- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] af2f93: flake8 contrib/ .
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af2f93b23609b367d15619471a18e3e6fd0c90e8 https://github.com/galaxyproject/galaxy/commit/af2f93b23609b367d15619471a18… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py Log Message: ----------- flake8 contrib/ . Commit: df808d0c1e8c46e45adebaafbd30e0a8a1cf9b55 https://github.com/galaxyproject/galaxy/commit/df808d0c1e8c46e45adebaafbd30… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.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/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.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/utility_containers/__init__.py M lib/tool_shed/grids/repository_grid_filter_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/scripts/api/add_repository_registry_entry.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/api/create_categories.py M lib/tool_shed/scripts/api/create_users.py M lib/tool_shed/scripts/api/export.py M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py M lib/tool_shed/scripts/api/import_capsule.py M lib/tool_shed/scripts/api/remove_repository_registry_entry.py M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- flake8 lib/tool_shed/ . Also: - use sys.exit() instead of exit() - fix sys.path manipulations. Commit: b1b710925a4c54f3081fc4b79963085e0c362d42 https://github.com/galaxyproject/galaxy/commit/b1b710925a4c54f3081fc4b79963… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.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/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.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/utility_containers/__init__.py M lib/tool_shed/grids/repository_grid_filter_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/scripts/api/add_repository_registry_entry.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/api/create_categories.py M lib/tool_shed/scripts/api/create_users.py M lib/tool_shed/scripts/api/export.py M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py M lib/tool_shed/scripts/api/import_capsule.py M lib/tool_shed/scripts/api/remove_repository_registry_entry.py M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Merge pull request #708 from nsoranzo/flake8_fixes flake8 contrib/ and lib/tool_shed/ . Compare: https://github.com/galaxyproject/galaxy/compare/5d79823a2d67...b1b710925a4c

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[galaxyproject/galaxy] 076af9: Upgrade sqlalchemy to 1.0.8. This was primarily d...
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 076af9bf487bfcef105a058c3f10cbe5c2e709b4 https://github.com/galaxyproject/galaxy/commit/076af9bf487bfcef105a058c3f10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M eggs.ini Log Message: ----------- Upgrade sqlalchemy to 1.0.8. This was primarily done in an attempt to fix a mysql-specific unicode bug (which it didn't fix). Commit: 5d79823a2d6703297503ed07e42cba75bec4b3df https://github.com/galaxyproject/galaxy/commit/5d79823a2d6703297503ed07e42c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M eggs.ini Log Message: ----------- Merge pull request #709 from dannon/sqlalchemy_update_108 Upgrade sqlalchemy to 1.0.8. Compare: https://github.com/galaxyproject/galaxy/compare/fa82f2ded3d0...5d79823a2d67

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[galaxyproject/galaxy] bbd31f: Add regex_replace tool dependency action.
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bbd31f70f165c860100bff4d892f8d96d7236e75 https://github.com/galaxyproject/galaxy/commit/bbd31f70f165c860100bff4d892f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add regex_replace tool dependency action. Commit: f80c7f88f96fd4a8e0c23599bef43477dd3909f5 https://github.com/galaxyproject/galaxy/commit/f80c7f88f96fd4a8e0c23599bef4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add documentation to the execute_step method. Commit: 938361cee04436c78b0729aed87f2646a34913dd https://github.com/galaxyproject/galaxy/commit/938361cee04436c78b0729aed87f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Improved memory usage for regex_replace action. Commit: a46ddd12211b6a0a33f19204095ac077062975ef https://github.com/galaxyproject/galaxy/commit/a46ddd12211b6a0a33f19204095a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Minor cleanup to regex_replace. - Iterate through the input file in a more pythonic way. - Flush the output file, just in case. Commit: fa82f2ded3d07ec9a60631809ad4596310d22bca https://github.com/galaxyproject/galaxy/commit/fa82f2ded3d07ec9a60631809ad4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #457 from davebx/td_regex_replace Add regex_replace tool dependency action. Compare: https://github.com/galaxyproject/galaxy/compare/2b43a271ed59...fa82f2ded3d0

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[galaxyproject/galaxy] 9a376d: Remove tool form downgrade option
by GitHub 09 Sep '15

09 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a376d1ae0a5bdad632b5ad0f280cddddbd2d54d https://github.com/galaxyproject/galaxy/commit/9a376d1ae0a5bdad632b5ad0f280… Author: guerler <aysam.guerler(a)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/6c805ccb988a47b2958e9bcaf7c5… Author: guerler <aysam.guerler(a)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/104bdcd7c8e8e5557b166d47c9dc… Author: guerler <aysam.guerler(a)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/5d8ad4249fc6198846bf8cdceabf… Author: guerler <aysam.guerler(a)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/09445359a4dbcedb2d996dd4c464… Author: guerler <aysam.guerler(a)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/9a44d780145b6a7b30b40b1a7e61… Author: guerler <aysam.guerler(a)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/11e6c9949e2bb58874eedb81d906… Author: guerler <aysam.guerler(a)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/aebf0c7fea2f276f68b77d27408c… Author: guerler <aysam.guerler(a)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/8cf76bd27e30a7b35ad3c7867fdc… Author: guerler <aysam.guerler(a)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/b1949c5805730d2f4ce53759dd56… Author: guerler <aysam.guerler(a)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/8444838a3eda2b2e361c32e165cb… Author: guerler <aysam.guerler(a)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/8d8df1ab5d741758a195eaa34b75… Author: guerler <aysam.guerler(a)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/c7bb8873ca46a67993ad5cb25a85… Author: guerler <aysam.guerler(a)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/d546d08c86fc506edb7912adefe7… Author: guerler <aysam.guerler(a)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/910f95188c3ea5fffc36e80aa5f8… Author: guerler <aysam.guerler(a)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/ad6fdc3dc226af9238b4e366ddc3… Author: guerler <aysam.guerler(a)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/b99b8f2853c49f432eb6e400c734… Author: guerler <aysam.guerler(a)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/df52c62f4d662cd73587cd8450c3… Author: guerler <aysam.guerler(a)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/521677623fae73e07aa98f67c6a6… Author: guerler <aysam.guerler(a)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 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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/a8ffdc523eebe21162e8e29cb631… Author: guerler <aysam.guerler(a)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/d0c77f17610c1361de1447840baf… Author: guerler <aysam.guerler(a)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/53b84fd17f662ba595d0a72ca79a… Author: guerler <aysam.guerler(a)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/92bdf0de2436549546951645a7f1… Author: guerler <aysam.guerler(a)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/3a94f35468622b6819c7f07c2a2f… Author: guerler <aysam.guerler(a)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/b8304e1ab7538b5bcc315f87905d… Author: guerler <aysam.guerler(a)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/94e8b312d4548be90f7ae4e89908… Author: guerler <aysam.guerler(a)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/93be500441a5c454168de3c504db… Author: guerler <aysam.guerler(a)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/5043dd2b7265e7b489428f285893… Author: guerler <aysam.guerler(a)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/c08aab0bd358a8568841a4b43af2… Author: guerler <aysam.guerler(a)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/823fd4ae47ccbf6ed1d19665a7a9… Author: guerler <aysam.guerler(a)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/192239f8d7832e24e9cca55f2ec2… Author: guerler <aysam.guerler(a)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/bcf77efb5aa79f20afd4cb110401… Author: guerler <aysam.guerler(a)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/2f08578ff607c67ddcfcf15f299e… Author: guerler <aysam.guerler(a)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/c948bc70caa9f241c56df0a0e1ff… Author: guerler <aysam.guerler(a)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/759c2142e744476c7bfa3164c34a… Author: guerler <aysam.guerler(a)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/359e812f4fbea0e207537b482b7a… Author: guerler <aysam.guerler(a)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/ac3fc394571da6d33eca6943d58f… Author: guerler <aysam.guerler(a)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/200c2e640b3665b7c63ce487ccde… Author: guerler <aysam.guerler(a)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/fcbd8b241024ea5a419287759f33… Author: guerler <aysam.guerler(a)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/00806d484b2007aaf0adb1efbf83… Author: guerler <aysam.guerler(a)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/e9009f63936cbef0248ef60638c9… Author: guerler <aysam.guerler(a)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/a47a5e89da8ef30b10115a96ade7… Author: guerler <aysam.guerler(a)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/cfbe362cb985f873bb7733e92542… Author: guerler <aysam.guerler(a)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/af6a51f0046e10aad46045fc513b… Author: guerler <aysam.guerler(a)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/4971a8f54003f38b427d6ebb3398… Author: guerler <aysam.guerler(a)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/1b86748a97c8eaa96882d370970d… Author: guerler <aysam.guerler(a)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/6f8dd18ede82d35b60f2b8c99e6d… Author: guerler <aysam.guerler(a)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/f99ff868657161a79e760760b73f… Author: guerler <aysam.guerler(a)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/514da84b07a78a24767d9f9318c7… Author: guerler <aysam.guerler(a)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/4bcc60b04484d7dc54a6bab3ab7c… Author: guerler <aysam.guerler(a)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/b62bf77d9612e98c6dbe39af0035… Author: guerler <aysam.guerler(a)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/bef379dfea1ec7b130fd20dc9dfc… Author: guerler <aysam.guerler(a)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/5bcc452a3718139f511d2097d18a… Author: guerler <aysam.guerler(a)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/2b43a271ed5987040731ae63df0f… Author: Dannon Baker <dannon.baker(a)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

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[galaxyproject/galaxy] d55c47: Optional argument id display (in workflow editor P...
by GitHub 09 Sep '15

09 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d55c47a14cca837ed775ff47a0c41a170c591c67 https://github.com/galaxyproject/galaxy/commit/d55c47a14cca837ed775ff47a0c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Optional argument id display (in workflow editor PJAs we don't care to see this, for example -- and this has been toggled off here) Commit: 434caeaf9515cee99e1f5ac4f9610bcc6a5e00cd https://github.com/galaxyproject/galaxy/commit/434caeaf9515cee99e1f5ac4f961… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Minor cleanup. Commit: e2542d7296adf1e9e5cf15fb7c9bc5f68db05002 https://github.com/galaxyproject/galaxy/commit/e2542d7296adf1e9e5cf15fb7c9b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Swap argument to pja_arg, being more indicative of how this is used. This also obviates the need for the togglable show_arg. Commit: ca5717d203cf93e0bc4dcb9bd6febd0d8c73d083 https://github.com/galaxyproject/galaxy/commit/ca5717d203cf93e0bc4dcb9bd6fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Address the regression in #674, add input name list back to rename PJA helptext. Commit: 8205bade71e1c4977ff9069bae22662fb5af159f https://github.com/galaxyproject/galaxy/commit/8205bade71e1c4977ff9069bae22… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Merge pull request #703 from dannon/optional_wf_args Workflow Editor PJA Argument Display + fix #674 Compare: https://github.com/galaxyproject/galaxy/compare/65f6d83459cd...8205bade71e1

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[galaxyproject/galaxy] e212f2: TabularData.set_peek() was missing parameters pres...
by GitHub 08 Sep '15

08 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e212f224703d4f63721eb51aa7214640c9e86c53 https://github.com/galaxyproject/galaxy/commit/e212f224703d4f63721eb51aa721… Author: Richard Burhans <burhans(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- TabularData.set_peek() was missing parameters present in Text.set_peek() Changed default value of skipchars in Text.set_peek() from [] to None Commit: 65f6d83459cd82c22b7308d7fdb9ba35b973aca7 https://github.com/galaxyproject/galaxy/commit/65f6d83459cd82c22b7308d7fdb9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #705 from richard-burhans/tabulardata Fix to get custom datatypes working after TabularData class was added Compare: https://github.com/galaxyproject/galaxy/compare/26c79e4aab5b...65f6d83459cd

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[galaxyproject/usegalaxy-playbook] bbbdad: Mutable configs on Test
by GitHub 08 Sep '15

08 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bbbdadec9ee8e3f7cddf4ca2e41a17a848afdc20 https://github.com/galaxyproject/usegalaxy-playbook/commit/bbbdadec9ee8e3f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Mutable configs on Test Commit: fb731fd2a8452a4401c1ffda40fca5e2cc33cfc2 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb731fd2a8452a44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Add reserved partition users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d1ea56bcd75e...…

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[galaxyproject/galaxy] 9850e4: Fix regression introduced in 6c82266546c77361f9d22...
by GitHub 08 Sep '15

08 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9850e45f07ebca6109084cfe3bd1338b47b361ae https://github.com/galaxyproject/galaxy/commit/9850e45f07ebca6109084cfe3bd1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix regression introduced in 6c82266546c77361f9d2265ab749db1446142150 . Fix traceback when calling galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed.update_to_changeset_revision() due to repository being None. Commit: 26c79e4aab5b8f9f0f7d0c5908352c776f12cef0 https://github.com/galaxyproject/galaxy/commit/26c79e4aab5b8f9f0f7d0c590835… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #701 from nsoranzo/fix_for_6c82266546c77361f9d2265ab749db1446142150 Fix regression introduced in 6c82266546c77361f9d2265ab749db1446142150 . Compare: https://github.com/galaxyproject/galaxy/compare/cafe2ece1e0a...26c79e4aab5b

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[galaxyproject/galaxy] 16a98b: Fixes to LDAP auth config sample.
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 16a98b50cce48150272289b409ae5a2a70fb9425 https://github.com/galaxyproject/galaxy/commit/16a98b50cce48150272289b409ae… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample Log Message: ----------- Fixes to LDAP auth config sample. Commit: b962a8ded0661b1df940400cb544a0ddbcfb0686 https://github.com/galaxyproject/galaxy/commit/b962a8ded0661b1df940400cb544… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Style fixes. Commit: 474d58809ab1a001a64cb2f540e896d2de22cda5 https://github.com/galaxyproject/galaxy/commit/474d58809ab1a001a64cb2f540e8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Fix commented-out code. Commit: cafe2ece1e0a71870be6c368e569ff2b4ceab096 https://github.com/galaxyproject/galaxy/commit/cafe2ece1e0a71870be6c368e569… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Merge pull request #696 from nsoranzo/dev Small fixes for LDAP auth. Compare: https://github.com/galaxyproject/galaxy/compare/2867f1149a01...cafe2ece1e0a

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Commit: 2284b2242c72183b8218717ea728bdc0d2420ac8 https://github.com/galaxyproject/galaxy/commit/2284b2242c72183b8218717ea728… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Commit: 2867f1149a019f840bc6f4d1da23b98aad702839 https://github.com/galaxyproject/galaxy/commit/2867f1149a019f840bc6f4d1da23… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/99e7ba43a0c4...2867f1149a01

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Commit: 2284b2242c72183b8218717ea728bdc0d2420ac8 https://github.com/galaxyproject/galaxy/commit/2284b2242c72183b8218717ea728… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/4557b27fea51...2284b2242c72

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Compare: https://github.com/galaxyproject/galaxy/compare/990501d2d947...1203ccc49cbf

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[galaxyproject/galaxy] 8430ca: UI, histories: correct allFetched setting in setCo...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8430ca4e3fc506db41357312db0cced248ee43dd https://github.com/galaxyproject/galaxy/commit/8430ca4e3fc506db41357312db0c… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js 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 Log Message: ----------- UI, histories: correct allFetched setting in setCollection to allow fetching after changing collection order Commit: b325966e65398b6f7ff6bf493c44e2ab691cd042 https://github.com/galaxyproject/galaxy/commit/b325966e65398b6f7ff6bf493c44… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- UI, histories: try to correct bootstrap popover dropdown width to keep caret inside button Commit: 99e7ba43a0c45a8777aafb0c5d0d9e773793d201 https://github.com/galaxyproject/galaxy/commit/99e7ba43a0c45a8777aafb0c5d0d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: 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 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 Log Message: ----------- Merge pull request #695 from carlfeberhard/multi-history.all-fetched Fix multi-history fetch flag to allow re-fetching after collection sort Compare: https://github.com/galaxyproject/galaxy/compare/9df1dfafebe3...99e7ba43a0c4

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[galaxyproject/galaxy] 85d4b7: Slight refactoring of parse_int, move to galaxy.ut...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85d4b747297f8bb2a2d7e39c8995d92e6e91911b https://github.com/galaxyproject/galaxy/commit/85d4b747297f8bb2a2d7e39c8995… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Slight refactoring of parse_int, move to galaxy.util and use default in invocation. Commit: 67322c5a440e2912be02c88d4d77e525fe8a7638 https://github.com/galaxyproject/galaxy/commit/67322c5a440e2912be02c88d4d77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Don't overload language builtins min, max in parse_int Commit: 65182d3a623630a783aff3a1d4ebba14bb106e81 https://github.com/galaxyproject/galaxy/commit/65182d3a623630a783aff3a1d4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Include second file of commit fixing min/max overloading Commit: 2afcc658c7f4b7f945413050b5b7bdcdd0b3abaf https://github.com/galaxyproject/galaxy/commit/2afcc658c7f4b7f945413050b5b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Support 'None' and raise the ValueError when appropriate. Commit: 9df1dfafebe31c84d546aee4146be1239cc793dc https://github.com/galaxyproject/galaxy/commit/9df1dfafebe31c84d546aee4146b… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #684 from dannon/minor_parseint_tweaks Minor parseint refactoring, tweaks Compare: https://github.com/galaxyproject/galaxy/compare/39c2854f6525...9df1dfafebe3

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[galaxyproject/galaxy] 152c81: Set a default value for copy history dialog radio ...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 152c81cf8acc45b1c686e26eba04ec87488c52a1 https://github.com/galaxyproject/galaxy/commit/152c81cf8acc45b1c686e26eba04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Set a default value for copy history dialog radio input (to copy *all*). Commit: 39c2854f652524f784a5179a7a2762fd375d67e5 https://github.com/galaxyproject/galaxy/commit/39c2854f652524f784a5179a7a27… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Merge pull request #693 from dannon/copy_history_default Set a default value for copy history dialog radio input (to copy *all*). Compare: https://github.com/galaxyproject/galaxy/compare/0785dedd854c...39c2854f6525

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[galaxyproject/galaxy] 4dc5ed: add alt to images; include GitHub issues for repor...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dc5ed52f9a85770e1652557a021a3e531f471c8 https://github.com/galaxyproject/galaxy/commit/4dc5ed52f9a85770e1652557a021… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- add alt to images; include GitHub issues for reporting Commit: 05f2c4bad0eaffa55782033a2c956f615ce955d8 https://github.com/galaxyproject/galaxy/commit/05f2c4bad0eaffa55782033a2c95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- switch links to https Commit: 0785dedd854c7f71c3360f1cbd8dfe3c1a9fb205 https://github.com/galaxyproject/galaxy/commit/0785dedd854c7f71c3360f1cbd8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #690 from martenson/readme-changes Readme changes Compare: https://github.com/galaxyproject/galaxy/compare/6edaf458e89b...0785dedd854c

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[galaxyproject/galaxy] cac794: Add a code of conduct for the project.
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cac7940706f74c0104611c4bfc7860ac93802261 https://github.com/galaxyproject/galaxy/commit/cac7940706f74c0104611c4bfc78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: A CODE_OF_CONDUCT.md Log Message: ----------- Add a code of conduct for the project. Commit: 7968f60d0374a15e0caf671867e711a66b8aabb4 https://github.com/galaxyproject/galaxy/commit/7968f60d0374a15e0caf671867e7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M CODE_OF_CONDUCT.md Log Message: ----------- Fix typo found by @nsoranzo. Commit: 6edaf458e89b3db7115c65f0242b781df7c77faa https://github.com/galaxyproject/galaxy/commit/6edaf458e89b3db7115c65f0242b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: A CODE_OF_CONDUCT.md Log Message: ----------- Merge pull request #646 from natefoo/code-of-conduct [PROCEDURES] Create a project code of conduct Compare: https://github.com/galaxyproject/galaxy/compare/88c57bf16b52...6edaf458e89b

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[galaxyproject/infrastructure-playbook] 365f48: Update users on n2
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 365f48597e1af187267850ae45e559daa4226a06 https://github.com/galaxyproject/infrastructure-playbook/commit/365f48597e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M galaxyenv/secret_host_vars/n2.galaxyproject.org.yml Log Message: ----------- Update users on n2

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[galaxyproject/galaxy] 2625bc: Fix flake8 broken when merging 041c94bf788bea09904...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2625bc4bc02f3b109c2340ca46b376fc9fbd9017 https://github.com/galaxyproject/galaxy/commit/2625bc4bc02f3b109c2340ca46b3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix flake8 broken when merging 041c94bf788bea0990401dab14e0ab717cec0c55 from release_15.07 . Commit: 88c57bf16b52c8d7edbe0c91eb30dda277d4f24b https://github.com/galaxyproject/galaxy/commit/88c57bf16b52c8d7edbe0c91eb30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #688 from nsoranzo/dev Fix flake8 broken when merging from release_15.07 . Compare: https://github.com/galaxyproject/galaxy/compare/bcbeb75a6895...88c57bf16b52

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[galaxyproject/galaxy] 8cd94b: When uploading tool_dependencies.xml to toolshed, ...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture. Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240 https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 19c85e070534f4318cca3e728c52c91a27163f4a https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52… Author: Jeremy Goecks <jgoecks(a)gwu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77 https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec296… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009 https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d08… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: d2e61e8af4c933b733c640f46f831bf424bc0197 https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934 https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b256… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 041c94bf788bea0990401dab14e0ab717cec0c55 https://github.com/galaxyproject/galaxy/commit/041c94bf788bea0990401dab14e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: 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 scripts/bootstrap_history.py Log Message: ----------- Release notes for 15.07. This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10. Commit: 4a05c07aa5cc8e386742bb638a6c44e839efc9bd https://github.com/galaxyproject/galaxy/commit/4a05c07aa5cc8e386742bb638a6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Fixup end of release items for release notes. Commit: 65f39b2eaf6b0c94b1044a92351c2b5799ca021a https://github.com/galaxyproject/galaxy/commit/65f39b2eaf6b0c94b1044a92351c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Typo noticed by @martenson. Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617 https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #657 from jmchilton/dev_1507_backports [15.07] Backport various dev fixes. Commit: a460ebd7d6b6132fe00238e834dcff0efb449ad8 https://github.com/galaxyproject/galaxy/commit/a460ebd7d6b6132fe00238e834dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst Log Message: ----------- Fix for explicit markup ending without a blank line Commit: 51534edc63bb7758d4fb4a7aaec13df7a1e5e8eb https://github.com/galaxyproject/galaxy/commit/51534edc63bb7758d4fb4a7aaec1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Deprecation notice for cloudlaunch Commit: 96840a3c57354690b9287e49dd2ef3400932b52e https://github.com/galaxyproject/galaxy/commit/96840a3c57354690b9287e49dd2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #9 from dannon/rn Deprecation notice for cloudlaunch. Commit: 82794e7ee7a8a6793438bf2021079515445bb873 https://github.com/galaxyproject/galaxy/commit/82794e7ee7a8a6793438bf202107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Fix cloudlaunch link. Commit: 36d262d7c695ba06c32f5c495a0a3ceb62d57731 https://github.com/galaxyproject/galaxy/commit/36d262d7c695ba06c32f5c495a0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #10 from dannon/rn Fix cloudlaunch link. Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975 https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload [release_15.07] Fix setting of toolshed repository attributes in special cases. Commit: 4dd6304f055706e38176823a4166c6536618a042 https://github.com/galaxyproject/galaxy/commit/4dd6304f055706e38176823a4166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Fix version parsing in tool form Commit: 3653bf5e37b13ea17cecd321fdbe9ce4fedcfbb8 https://github.com/galaxyproject/galaxy/commit/3653bf5e37b13ea17cecd321fdbe… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #677 from guerler/fix_version_002 [15.07] Fix version handling in tool form Commit: f4605937e3bb1e0e993c66ac86deabff374034c4 https://github.com/galaxyproject/galaxy/commit/f4605937e3bb1e0e993c66ac86de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: 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 scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Merge pull request #642 from jmchilton/rn [15.07] Release notes for 15.07. Commit: f6b5558c11698069c4eebb1b28f089a3ecc32c40 https://github.com/galaxyproject/galaxy/commit/f6b5558c11698069c4eebb1b28f0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: 099d61ef21e9cf1eae364cf807aa7e3705d8d787 https://github.com/galaxyproject/galaxy/commit/099d61ef21e9cf1eae364cf807aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix for raising error when trying to compare unknown column types in CSV. Commit: 566acab16e52d3e9a1969366a2a52e02bf8c1eb9 https://github.com/galaxyproject/galaxy/commit/566acab16e52d3e9a1969366a2a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #680 from blankenberg/csv_fix [15.07] For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: c2c1c723569db7076772235594f59e0dfe3a8c41 https://github.com/galaxyproject/galaxy/commit/c2c1c723569db7076772235594f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 990501d2d94741a3ac16016b8a37e48e84acf018 https://github.com/galaxyproject/galaxy/commit/990501d2d94741a3ac16016b8a37… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #687 from dannon/release_15.07 Backport of Fix issue #525 Commit: 4557b27fea515934fa5a9296c5993423aa482dd7 https://github.com/galaxyproject/galaxy/commit/4557b27fea515934fa5a9296c599… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js 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 lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/workflows.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/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge branch 'release_15.07' Commit: bcbeb75a68952597e89563d316dc0ec2d945f49c https://github.com/galaxyproject/galaxy/commit/bcbeb75a68952597e89563d316dc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js 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 lib/galaxy/datatypes/tabular.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/tool_shed/dependencies/tool/tag_attribute_handler.py Compare: https://github.com/galaxyproject/galaxy/compare/f48dd9942567...bcbeb75a6895

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[galaxyproject/galaxy] 8cd94b: When uploading tool_dependencies.xml to toolshed, ...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture. Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240 https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 19c85e070534f4318cca3e728c52c91a27163f4a https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52… Author: Jeremy Goecks <jgoecks(a)gwu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77 https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec296… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009 https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d08… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: d2e61e8af4c933b733c640f46f831bf424bc0197 https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934 https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b256… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 041c94bf788bea0990401dab14e0ab717cec0c55 https://github.com/galaxyproject/galaxy/commit/041c94bf788bea0990401dab14e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: 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 scripts/bootstrap_history.py Log Message: ----------- Release notes for 15.07. This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10. Commit: 4a05c07aa5cc8e386742bb638a6c44e839efc9bd https://github.com/galaxyproject/galaxy/commit/4a05c07aa5cc8e386742bb638a6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Fixup end of release items for release notes. Commit: 65f39b2eaf6b0c94b1044a92351c2b5799ca021a https://github.com/galaxyproject/galaxy/commit/65f39b2eaf6b0c94b1044a92351c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Typo noticed by @martenson. Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617 https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #657 from jmchilton/dev_1507_backports [15.07] Backport various dev fixes. Commit: a460ebd7d6b6132fe00238e834dcff0efb449ad8 https://github.com/galaxyproject/galaxy/commit/a460ebd7d6b6132fe00238e834dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst Log Message: ----------- Fix for explicit markup ending without a blank line Commit: 51534edc63bb7758d4fb4a7aaec13df7a1e5e8eb https://github.com/galaxyproject/galaxy/commit/51534edc63bb7758d4fb4a7aaec1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Deprecation notice for cloudlaunch Commit: 96840a3c57354690b9287e49dd2ef3400932b52e https://github.com/galaxyproject/galaxy/commit/96840a3c57354690b9287e49dd2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #9 from dannon/rn Deprecation notice for cloudlaunch. Commit: 82794e7ee7a8a6793438bf2021079515445bb873 https://github.com/galaxyproject/galaxy/commit/82794e7ee7a8a6793438bf202107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Fix cloudlaunch link. Commit: 36d262d7c695ba06c32f5c495a0a3ceb62d57731 https://github.com/galaxyproject/galaxy/commit/36d262d7c695ba06c32f5c495a0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #10 from dannon/rn Fix cloudlaunch link. Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975 https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload [release_15.07] Fix setting of toolshed repository attributes in special cases. Commit: 4dd6304f055706e38176823a4166c6536618a042 https://github.com/galaxyproject/galaxy/commit/4dd6304f055706e38176823a4166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Fix version parsing in tool form Commit: 3653bf5e37b13ea17cecd321fdbe9ce4fedcfbb8 https://github.com/galaxyproject/galaxy/commit/3653bf5e37b13ea17cecd321fdbe… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #677 from guerler/fix_version_002 [15.07] Fix version handling in tool form Commit: f4605937e3bb1e0e993c66ac86deabff374034c4 https://github.com/galaxyproject/galaxy/commit/f4605937e3bb1e0e993c66ac86de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: 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 scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Merge pull request #642 from jmchilton/rn [15.07] Release notes for 15.07. Commit: f6b5558c11698069c4eebb1b28f089a3ecc32c40 https://github.com/galaxyproject/galaxy/commit/f6b5558c11698069c4eebb1b28f0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: 099d61ef21e9cf1eae364cf807aa7e3705d8d787 https://github.com/galaxyproject/galaxy/commit/099d61ef21e9cf1eae364cf807aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix for raising error when trying to compare unknown column types in CSV. Commit: 566acab16e52d3e9a1969366a2a52e02bf8c1eb9 https://github.com/galaxyproject/galaxy/commit/566acab16e52d3e9a1969366a2a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #680 from blankenberg/csv_fix [15.07] For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: c2c1c723569db7076772235594f59e0dfe3a8c41 https://github.com/galaxyproject/galaxy/commit/c2c1c723569db7076772235594f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 990501d2d94741a3ac16016b8a37e48e84acf018 https://github.com/galaxyproject/galaxy/commit/990501d2d94741a3ac16016b8a37… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #687 from dannon/release_15.07 Backport of Fix issue #525 Commit: 4557b27fea515934fa5a9296c5993423aa482dd7 https://github.com/galaxyproject/galaxy/commit/4557b27fea515934fa5a9296c599… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js 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 lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/workflows.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/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/224c20d4b2cf...4557b27fea51

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[galaxyproject/galaxy] c2c1c7: Fix issue #525. Repo info dicts and tsr_ids were f...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: c2c1c723569db7076772235594f59e0dfe3a8c41 https://github.com/galaxyproject/galaxy/commit/c2c1c723569db7076772235594f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 990501d2d94741a3ac16016b8a37e48e84acf018 https://github.com/galaxyproject/galaxy/commit/990501d2d94741a3ac16016b8a37… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #687 from dannon/release_15.07 Backport of Fix issue #525 Compare: https://github.com/galaxyproject/galaxy/compare/566acab16e52...990501d2d947

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[galaxyproject/galaxy] 9a9d19: Refactored line lengths
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a9d193eace1646c7dc0e74991ddc14ebd18c37d https://github.com/galaxyproject/galaxy/commit/9a9d193eace1646c7dc0e74991dd… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css 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_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 Log Message: ----------- Refactored line lengths Fixed sorting bug in workflows per user sorting Commit: c057bfa1d8fe4c921e80260f5205fe35f5d1e8b8 https://github.com/galaxyproject/galaxy/commit/c057bfa1d8fe4c921e80260f5205… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/users_last_access_date.mako Log Message: ----------- Fixed format issue in date of last login page Commit: f48dd9942567b23326227b2538d350cd4c118ba3 https://github.com/galaxyproject/galaxy/commit/f48dd9942567b23326227b2538d3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css 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_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 Log Message: ----------- Merge pull request #678 from Airistotal/dev Reports Refactoring Compare: https://github.com/galaxyproject/galaxy/compare/291d16f3fcf7...f48dd9942567

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[galaxyproject/galaxy] 6273fa: Use standard Galaxy message box styles on tool hel...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6273fa8a5da7bae8c4f4cdda281cc096ee21f70a https://github.com/galaxyproject/galaxy/commit/6273fa8a5da7bae8c4f4cdda281c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Use standard Galaxy message box styles on tool help texts that use rST admonitions. Commit: 291d16f3fcf7f4b7c70f47aa568a08f60262a806 https://github.com/galaxyproject/galaxy/commit/291d16f3fcf7f4b7c70f47aa568a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #685 from natefoo/help-message-css Use standard Galaxy message box styles on tool help texts that use rST admonitions Compare: https://github.com/galaxyproject/galaxy/compare/e584a3527323...291d16f3fcf7

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[galaxyproject/galaxy] ee4694: Fix issue #525. Repo info dicts and tsr_ids were f...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee46947c3d58a98d0c6640ba3eea3ef405d8c9c3 https://github.com/galaxyproject/galaxy/commit/ee46947c3d58a98d0c6640ba3eea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: e584a3527323a0b801e50a86f6fc2032d84b06ed https://github.com/galaxyproject/galaxy/commit/e584a3527323a0b801e50a86f6fc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #681 from mvdbeek/dev Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-ins… Compare: https://github.com/galaxyproject/galaxy/compare/d00b5507c0d3...e584a3527323

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