Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e074e28807f62544212adb79a2dd8fefa39c9cda https://github.com/galaxyproject/galaxy/commit/e074e28807f62544212adb79a2dd8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Downgrade WebError. This fixes the interactive debugger (for now -- to be replaced w/ werkzeug eventually) Commit: b5c4a3de7060e7c5a77414cc4d638e1eae0a31d9 https://github.com/galaxyproject/galaxy/commit/b5c4a3de7060e7c5a77414cc4d638... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove weberror/pygments from unconditional dependencies list Commit: d4ca44c898d173b9a32c3bdc7c7cce313ecbfa73 https://github.com/galaxyproject/galaxy/commit/d4ca44c898d173b9a32c3bdc7c7cc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add pygments back, since it's a dependency of a conditional dependency. Commit: 063390097e23e0f9c8d956ca8a4e493e41b3b38b https://github.com/galaxyproject/galaxy/commit/063390097e23e0f9c8d956ca8a4e4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M .ci/flake8_wrapper.sh M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-panel.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.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/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M run.sh A scripts/check_eggs.py A scripts/fetch_eggs.py M static/maps/galaxy-app-base.js.map M static/maps/libs/jquery/select2.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/history-content-model.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/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.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/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/deferred.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.panels.js M static/scripts/libs/jquery/select2.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M templates/galaxy_client_app.mako M test/api/helpers.py M test/qunit/tests/galaxy-app-base.js M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge and resolve conflicts Commit: 6dfacb6fe648097c94fb32db2df5e643cdcc45e1 https://github.com/galaxyproject/galaxy/commit/6dfacb6fe648097c94fb32db2df5e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1017 from dannon/weberror_downgrade Downgrade WebError. Compare: https://github.com/galaxyproject/galaxy/compare/1333f8037572...6dfacb6fe648