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/components/RuleCollectionBuilder.vue M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Fix test cases Commit: cb9cbfe796ecf4e5f077c6a4e0ebe97d0102c3b5 https://github.com/galaxyproject/galaxy/commit/cb9cbfe796ecf4e5f077c6a4e0eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/plugins/tours/core.galaxy_ui.yaml M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_stock_tours.py Log Message: ----------- Fix tour tests. Commit: 3eb266a5dceaa873602a792ceefe45a412daa866 https://github.com/galaxyproject/galaxy/commit/3eb266a5dceaa873602a792ceefe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Remove unused variable, revisit issue in later Commit: f6d3059f7e1b08141f99b36aa555c10df3886305 https://github.com/galaxyproject/galaxy/commit/f6d3059f7e1b08141f99b36aa555… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/frame.scss R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss R client/galaxy/style/scss/galaxy_bootstrap/variables.scss R client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/theme/blue.scss R client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss A client/galaxy/style/source_material/error_icon.svg M client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/info_icon.svg A client/galaxy/style/source_material/ok_icon.svg A client/galaxy/style/source_material/wait_icon.svg A client/galaxy/style/source_material/warn_icon.svg M config/plugins/tours/core.galaxy_ui.yaml M static/style/blue/base.css M static/style/blue/library.css M templates/display_base.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #6422 from jxtx/styles-refresh-2018 Initial work on updating styles Compare: https://github.com/galaxyproject/galaxy/compare/7481d97a33ba...f6d3059f7e1b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 5f32ac: Automatically determine the correct Jetstream imag...
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5f32ac85ecb6b8cef89ffb68f7221d96f2c8857d https://github.com/galaxyproject/infrastructure-playbook/commit/5f32ac85ecb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M roles/slurmscale/files/group_vars/all/spawn.yml M roles/slurmscale/files/resume.yml M roles/slurmscale/tasks/main.yml Log Message: ----------- Automatically determine the correct Jetstream image since it changes. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] e0b35d: Disable new objectstore feature temporarily due to...
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e0b35d32e8cda56e28a1993d991e72a2242e457d https://github.com/galaxyproject/usegalaxy-playbook/commit/e0b35d32e8cda56e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable new objectstore feature temporarily due to bugs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f65e61: Use mapped-over collectionType when inferring coll...
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: f65e616c1afe6d9ec0bb9680fa90ee8e9d311900 https://github.com/galaxyproject/galaxy/commit/f65e616c1afe6d9ec0bb9680fa90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Use mapped-over collectionType when inferring collectionType through format_source Commit: 3ffbf5b4b6138177ed7581d7845432bec138ee23 https://github.com/galaxyproject/galaxy/commit/3ffbf5b4b6138177ed7581d78454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Append mapped-over collection type to output collection type So if for instance the connected input is a regular input with a list:list input and the output is a paired collection we set the output collection type to list:list:paired. Commit: eb37ad3752f5dbe4806e74f85b4fcee63ab407fa https://github.com/galaxyproject/galaxy/commit/eb37ad3752f5dbe4806e74f85b4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Only reset the right hand side of a connection on disconnect Commit: e10180dea108785a017b7be37b7ff5d85a2eebf1 https://github.com/galaxyproject/galaxy/commit/e10180dea108785a017b7be37b7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- (minor) client-format Commit: 8a4fe72f6710270ca453b75d61e8dbc96feadcc5 https://github.com/galaxyproject/galaxy/commit/8a4fe72f6710270ca453b75d61e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'collection_type_source_followup' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/0fb115e046b3...8a4fe72f6710 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7eac08: Undo auto-propagation of group tags.
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 7eac08979b1f474254e9a6a0b2005d365e09c143 https://github.com/galaxyproject/galaxy/commit/7eac08979b1f474254e9a6a0b200… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Undo auto-propagation of group tags. @mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool. Commit: 0fb115e046b3a492db6b592d8b38459104d696bf https://github.com/galaxyproject/galaxy/commit/0fb115e046b3a492db6b592d8b38… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6750 from jmchilton/1809_tags_walkback [18.09] Undo auto-propagation of group tags. Compare: https://github.com/galaxyproject/galaxy/compare/9b5045a05c88...0fb115e046b3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] 3e60d5: init travis script and test playbook
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3e60d5801b0577e0e3574a514838ce13e65a3d4c https://github.com/galaxyproject/ansible-galaxy/commit/3e60d5801b0577e0e357… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: A .travis.yml A tests/test_playbook.yml Log Message: ----------- init travis script and test playbook Commit: 2f9de4a553d3561743b47cff34b579f2fce03c3e https://github.com/galaxyproject/ansible-galaxy/commit/2f9de4a553d3561743b4… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M defaults/main.yml Log Message: ----------- Added variables for folder ownership and permissions Commit: 85b579c12319ec4d9d14a81992157aa2875e2213 https://github.com/galaxyproject/ansible-galaxy/commit/85b579c12319ec4d9d14… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/database.yml Log Message: ----------- Added become statements and setting database dir ownership & permissions Commit: 5febd3ca7e3a879ec20eb7b0bded8d5077e2e7b9 https://github.com/galaxyproject/ansible-galaxy/commit/5febd3ca7e3a879ec20e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Added become statements Commit: 26871a0cc59083a21fe9c098c9ac73fed3d00ef4 https://github.com/galaxyproject/ansible-galaxy/commit/26871a0cc59083a21fe9… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/mutable_setup.yml Log Message: ----------- Added become statements and setting config & shed tools dir ownership & permissions Commit: e01155439ed882666d7d663e39b537aa2f076582 https://github.com/galaxyproject/ansible-galaxy/commit/e01155439ed882666d7d… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Added become statements Commit: 0745f52b597067844c27afac52277e020226764d https://github.com/galaxyproject/ansible-galaxy/commit/0745f52b597067844c27… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/clone.yml Log Message: ----------- Added become statements and setting galaxy dir ownership & permissions Commit: cac16f1209e2e02b4a8167801c7cc41610585703 https://github.com/galaxyproject/ansible-galaxy/commit/cac16f1209e2e02b4a81… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- removed unnecessary docker lines Commit: dafe6ad12abf0f471d2954d2ed0be8d193bcac10 https://github.com/galaxyproject/ansible-galaxy/commit/dafe6ad12abf0f471d29… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml Log Message: ----------- added become statements which apply outside of travis Commit: 78d9bd9754c57258c5a13af1c873ef4509de0d16 https://github.com/galaxyproject/ansible-galaxy/commit/78d9bd9754c57258c5a1… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Update .travis.yml Commit: 1b54661490b9660f554b2a681fdb040aa9ba816f https://github.com/galaxyproject/ansible-galaxy/commit/1b54661490b9660f554b… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- pinning Ansible version to 2.4 https://github.com/galaxyproject/ansible-galaxy/pull/38/files/dafe6ad12abf0… Commit: 838cd85876d7bd6e3d3e10dde6b377ac6a3ab02b https://github.com/galaxyproject/ansible-galaxy/commit/838cd85876d7bd6e3d3e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Install an upgraded pip and virtualenv Commit: fccea6b2cde19e3c961e2c7d2d9672d5d12f57ae https://github.com/galaxyproject/ansible-galaxy/commit/fccea6b2cde19e3c961e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Install git Commit: a74e098c29917cf7c5120e5bec6f788238a4d7a5 https://github.com/galaxyproject/ansible-galaxy/commit/a74e098c29917cf7c512… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Drop unnecessary become Commit: bdafc7e265a16fec35e74a30a47e557e46b38e06 https://github.com/galaxyproject/ansible-galaxy/commit/bdafc7e265a16fec35e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tests/test_playbook.yml Log Message: ----------- Add become on play level Commit: cbd0201114858f0af391c03ddd9f3f54a8e70fa0 https://github.com/galaxyproject/ansible-galaxy/commit/cbd0201114858f0af391… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml M tests/test_playbook.yml Log Message: ----------- Merge pull request #5 from mvdbeek/drop_become Thank you! Commit: f606476bbaa96fbfc472a973dadd023fbebaad0c https://github.com/galaxyproject/ansible-galaxy/commit/f606476bbaa96fbfc472… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M defaults/main.yml M tasks/clone.yml M tasks/database.yml M tasks/mutable_setup.yml M tasks/static_setup.yml Log Message: ----------- drop unnecessary file and variable Commit: 9ee412e2d63d706437134f3a307774af7eeb8fd8 https://github.com/galaxyproject/ansible-galaxy/commit/9ee412e2d63d70643713… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: A .travis.yml M tasks/clone.yml M tasks/static_setup.yml A tests/test_playbook.yml Log Message: ----------- Merge pull request #38 from eslerm/travis Travis-CI Compare: https://github.com/galaxyproject/ansible-galaxy/compare/fa0df02a3eaf...9ee4… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eae35f: Deduplicate pgcleanup.py
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eae35fab3304224ab6d55ffeae40d6b6611a99cb https://github.com/galaxyproject/galaxy/commit/eae35fab3304224ab6d55ffeae40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Deduplicate pgcleanup.py Commit: 7b8af87091eb5686ad390073f678d9088f6af10b https://github.com/galaxyproject/galaxy/commit/7b8af87091eb5686ad390073f678… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Add a pgcleanup function for purging error HDAs Commit: 7481d97a33ba7fb2a003ae2ad51414c04ae826b0 https://github.com/galaxyproject/galaxy/commit/7481d97a33ba7fb2a003ae2ad514… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6736 from natefoo/pgcleanup pgcleanup.py enhancements Compare: https://github.com/galaxyproject/galaxy/compare/bae08f3ca226...7481d97a33ba **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 649390: Increase Toolshed uWSGI proxy timeout
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6493903ab85efa59019c9b9e056e2ae97319d300 https://github.com/galaxyproject/usegalaxy-playbook/commit/6493903ab85efa59… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- Increase Toolshed uWSGI proxy timeout **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b5e221: Fix page editor height for flex panels.
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b5e221929687809adfb30cad8280767f3a8412c5 https://github.com/galaxyproject/galaxy/commit/b5e221929687809adfb30cad8280… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Fix page editor height for flex panels. Commit: 9b5045a05c882c652935d9daaf589a10d776190c https://github.com/galaxyproject/galaxy/commit/9b5045a05c882c652935d9daaf58… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6747 from dannon/fix_page_editor_height [18.09] Fix page editor height for flex panels. Compare: https://github.com/galaxyproject/galaxy/compare/287648f5d9f9...9b5045a05c88 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0