Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e4e30fda24316033c28cad01b0f639d826afbd97 https://github.com/galaxyproject/galaxy/commit/e4e30fda24316033c28cad01b0f63... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add tabs, unify installation UI. Commit: 10af8ce2b299d8f732cd1eeff538b3a24f55355d https://github.com/galaxyproject/galaxy/commit/10af8ce2b299d8f732cd1eeff538b... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Finished repository details. Commit: 1c093a9771b196b3e6faaa76f1ca803d7f5b3089 https://github.com/galaxyproject/galaxy/commit/1c093a9771b196b3e6faaa76f1ca8... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.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.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-model.js M client/galaxy/scripts/mvc/form/form-data.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/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.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-model.js A 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/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.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/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.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-tabs.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-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/ui/search-input.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/error-modal.less M client/galaxy/style/less/ui/search-input.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js R config/plugins/visualizations/charts/static/models/group.js R config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css M config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/group.js A config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js M config/tool_data_table_conf.xml.sample A config/tool_destinations.yml.sample A display_applications/ucsc/trackhub.xml A doc/source/admin/grt.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.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/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.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/tools/deps/views.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/history_contents.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/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh M scripts/bootstrap_history.py A scripts/communication/communication_server.py A scripts/communication/template/communication.css A scripts/communication/template/communication.html A scripts/communication/template/communication.js A scripts/grt.py A scripts/grt.yml.sample M scripts/nosetests.py M setup.cfg A static/maps/layout/generic-nav-view.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-li-edit.js.map M 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static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-data.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/history/copy-dialog.js M static/scripts/mvc/history/hda-model.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-model.js A 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/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.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/ui/error-modal.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.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-tabs.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-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/ui/search-input.js M static/scripts/utils/ajax-queue.js A static/style/base.css M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css M templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/user/change_password.mako A templates/user/communication_settings.mako M templates/user/index.mako M templates/user/register.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/workflow/run.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako A test-data/neostore.zip M test/api/test_workflows.py M test/base/driver_util.py M test/base/twilltestcase.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_resolvers.py M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_tool_deps.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into Merge remote-tracking branch 'upstream/dev' into api_install_performance. Commit: 8e83d3178452cc55ca5938dcf1ed0162764142b7 https://github.com/galaxyproject/galaxy/commit/8e83d3178452cc55ca5938dcf1ed0... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Additional minor cleanup. Commit: c52b046764a95bf237f9af6212565ea6e3c64e15 https://github.com/galaxyproject/galaxy/commit/c52b046764a95bf237f9af6212565... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Even more cleanup. - Removed dangling code. - Restored Marius' changes. - Fixed the repository-wide tool panel selection. Commit: 5425f99ee8471ee59dff84835c5f03744001e1bc https://github.com/galaxyproject/galaxy/commit/5425f99ee8471ee59dff84835c5f0... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/style/less/base.less M config/tool_shed.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance Commit: 5ed67c0ab05e82fe1b388711c7291e58d3b7a4a1 https://github.com/galaxyproject/galaxy/commit/5ed67c0ab05e82fe1b388711c7291... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/tool_shed/api/common.py M setup.cfg M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.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/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js R static/style/blue/tool_menu.css M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance Commit: fe3112fea5d1bfde89317054a818b8a0f244c28e https://github.com/galaxyproject/galaxy/commit/fe3112fea5d1bfde89317054a818b... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix installation, incorporate Marius' conda changes. Commit: b6bdbdbd6d6193524cab3e058dd6e450dcf5eb52 https://github.com/galaxyproject/galaxy/commit/b6bdbdbd6d6193524cab3e058dd6e... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix repository details updating when revision is selected. Commit: 786c50505ed509354ac7a126647eabc3824bd0b9 https://github.com/galaxyproject/galaxy/commit/786c50505ed509354ac7a126647ea... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M Makefile M client/galaxy/scripts/mvc/history/hdca-model.js M config/tool_shed.ini.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M scripts/common_startup.sh M static/maps/mvc/history/hdca-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hdca-model.js M test/shed_functional/functional/test_0310_hg_api_features.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance Commit: 21bfcecf477d065c2b2d1ac99b5b2fbf4ef5cace https://github.com/galaxyproject/galaxy/commit/21bfcecf477d065c2b2d1ac99b5b2... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Implement most of the repo installation queue. - Adding repositories to the queue. Removing repositories from the queue. - Installation of individual repositories from the queue. Installing everything in the queue does not yet work. Commit: 4965c17174778e721b9e9dee5809f6066ca0dd7d https://github.com/galaxyproject/galaxy/commit/4965c17174778e721b9e9dee5809f... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Implement batch installation of the repository queue. Commit: eada11e9fc36b9dc62a25028370cfe9295489dd9 https://github.com/galaxyproject/galaxy/commit/eada11e9fc36b9dc62a25028370cf... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: 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-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance Commit: fab2c3ecc3b70c824ea5d5d89e4cd4733d98a411 https://github.com/galaxyproject/galaxy/commit/fab2c3ecc3b70c824ea5d5d89e4cd... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Improve travis' mood. Commit: 5081cdc07d9d74bd8d68f2cc32128bfcdae45eee https://github.com/galaxyproject/galaxy/commit/5081cdc07d9d74bd8d68f2cc32128... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix tabs. Commit: 32da285d5c4d5e479eeeaa7465ddfaf2e5ac1dc1 https://github.com/galaxyproject/galaxy/commit/32da285d5c4d5e479eeeaa7465ddf... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M .ci/first_startup.sh M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.ini.sample A doc/source/dev/build_a_job_runner.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/datasets.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M run.sh M scripts/common_startup.sh M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance Commit: 571dc2a4dbedad1e0f140ddbf86216b033266015 https://github.com/galaxyproject/galaxy/commit/571dc2a4dbedad1e0f140ddbf8621... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/less/library.less M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/update_repository_manager.py 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/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance Commit: 46136787e45160e7101b941f8fc1b56a2f3ec6d4 https://github.com/galaxyproject/galaxy/commit/46136787e45160e7101b941f8fc1b... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Text fixes, make the queue and its tab always visible. Commit: 54e589ebad000535c384850df7abe6c195fbe5f5 https://github.com/galaxyproject/galaxy/commit/54e589ebad000535c384850df7abe... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #2769 from davebx/api_install_performance Cleanup of and performance enhancements to the API installation of repositories. Compare: https://github.com/galaxyproject/galaxy/compare/ba6a0a36476c...54e589ebad00