Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e591288cadf5af3acb0700f01cbac1188f07abb1 https://github.com/galaxyproject/galaxy/commit/e591288cadf5af3acb0700f01cbac... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Swap to a more flexible bibtex library. Commit: b9ff347e9b2330d2ed87be5f1ada15834535b1cb https://github.com/galaxyproject/galaxy/commit/b9ff347e9b2330d2ed87be5f1ada1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M Makefile M client/.babelrc 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/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.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/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.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/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.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/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.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-modal.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-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.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-select.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/ui/ui-thumbnails.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-button.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-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M 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static/maps/mvc/tours.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/de/locale.js.map M static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.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/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M 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/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M static/style/blue/base.css R templates/admin/package_tool.mako R templates/admin/reload_tool.mako M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/citations.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/group/index.mako M test/api/test_dataset_collections.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary M test/galaxy_selenium/driver_factory.py M test/qunit/test-app.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_published_histories_grid.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: f7fc785eeb711f6ac86cc96fe124178009fe5b9d https://github.com/galaxyproject/galaxy/commit/f7fc785eeb711f6ac86cc96fe1241... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/package.json M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js R templates/webapps/galaxy/history/citations.mako Log Message: ----------- Citations work; add client route, remove mako and make it all js-driven. Commit: 3e69d275433da474e68d5bd8b10ed327416c99e6 https://github.com/galaxyproject/galaxy/commit/3e69d275433da474e68d5bd8b10ed... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- arrow functions and formatting in analysis.js Commit: b52051e35d3e9d76b99f1ec5bd1f2480073eb3ad https://github.com/galaxyproject/galaxy/commit/b52051e35d3e9d76b99f1ec5bd1f2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Cleanup in citation-model.js Commit: 1f0f731a4f1b1df455cff49c1d59813d9315cad3 https://github.com/galaxyproject/galaxy/commit/1f0f731a4f1b1df455cff49c1d598... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- parseBibtex->bibtexParse, remove cruft. Commit: 3b7b294acf7d8967125b69c9e9c5db45bd7cbdc1 https://github.com/galaxyproject/galaxy/commit/3b7b294acf7d8967125b69c9e9c5d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/citations.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A static/maps/mvc/citations.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js A static/scripts/mvc/citations.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Convert to a single citations module; this is much easier to manage. We're shifting *more* towards encapsulated components and having all this stuff split up makes it more difficult to wrangle. Commit: 83e142170b1cf921c911f5d1595ad9a7da535ec0 https://github.com/galaxyproject/galaxy/commit/83e142170b1cf921c911f5d1595ad... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Remove super chatty collection view creation console.log (if we really need this, it should be using our scoped logger, but I don't thinkwe do) Commit: 4454d50909ea5dca041b52c96c36b5d06e4c1f25 https://github.com/galaxyproject/galaxy/commit/4454d50909ea5dca041b52c96c36b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fetch isn't built into the citations model, requires a manual fetch here. Commit: 4071c81a9295f0555653c46861930a899301cc9b https://github.com/galaxyproject/galaxy/commit/4071c81a9295f0555653c46861930... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock A static/scripts/libs/vue.js Log Message: ----------- Vue lib+build; fixes setimmediate polyfill injection. Commit: 3091994a02d919d486432f917646f76fe35be149 https://github.com/galaxyproject/galaxy/commit/3091994a02d919d486432f917646f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Segmented out single file component build infra for vue Commit: 886cd6c62e08177cb2458bd4ea6f82e93b1484f4 https://github.com/galaxyproject/galaxy/commit/886cd6c62e08177cb2458bd4ea6f8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citations.js M client/package.json M client/webpack.config.js M client/yarn.lock M static/maps/mvc/citations.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citations.js Log Message: ----------- Better, more robust latex conversion. Commit: c903e9fe1acbe3b90b3cd60c8ffc1d6880f74742 https://github.com/galaxyproject/galaxy/commit/c903e9fe1acbe3b90b3cd60c8ffc1... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/mvc/user/user_api_keys.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/user/user_api_keys.js M static/style/blue/base.css R templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Showcase Vue JS by transforming a mako file to javascript Commit: 8e5f62673d3b6a48df6214d91e00b75f86826a62 https://github.com/galaxyproject/galaxy/commit/8e5f62673d3b6a48df6214d91e00b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/user/user_api_keys.js M static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user_api_keys.js Log Message: ----------- Fix up admin apikey imports, formatting. Commit: c046565fbfc33a2ded14d41d42272c1cd5aa2d61 https://github.com/galaxyproject/galaxy/commit/c046565fbfc33a2ded14d41d42272... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citations.js M static/maps/mvc/citations.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Citations formatting. Commit: 0ca4aa7e933de4e9c5471ba110b23d0299ee01bb https://github.com/galaxyproject/galaxy/commit/0ca4aa7e933de4e9c5471ba110b23... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/userskeys.py Log Message: ----------- Fixing build fail issues Commit: 3a931e744831a0216d5c1c99db25ec486eced972 https://github.com/galaxyproject/galaxy/commit/3a931e744831a0216d5c1c99db25e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/userskeys.py Log Message: ----------- Remove unused import from userkeys.py Commit: 8810bd0f7c08d9216b85d52a147da44187c4c355 https://github.com/galaxyproject/galaxy/commit/8810bd0f7c08d9216b85d52a147da... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Add axios Commit: a41c9af3a17853e17f127ebc9a79df1e813d3ec9 https://github.com/galaxyproject/galaxy/commit/a41c9af3a17853e17f127ebc9a79d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/layout/panel.js M static/maps/layout/panel.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/panel.js Log Message: ----------- Allow views *or* elements for panel display method. Commit: 1013f6b005bf882acc9dce98c23bb4c1edaffc7f https://github.com/galaxyproject/galaxy/commit/1013f6b005bf882acc9dce98c23bb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/components/user_api_keys.vue R client/galaxy/scripts/mvc/user/user_api_keys.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map R static/scripts/mvc/user/user_api_keys.js Log Message: ----------- Vue SFC for admin/user_api_keys. Commit: 1beda0eb7a966cfee408728b0cc0a0dfd8899ac4 https://github.com/galaxyproject/galaxy/commit/1beda0eb7a966cfee408728b0cc0a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/components/user_api_keys.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Bit of cleanup in user_api_keys SFC Commit: ad26832461bb27aced41f0530ba5f528412b576a https://github.com/galaxyproject/galaxy/commit/ad26832461bb27aced41f0530ba5f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/components/user_api_keys.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- More cleanup. Commit: f79ae1d1a1a04d72731206fad06b6d0fcc3c6547 https://github.com/galaxyproject/galaxy/commit/f79ae1d1a1a04d72731206fad06b6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.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/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.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/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.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/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/trackster.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml A lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/datatypes/text.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/admin.toolshed.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/i18n.js.map M static/maps/layout/modal.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/library/library-util.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/ja/locale.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/search-input.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/localization.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map 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/grid/grid-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/trackster.css M templates/webapps/reports/run_stats.mako M test/api/test_history_contents.py M test/base/populators.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.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/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: c03d011914b7246a587ecaa3e46fa1646570bdd5 https://github.com/galaxyproject/galaxy/commit/c03d011914b7246a587ecaa3e46fa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Simplify Vue creation from SFC, no need to specify template/component separately here. Commit: fc58c45a7e79455c5b51d6d442241c312cae9cb5 https://github.com/galaxyproject/galaxy/commit/fc58c45a7e79455c5b51d6d442241... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/citations.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- WIP Citations/Vue Commit: 740234534509cebeadbaf927c97e5031ab955640 https://github.com/galaxyproject/galaxy/commit/740234534509cebeadbaf927c97e5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/utils/ajax-queue.js M config/galaxy.ini.sample M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/hash_util.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/hg_util.py M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/ajax-queue.js R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M test/unit/jobs/test_runner_local.py M test/unit/shed_unit/test_tool_panel_manager.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: a853d54b39b68439374df043f17cf049a06b33e3 https://github.com/galaxyproject/galaxy/commit/a853d54b39b68439374df043f17cf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/yarn.lock M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting Commit: 2718f93ab0751042a191941371567a97319ae9bb https://github.com/galaxyproject/galaxy/commit/2718f93ab0751042a191941371567... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Stray console.debug removed. Commit: af2fe1805dd653880eaa8045f238fa326de27bb4 https://github.com/galaxyproject/galaxy/commit/af2fe1805dd653880eaa8045f238f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R client/galaxy/scripts/mvc/citations.js R static/scripts/mvc/citations.js Log Message: ----------- Remove unused citations.js; this was all pushed into the component. (we may want to pull some of the storage logic back out, elsewhere, but this is an incremental step forward) Commit: 3b2e21373917516c1b192cc27e6274c5adff4804 https://github.com/galaxyproject/galaxy/commit/3b2e21373917516c1b192cc27e627... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove some unused styles, push others into component. Commit: 951d8ab4bbef5ed4e459dd624af46f70bfc31ba1 https://github.com/galaxyproject/galaxy/commit/951d8ab4bbef5ed4e459dd624af46... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix citations display differentiation w/ histories vs specific tool. Commit: e385b7f79570a078b9198d37c458559d0fa70e92 https://github.com/galaxyproject/galaxy/commit/e385b7f79570a078b9198d37c4585... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: A client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Add basic workflow editor app, bundle, entry. Doesn't work yet, need to disentangle all the other bits. Commit: d9897567f93d3005fd1ff186f3ba391a10ae2d10 https://github.com/galaxyproject/galaxy/commit/d9897567f93d3005fd1ff186f3ba3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Repack. Commit: c2b6d7b7dc63add49d17667cc887b059538d6b2d https://github.com/galaxyproject/galaxy/commit/c2b6d7b7dc63add49d17667cc887b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Bundle masthead into application, dramatically cutting down on load time on older pages like workflow editor, etc, in addition to allowing newer features. Commit: d166e41204074d60beec15c305cb8c0eb395996b https://github.com/galaxyproject/galaxy/commit/d166e41204074d60beec15c305cb8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: A client/galaxy/scripts/apps/masthead.js A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/workflow.bundled.js A static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Actually add masthead and workflow bundles. Commit: a9db144e62c8614c477a3338afa2be90f524997f https://github.com/galaxyproject/galaxy/commit/a9db144e62c8614c477a3338afa2b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M 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lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py A lib/galaxy/util/script.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/schedulers/core.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M scripts/common_startup.sh M scripts/functional_tests.py M scripts/manage_tool_dependencies.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/tool/tool-form-base.js R templates/search/index.mako M templates/show_params.mako M templates/user/register.mako M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: a11cffd67886a44ea0df5b96e9bb7795ddb61ef2 https://github.com/galaxyproject/galaxy/commit/a11cffd67886a44ea0df5b96e9bb7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M .travis.yml Log Message: ----------- Allow qunit travis failures. *TEMPORARY* Commit: 6637c52864292c7c97e46c71c09faf7dc569b13b https://github.com/galaxyproject/galaxy/commit/6637c52864292c7c97e46c71c09fa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M .travis.yml Log Message: ----------- Try again to allow travis failures. Commit: 4c595798b8a68863976d5715d607784150e0e028 https://github.com/galaxyproject/galaxy/commit/4c595798b8a68863976d5715d6077... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/galaxy.library.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-libraryrow-view.js M static/maps/galaxy.library.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-libraryrow-view.js.map M static/scripts/galaxy.library.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-libraryrow-view.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Clean up some library imports to slim down require'd components. Kick off masthead correctly w/ galaxy.root settings. Commit: 00147bafc7cc4738ff70ec7a4156363613c54559 https://github.com/galaxyproject/galaxy/commit/00147bafc7cc4738ff70ec7a41563... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/karma.config.js M client/package.json M run_tests.sh R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Run qunit tests under Karma. Commit: 699e10bdecf542c994460282d399e5c20ef97b3f https://github.com/galaxyproject/galaxy/commit/699e10bdecf542c994460282d399e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/karma.config.js M client/package.json M run_tests.sh R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge pull request #22 from jmchilton/bibtex-replacement-lib Run qunit tests under Karma. Commit: 01f3cc1c1adacb5c688d17832235f77ae7d7e3a1 https://github.com/galaxyproject/galaxy/commit/01f3cc1c1adacb5c688d17832235f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Move testing dependencies to devDependencies, use yarn. Commit: baec91349f521103593a0658285f758421b789b2 https://github.com/galaxyproject/galaxy/commit/baec91349f521103593a0658285f7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json Log Message: ----------- Remove bin path from package.json for karma. Commit: c871ba605a53ef88a317196ba620eaae315afb95 https://github.com/galaxyproject/galaxy/commit/c871ba605a53ef88a317196ba620e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Work around https://github.com/karma-runner/karma-qunit/issues/98 for now, use qunitjs dep Commit: 4bdbe28e79ce6a4889ad6e504b49b10fe32e1c70 https://github.com/galaxyproject/galaxy/commit/4bdbe28e79ce6a4889ad6e504b49b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/karma.config.js M client/package.json Log Message: ----------- Fix two more of the qunit tests for webpack setup. Using karma-polyfill. Commit: 0f266997f222ff7d0deb0ba3da540f80432ae61c https://github.com/galaxyproject/galaxy/commit/0f266997f222ff7d0deb0ba3da540... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Swap karma-polyfill to devDependencies Commit: 6d9b21776e502dc0225bac6a7677bbbe4f143231 https://github.com/galaxyproject/galaxy/commit/6d9b21776e502dc0225bac6a7677b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/gulpfile.js Log Message: ----------- Gulp should ignore the qunit directory here. Commit: e81d89f74faa2678413ecb4b6b89689ba8cc4f11 https://github.com/galaxyproject/galaxy/commit/e81d89f74faa2678413ecb4b6b896... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: A client/galaxy/scripts/apps/trackster.js M client/webpack.config.js Log Message: ----------- WIP Trackster entrypoint; more entangled than expected so it needs help. Commit: 8d9998c50f9beb47eb23a67ad040b8721310dee9 https://github.com/galaxyproject/galaxy/commit/8d9998c50f9beb47eb23a67ad040b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M client/galaxy/scripts/apps/trackster.js M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/trackster.bundled.js A static/scripts/bundled/trackster.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Trackster app entrypoint fix. Commit: 07ea8029a2b85876e064f4e4ba336e0397ee4e0c https://github.com/galaxyproject/galaxy/commit/07ea8029a2b85876e064f4e4ba336... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy-app-base.js M client/galaxy/scripts/qunit/tests/graph.js M client/galaxy/scripts/qunit/tests/hda-base.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job-dag.js M client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics-logger.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M 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/scripts/qunit/tests/utils_test.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Client-format for tests. Commit: 380e82c5dc9aadec15eccb07c9c778fc7b9c0f29 https://github.com/galaxyproject/galaxy/commit/380e82c5dc9aadec15eccb07c9c77... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: R client/galaxy/scripts/apps/trackster.js A client/galaxy/scripts/apps/viz.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map R static/scripts/bundled/trackster.bundled.js R static/scripts/bundled/trackster.bundled.js.map A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Bundle trackster/circster together as 'viz'. Commit: c92d958c0a3c11b8a6f442abe9a59c127a5b1572 https://github.com/galaxyproject/galaxy/commit/c92d958c0a3c11b8a6f442abe9a59... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: A client/galaxy/scripts/apps/library.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/library.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/library.bundled.js A static/scripts/bundled/library.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Bundle libraries. Commit: 76f0eb41726424829f2e93efa08d8336266b7c50 https://github.com/galaxyproject/galaxy/commit/76f0eb41726424829f2e93efa08d8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/library.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/library.bundled.js M static/scripts/bundled/library.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Bundle admin toolshed beta interface. Commit: 953d4859750874b2cedf1351c344cba2da7b5c7f https://github.com/galaxyproject/galaxy/commit/953d4859750874b2cedf1351c344c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Slight rewording of citation reminder/prompt, change to an infomessage. Commit: d4f33c4bf8a0e488536099e0fe3d155b4ec15f39 https://github.com/galaxyproject/galaxy/commit/d4f33c4bf8a0e488536099e0fe3d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow onclicks. Commit: 283afd984bca6f36d604e4e48e028ee17fc67719 https://github.com/galaxyproject/galaxy/commit/283afd984bca6f36d604e4e48e028... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue Log Message: ----------- Add a tag to formatted references in citations.vue. No style associated with it yet but it makes it easier to identify for tours and tests. Commit: 7594ae7febf653aa3f08548d4157f73012e15e95 https://github.com/galaxyproject/galaxy/commit/7594ae7febf653aa3f08548d4157f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Rebuild after merges. Commit: 2950bf992446da7d05d2210576f9bcfa86ae977b https://github.com/galaxyproject/galaxy/commit/2950bf992446da7d05d2210576f9b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Only show citations infomessage blurb for the full history view. Commit: 5b531472f7319c07a3847879e427a2a752b5b13e https://github.com/galaxyproject/galaxy/commit/5b531472f7319c07a3847879e427a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Slight reformatting in message display for history-level citations. Commit: 8426158499d4b1a8fa0c960b964b3ac220c6bac6 https://github.com/galaxyproject/galaxy/commit/8426158499d4b1a8fa0c960b964b3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/scheduling_manager.py M run_tests.sh M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M test/api/test_configuration.py M test/api/test_history_contents.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: 6c47f17857d27ba5c10f54ac520a1adadb493da3 https://github.com/galaxyproject/galaxy/commit/6c47f17857d27ba5c10f54ac520a1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- rebundle Commit: 4d416dcb21cdaac9396cf4c8a76ae7bf251d3a79 https://github.com/galaxyproject/galaxy/commit/4d416dcb21cdaac9396cf4c8a76ae... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/library.js A client/galaxy/scripts/apps/masthead.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/viz.js A client/galaxy/scripts/apps/workflow.js A client/galaxy/scripts/components/citations.vue A client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/panel.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.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-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/style/less/base.less M client/gulpfile.js A client/karma.config.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/galaxy.library.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/citations.js.map M static/maps/mvc/history/options-menu.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-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/library.bundled.js A static/scripts/bundled/library.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 M static/scripts/bundled/login.bundled.js.map A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/viz.bundled.js.map A static/scripts/bundled/workflow.bundled.js A static/scripts/bundled/workflow.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/panel.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js A static/scripts/libs/vue.js R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.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-libraryrow-view.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/workflow/editor.mako R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge pull request #4978 from dannon/bibtex-replacement-lib Vue integration, bibtex replacement Compare: https://github.com/galaxyproject/galaxy/compare/ce4584956b72...4d416dcb21cd