Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d98c8965eb3433b9dbf26e9aa96a26818f8fc0fb https://github.com/galaxyproject/galaxy/commit/d98c8965eb3433b9dbf26e9aa96a2... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Move metadata-related methods from shed_util_common to metadata_util. Commit: 03102e5565319b7a38993fae934f7a27337adbd0 https://github.com/galaxyproject/galaxy/commit/03102e5565319b7a38993fae934f7... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct travis errors and missing imports. Commit: 64f6a8bc7d09b61e7337e18011a7f852cea5c978 https://github.com/galaxyproject/galaxy/commit/64f6a8bc7d09b61e7337e18011a7f... Author: Dave B <dave@bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py Log Message: ----------- Update method call. Commit: abb6176a4e1356595d33284a769245e63ece24d0 https://github.com/galaxyproject/galaxy/commit/abb6176a4e1356595d33284a76924... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py Log Message: ----------- Fix category/repositories API endpoint. Add test. Commit: d78fd5f20c75a77b96d0dd9d54c477ad5ca9fe54 https://github.com/galaxyproject/galaxy/commit/d78fd5f20c75a77b96d0dd9d54c47... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M test/shed_functional/functional/test_0000_basic_repository_features.py Log Message: ----------- Placate Travis. Commit: acaedd470be1fbc53ac6f4cf8e6e7c109c9bcb29 https://github.com/galaxyproject/galaxy/commit/acaedd470be1fbc53ac6f4cf8e6e7... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M test/shed_functional/functional/test_1000_install_basic_repository.py Log Message: ----------- Refactor out repository-related methods from shed_util_common. Commit: e1d9ce920d3272614b335002ed7d54d6dba2ffc1 https://github.com/galaxyproject/galaxy/commit/e1d9ce920d3272614b335002ed7d5... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Move more methods from shed_util_common to repository_util. Commit: 0400c172d6ba7f0fff2bd5a597b814eadf70500a https://github.com/galaxyproject/galaxy/commit/0400c172d6ba7f0fff2bd5a597b81... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/admin/tool_shed_repository/repair_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Move a lot more things from shed_util_common to repository_util. Commit: 26396ffc82762edcaadb76eac31b1bdec675ba40 https://github.com/galaxyproject/galaxy/commit/26396ffc82762edcaadb76eac31b1... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Fix travis errors. Commit: 9f9e008d9f63d6fa19255a52122c6cf6e374058c https://github.com/galaxyproject/galaxy/commit/9f9e008d9f63d6fa19255a52122c6... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py Log Message: ----------- Remove another unused import. Commit: ac2fb6d745522d68b063226b622f25893052e1df https://github.com/galaxyproject/galaxy/commit/ac2fb6d745522d68b063226b622f2... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M README.rst M client/README.md M client/bower.json M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M 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static/style/blue/base.css M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/composite_output_expected_log M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/functional/tools/composite_output.xml M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/fakeserver.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_objectstore.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into refactor_suc Commit: 8eb4f90be0e49b2ceda230a68ff3a888aaad1e9d https://github.com/galaxyproject/galaxy/commit/8eb4f90be0e49b2ceda230a68ff3a... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Remove merge conflict aftereffects. Commit: 964779373e82b4096ffd4fe34acf9b9ce7161400 https://github.com/galaxyproject/galaxy/commit/964779373e82b4096ffd4fe34acf9... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix another incorrectly resolved merge conflict. Commit: 9ee0d880db830c6a59ed9e9efffc2fce9aaf90c6 https://github.com/galaxyproject/galaxy/commit/9ee0d880db830c6a59ed9e9efffc2... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Fix missing import and unused import. Commit: 172a4778c3a5fb54f8eec91a071b8f0a43bd2c3a https://github.com/galaxyproject/galaxy/commit/172a4778c3a5fb54f8eec91a071b8... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M test/shed_functional/functional/test_1000_install_basic_repository.py Log Message: ----------- Create categories in the right order. Commit: c0b5a2840bc954b199bb4cf0db4dafc81116df46 https://github.com/galaxyproject/galaxy/commit/c0b5a2840bc954b199bb4cf0db4da... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/admin/tool_shed_repository/repair_repository.mako M templates/webapps/tool_shed/repository/common.mako M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_1000_install_basic_repository.py Log Message: ----------- Merge pull request #2269 from davebx/refactor_suc Move specific methods from shed_util_common.py to specific_util.py Compare: https://github.com/galaxyproject/galaxy/compare/e2f219335532...c0b5a2840bc9