Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a376d1ae0a5bdad632b5ad0f280cddddbd2d54d https://github.com/galaxyproject/galaxy/commit/9a376d1ae0a5bdad632b5ad0f280c... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/tool_form.mako Log Message: ----------- Remove tool form downgrade option Commit: 6c805ccb988a47b2958e9bcaf7c56faed13c1fd0 https://github.com/galaxyproject/galaxy/commit/6c805ccb988a47b2958e9bcaf7c56... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt 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-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/util/jstree.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/capsule/capsule_manager.py 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-view.js.map M static/maps/reports_webapp/run_stats.js.map 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-view.js M static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000 Commit: 104bdcd7c8e8e5557b166d47c9dcdfdadf22cdf6 https://github.com/galaxyproject/galaxy/commit/104bdcd7c8e8e5557b166d47c9dcd... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-check.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-button-check.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-options.js.map M static/scripts/mvc/ui/ui-button-check.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-options.js Log Message: ----------- Minor code cleanup for ui elements Commit: 5d8ad4249fc6198846bf8cdceabf3fb91acc2973 https://github.com/galaxyproject/galaxy/commit/5d8ad4249fc6198846bf8cdceabf3... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/mvc/ui/ui-color-picker.js Log Message: ----------- Remove unnecessary condition Commit: 09445359a4dbcedb2d996dd4c46469f462ca6809 https://github.com/galaxyproject/galaxy/commit/09445359a4dbcedb2d996dd4c4646... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M test/qunit/tests/upload_dialog_tests.js M test/unit/test_galaxy_mapping.py R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000 Commit: 9a44d780145b6a7b30b40b1a7e61b7df5e526dbc https://github.com/galaxyproject/galaxy/commit/9a44d780145b6a7b30b40b1a7e61b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/workflow/render.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/common_util.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000 Commit: 11e6c9949e2bb58874eedb81d9066c1f460fa34a https://github.com/galaxyproject/galaxy/commit/11e6c9949e2bb58874eedb81d9066... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M templates/base.mako Log Message: ----------- Make sure global Galaxy object exists Commit: aebf0c7fea2f276f68b77d27408c45e330aa629b https://github.com/galaxyproject/galaxy/commit/aebf0c7fea2f276f68b77d27408c4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M static/maps/galaxy.panels.js.map M templates/base.mako M templates/webapps/galaxy/root/index.mako Log Message: ----------- Add modified index handling Commit: 8cf76bd27e30a7b35ad3c7867fdc43bd44a4b661 https://github.com/galaxyproject/galaxy/commit/8cf76bd27e30a7b35ad3c7867fdc4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M static/maps/galaxy.panels.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy.panels.js M static/scripts/utils/uploadbox.js M templates/base.mako Log Message: ----------- Note root in Galaxy object Commit: b1949c5805730d2f4ce53759dd5636449a0b08f5 https://github.com/galaxyproject/galaxy/commit/b1949c5805730d2f4ce53759dd563... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/app/app-panel-center.js A client/galaxy/scripts/mvc/app/app-panel-history.js A client/galaxy/scripts/mvc/app/app-panel-tool.js A client/galaxy/scripts/mvc/app/app-view.js A static/maps/mvc/app/app-panel-center.js.map A static/maps/mvc/app/app-panel-history.js.map A static/maps/mvc/app/app-panel-tool.js.map A static/maps/mvc/app/app-view.js.map A static/scripts/mvc/app/app-panel-center.js A static/scripts/mvc/app/app-panel-history.js A static/scripts/mvc/app/app-panel-tool.js A static/scripts/mvc/app/app-view.js M templates/base.mako M templates/webapps/galaxy/root/index.mako Log Message: ----------- Add script files, continue ui replication Commit: 8444838a3eda2b2e361c32e165cb65ad3a198cc5 https://github.com/galaxyproject/galaxy/commit/8444838a3eda2b2e361c32e165cb6... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Fix panel handlers Commit: 8d8df1ab5d741758a195eaa34b75b49c1339a948 https://github.com/galaxyproject/galaxy/commit/8d8df1ab5d741758a195eaa34b75b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map R static/maps/mvc/ui/ui-button-check.js.map R static/maps/mvc/ui/ui-button-menu.js.map A static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js R static/scripts/mvc/ui/ui-button-check.js R static/scripts/mvc/ui/ui-button-menu.js A static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Revise/unify buttons, cleanup default ui element code, add panel button Commit: c7bb8873ca46a67993ad5cb25a85bc81bb780777 https://github.com/galaxyproject/galaxy/commit/c7bb8873ca46a67993ad5cb25a85b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Add buttons to panel history builder, apply coding conventions Commit: d546d08c86fc506edb7912adefe723c60e0738fb https://github.com/galaxyproject/galaxy/commit/d546d08c86fc506edb7912adefe72... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M static/maps/mvc/app/app-panel-history.js.map M static/scripts/mvc/app/app-panel-history.js Log Message: ----------- Minor fix Commit: 910f95188c3ea5fffc36e80aa5f8d689e4450ddf https://github.com/galaxyproject/galaxy/commit/910f95188c3ea5fffc36e80aa5f8d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix tool panel handling Commit: ad6fdc3dc226af9238b4e366ddc3f246db1e5a87 https://github.com/galaxyproject/galaxy/commit/ad6fdc3dc226af9238b4e366ddc3f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Add history panel specific css style Commit: b99b8f2853c49f432eb6e400c734ef087ce36af2 https://github.com/galaxyproject/galaxy/commit/b99b8f2853c49f432eb6e400c734e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js Log Message: ----------- Remove unnecessary div Commit: df52c62f4d662cd73587cd8450c33f86799ff79e https://github.com/galaxyproject/galaxy/commit/df52c62f4d662cd73587cd8450c33... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Reinsert message divs Commit: 521677623fae73e07aa98f67c6a65c1913885150 https://github.com/galaxyproject/galaxy/commit/521677623fae73e07aa98f67c6a65... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/reports.less M config/tool_data_table_conf.xml.sample A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M doc/source/ts_api_doc.rst M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py 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 M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.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/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/shed_util_common.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tools/tools-form.js M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/qunit/README.txt M test/qunit/package.json M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar M test/unit/managers/test_DatasetManager.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox_filters.py M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ui_revision_000 Commit: a8ffdc523eebe21162e8e29cb6311200d7a2816b https://github.com/galaxyproject/galaxy/commit/a8ffdc523eebe21162e8e29cb6311... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-panel-center.js R client/galaxy/scripts/mvc/app/app-panel-history.js R client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js R static/maps/mvc/app/app-panel-center.js.map R static/maps/mvc/app/app-panel-history.js.map R static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map R static/scripts/mvc/app/app-panel-center.js R static/scripts/mvc/app/app-panel-history.js R static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Group analysis panels Commit: d0c77f17610c1361de1447840bafae9cea3a575d https://github.com/galaxyproject/galaxy/commit/d0c77f17610c1361de1447840bafa... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js Log Message: ----------- Revise page building Commit: 53b84fd17f662ba595d0a72ca79a24d5792ec0f8 https://github.com/galaxyproject/galaxy/commit/53b84fd17f662ba595d0a72ca79a2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M templates/webapps/galaxy/root/index.mako Log Message: ----------- Style fixes, generalizations Commit: 92bdf0de2436549546951645a7f1e8d852715e49 https://github.com/galaxyproject/galaxy/commit/92bdf0de2436549546951645a7f1e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Remove unused styles Commit: 3a94f35468622b6819c7f07c2a2f95a85ca03870 https://github.com/galaxyproject/galaxy/commit/3a94f35468622b6819c7f07c2a2f9... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: R templates/webapps/galaxy/root/tool_menu.mako Log Message: ----------- Remove tool menu mako Commit: b8304e1ab7538b5bcc315f87905d242554b2171a https://github.com/galaxyproject/galaxy/commit/b8304e1ab7538b5bcc315f87905d2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Reinsert active view identifier Commit: 94e8b312d4548be90f7ae4e899080298f87380f5 https://github.com/galaxyproject/galaxy/commit/94e8b312d4548be90f7ae4e899080... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Reinsert message classes Commit: 93be500441a5c454168de3c504db341709be7191 https://github.com/galaxyproject/galaxy/commit/93be500441a5c454168de3c504db3... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/app/app-analysis.js A static/maps/mvc/app/app-analysis.js.map A static/scripts/mvc/app/app-analysis.js Log Message: ----------- Add unified panel script Commit: 5043dd2b7265e7b489428f2858936cd7edac75d3 https://github.com/galaxyproject/galaxy/commit/5043dd2b7265e7b489428f2858936... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/app/app-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix panel notifications Commit: c08aab0bd358a8568841a4b43af2e416dec5a513 https://github.com/galaxyproject/galaxy/commit/c08aab0bd358a8568841a4b43af2e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map Log Message: ----------- Code style fix Commit: 823fd4ae47ccbf6ed1d19665a7a921d53441833c https://github.com/galaxyproject/galaxy/commit/823fd4ae47ccbf6ed1d19665a7a92... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: A CODE_OF_CONDUCT.md M README.rst M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ui_revision_000 Conflicts: static/style/blue/base.css Commit: 192239f8d7832e24e9cca55f2ec20c6e3f8e4773 https://github.com/galaxyproject/galaxy/commit/192239f8d7832e24e9cca55f2ec20... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M static/maps/mvc/ui/ui-color-picker.js.map Log Message: ----------- Fix codestyle color picker Commit: bcf77efb5aa79f20afd4cb1104013892fac97959 https://github.com/galaxyproject/galaxy/commit/bcf77efb5aa79f20afd4cb1104013... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Remove fixed message Commit: 2f08578ff607c67ddcfcf15f299e26ea99008ecb https://github.com/galaxyproject/galaxy/commit/2f08578ff607c67ddcfcf15f299e2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix center panel Commit: c948bc70caa9f241c56df0a0e1ff7e542bdabee3 https://github.com/galaxyproject/galaxy/commit/c948bc70caa9f241c56df0a0e1ff7... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map Log Message: ----------- Remove gap Commit: 759c2142e744476c7bfa3164c34ac351bfb37fa0 https://github.com/galaxyproject/galaxy/commit/759c2142e744476c7bfa3164c34ac... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/galaxy.menu.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix user object usage Commit: 359e812f4fbea0e207537b482b7ab601aa5a3d8f https://github.com/galaxyproject/galaxy/commit/359e812f4fbea0e207537b482b7ab... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Adjust old masthead config Commit: ac3fc394571da6d33eca6943d58f18aeb5e00814 https://github.com/galaxyproject/galaxy/commit/ac3fc394571da6d33eca6943d58f1... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix masthead Commit: 200c2e640b3665b7c63ce487ccdee044b7c9b054 https://github.com/galaxyproject/galaxy/commit/200c2e640b3665b7c63ce487ccdee... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix tabs Commit: fcbd8b241024ea5a419287759f33b622e94af4fa https://github.com/galaxyproject/galaxy/commit/fcbd8b241024ea5a419287759f33b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Remove unused user json Commit: 00806d484b2007aaf0adb1efbf83db49c8dc5ff4 https://github.com/galaxyproject/galaxy/commit/00806d484b2007aaf0adb1efbf83d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Use Galaxy object instead of galaxy_config Commit: e9009f63936cbef0248ef60638c9de7d6ffb034b https://github.com/galaxyproject/galaxy/commit/e9009f63936cbef0248ef60638c9d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Start adding workflows back into tool panel Commit: a47a5e89da8ef30b10115a96ade74e2efb6fbf1f https://github.com/galaxyproject/galaxy/commit/a47a5e89da8ef30b10115a96ade74... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix workflow links in tool panel Commit: cfbe362cb985f873bb7733e92542bf97ee2ec1bc https://github.com/galaxyproject/galaxy/commit/cfbe362cb985f873bb7733e92542b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix links Commit: af6a51f0046e10aad46045fc513b3ea2af77995b https://github.com/galaxyproject/galaxy/commit/af6a51f0046e10aad46045fc513b3... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Fix admin check Commit: 4971a8f54003f38b427d6ebb3398f88182912174 https://github.com/galaxyproject/galaxy/commit/4971a8f54003f38b427d6ebb3398f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Disable iframe for tool form Commit: 1b86748a97c8eaa96882d370970d99603c967303 https://github.com/galaxyproject/galaxy/commit/1b86748a97c8eaa96882d370970d9... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Insert bibtex support Commit: 6f8dd18ede82d35b60f2b8c99e6d8781f9b9d085 https://github.com/galaxyproject/galaxy/commit/6f8dd18ede82d35b60f2b8c99e6d8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix style Commit: f99ff868657161a79e760760b73fba0ad1368c9e https://github.com/galaxyproject/galaxy/commit/f99ff868657161a79e760760b73fb... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js Log Message: ----------- Fix select2 leak Commit: 514da84b07a78a24767d9f9318c735d52fc77d32 https://github.com/galaxyproject/galaxy/commit/514da84b07a78a24767d9f9318c73... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Fix scrolling Commit: 4bcc60b04484d7dc54a6bab3ab7c48de27838f9e https://github.com/galaxyproject/galaxy/commit/4bcc60b04484d7dc54a6bab3ab7c4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix stored workflow list Commit: b62bf77d9612e98c6dbe39af0035e0c7f6b18875 https://github.com/galaxyproject/galaxy/commit/b62bf77d9612e98c6dbe39af0035e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Empty center div before hiding it Commit: bef379dfea1ec7b130fd20dc9dfce59f009ce6e4 https://github.com/galaxyproject/galaxy/commit/bef379dfea1ec7b130fd20dc9dfce... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Avoid blank screen when switching between tools Commit: 5bcc452a3718139f511d2097d18ab5644e0a86c2 https://github.com/galaxyproject/galaxy/commit/5bcc452a3718139f511d2097d18ab... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Reset scrolling when display is called Commit: 2b43a271ed5987040731ae63df0fe997b9af28e6 https://github.com/galaxyproject/galaxy/commit/2b43a271ed5987040731ae63df0fe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A 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-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/base.less M config/galaxy.ini.sample M static/maps/galaxy.menu.js.map M static/maps/galaxy.panels.js.map A static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/ui/ui-button-check.js.map R static/maps/mvc/ui/ui-button-menu.js.map A static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/galaxy.menu.js M static/scripts/galaxy.panels.js A static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/ui/ui-button-check.js R static/scripts/mvc/ui/ui-button-menu.js A static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M templates/base.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/root/index.mako R templates/webapps/galaxy/root/tool_menu.mako M templates/webapps/galaxy/tool_form.mako Log Message: ----------- Merge pull request #706 from guerler/ui_revision_000 UI revision (panel rendering, iframes and tool forms) Compare: https://github.com/galaxyproject/galaxy/compare/8205bade71e1...2b43a271ed59