[galaxy-commits] [galaxyproject/galaxy] 2cd95c: Fix import order everywhere

14 Nov 2017

      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 2cd95c48f6dabfe79ec9a5c440bff8cfc29c68df
      https://github.com/galaxyproject/galaxy/commit/2cd95c48f6dabfe79ec9a5c440bff...
  Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
  Date:   2017-11-14 (Tue, 14 Nov 2017)

  Changed paths:
    R .ci/flake8_lint_include_list.txt
    R .ci/flake8_wrapper_imports.sh
    M .travis.yml
    M lib/galaxy/app.py
    M lib/galaxy/config.py
    M lib/galaxy/dataset_collections/matching.py
    M lib/galaxy/dataset_collections/registry.py
    M lib/galaxy/dataset_collections/types/list.py
    M lib/galaxy/dataset_collections/types/paired.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/dataproviders/dataset.py
    M lib/galaxy/datatypes/display_applications/application.py
    M lib/galaxy/datatypes/graph.py
    M lib/galaxy/datatypes/interval.py
    M lib/galaxy/datatypes/registry.py
    M lib/galaxy/datatypes/sequence.py
    M lib/galaxy/datatypes/tabular.py
    M lib/galaxy/datatypes/tracks.py
    M lib/galaxy/datatypes/util/gff_util.py
    M lib/galaxy/dependencies/pipfiles/flake8/Pipfile
    M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
    M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
    M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
    R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile
    R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock
    R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt
    R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt
    M lib/galaxy/dependencies/pipfiles/update.sh
    M lib/galaxy/external_services/actions.py
    M lib/galaxy/external_services/service.py
    M lib/galaxy/forms/forms.py
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/dynamic_tool_destination.py
    M lib/galaxy/jobs/mapper.py
    M lib/galaxy/jobs/metrics/__init__.py
    M lib/galaxy/jobs/metrics/collectl/processes.py
    M lib/galaxy/jobs/metrics/instrumenters/collectl.py
    M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
    M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
    M lib/galaxy/jobs/rule_helper.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/chronos.py
    M lib/galaxy/jobs/runners/cli.py
    M lib/galaxy/jobs/runners/local.py
    M lib/galaxy/jobs/runners/state_handlers/resubmit.py
    M lib/galaxy/jobs/runners/util/__init__.py
    M lib/galaxy/jobs/splitters/multi.py
    M lib/galaxy/managers/citations.py
    M lib/galaxy/managers/configuration.py
    M lib/galaxy/managers/containers.py
    M lib/galaxy/managers/datasets.py
    M lib/galaxy/managers/folders.py
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/hdcas.py
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/history_contents.py
    M lib/galaxy/managers/library_datasets.py
    M lib/galaxy/managers/pages.py
    M lib/galaxy/managers/ratable.py
    M lib/galaxy/managers/rbac_secured.py
    M lib/galaxy/managers/roles.py
    M lib/galaxy/managers/sharable.py
    M lib/galaxy/managers/tags.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/managers/visualizations.py
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/migrate/check.py
    M lib/galaxy/objectstore/__init__.py
    M lib/galaxy/objectstore/azure_blob.py
    M lib/galaxy/objectstore/pithos.py
    M lib/galaxy/objectstore/rods.py
    M lib/galaxy/objectstore/s3.py
    M lib/galaxy/objectstore/s3_multipart_upload.py
    M lib/galaxy/openid/providers.py
    M lib/galaxy/queue_worker.py
    M lib/galaxy/queues.py
    M lib/galaxy/sample_tracking/request_types.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/metadata.py
    M lib/galaxy/tools/actions/upload.py
    M lib/galaxy/tools/cwl/parser.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/mulled/mulled_build.py
    M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
    M lib/galaxy/tools/deps/mulled/util.py
    M lib/galaxy/tools/deps/resolvers/__init__.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
    M lib/galaxy/tools/error_reports/plugins/biostars.py
    M lib/galaxy/tools/error_reports/plugins/email.py
    M lib/galaxy/tools/error_reports/plugins/github.py
    M lib/galaxy/tools/error_reports/plugins/influxdb.py
    M lib/galaxy/tools/error_reports/plugins/json.py
    M lib/galaxy/tools/error_reports/plugins/sentry.py
    M lib/galaxy/tools/lint.py
    M lib/galaxy/tools/linters/inputs.py
    M lib/galaxy/tools/locations/__init__.py
    M lib/galaxy/tools/locations/dockstore.py
    M lib/galaxy/tools/locations/http.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/dynamic_options.py
    M lib/galaxy/tools/parameters/output_collect.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/parser/factory.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/parser/yaml.py
    M lib/galaxy/tools/toolbox/__init__.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/filters/__init__.py
    M lib/galaxy/tools/toolbox/lineages/factory.py
    M lib/galaxy/tools/toolbox/lineages/interface.py
    M lib/galaxy/tools/toolbox/panel.py
    M lib/galaxy/tools/verify/__init__.py
    M lib/galaxy/tools/verify/test_data.py
    M lib/galaxy/tours/__init__.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/biostar.py
    M lib/galaxy/util/object_wrapper.py
    M lib/galaxy/util/pastescript/loadwsgi.py
    M lib/galaxy/util/properties.py
    M lib/galaxy/util/submodules.py
    M lib/galaxy/util/xml_macros.py
    M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
    M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
    M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
    M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
    M lib/galaxy/visualization/data_providers/registry.py
    M lib/galaxy/visualization/plugins/config_parser.py
    M lib/galaxy/visualization/plugins/registry.py
    M lib/galaxy/visualization/plugins/resource_parser.py
    M lib/galaxy/web/form_builder.py
    M lib/galaxy/web/framework/formbuilder.py
    M lib/galaxy/web/framework/helpers/__init__.py
    M lib/galaxy/web/framework/middleware/batch.py
    M lib/galaxy/web/framework/middleware/graphite.py
    M lib/galaxy/web/framework/middleware/profile.py
    M lib/galaxy/web/framework/middleware/remoteuser.py
    M lib/galaxy/web/framework/openid_manager.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/web/security/__init__.py
    M lib/galaxy/webapps/config_manage.py
    M lib/galaxy/webapps/galaxy/api/annotations.py
    M lib/galaxy/webapps/galaxy/api/configuration.py
    M lib/galaxy/webapps/galaxy/api/dataset_collections.py
    M lib/galaxy/webapps/galaxy/api/datasets.py
    M lib/galaxy/webapps/galaxy/api/datatypes.py
    M lib/galaxy/webapps/galaxy/api/extended_metadata.py
    M lib/galaxy/webapps/galaxy/api/folder_contents.py
    M lib/galaxy/webapps/galaxy/api/folders.py
    M lib/galaxy/webapps/galaxy/api/forms.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/api/item_tags.py
    M lib/galaxy/webapps/galaxy/api/job_files.py
    M lib/galaxy/webapps/galaxy/api/libraries.py
    M lib/galaxy/webapps/galaxy/api/library_contents.py
    M lib/galaxy/webapps/galaxy/api/metrics.py
    M lib/galaxy/webapps/galaxy/api/page_revisions.py
    M lib/galaxy/webapps/galaxy/api/pages.py
    M lib/galaxy/webapps/galaxy/api/provenance.py
    M lib/galaxy/webapps/galaxy/api/quotas.py
    M lib/galaxy/webapps/galaxy/api/remote_files.py
    M lib/galaxy/webapps/galaxy/api/search.py
    M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/toolshed.py
    M lib/galaxy/webapps/galaxy/api/visualizations.py
    M lib/galaxy/webapps/galaxy/api/webhooks.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/biostar.py
    M lib/galaxy/webapps/galaxy/controllers/library.py
    M lib/galaxy/webapps/galaxy/controllers/tag.py
    M lib/galaxy/webapps/galaxy/controllers/user.py
    M lib/galaxy/webapps/galaxy/controllers/visualization.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/reports/app.py
    M lib/galaxy/webapps/reports/controllers/history.py
    M lib/galaxy/webapps/reports/controllers/home.py
    M lib/galaxy/webapps/reports/controllers/jobs.py
    M lib/galaxy/webapps/reports/controllers/root.py
    M lib/galaxy/webapps/reports/controllers/sample_tracking.py
    M lib/galaxy/webapps/reports/controllers/users.py
    M lib/galaxy/webapps/reports/controllers/workflows.py
    M lib/galaxy/webapps/tool_shed/api/authenticate.py
    M lib/galaxy/webapps/tool_shed/api/categories.py
    M lib/galaxy/webapps/tool_shed/api/configuration.py
    M lib/galaxy/webapps/tool_shed/api/groups.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/api/tools.py
    M lib/galaxy/webapps/tool_shed/api/users.py
    M lib/galaxy/webapps/tool_shed/app.py
    M lib/galaxy/webapps/tool_shed/controllers/admin.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/controllers/user.py
    M lib/galaxy/webapps/tool_shed/search/tool_search.py
    M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
    M lib/galaxy/workflow/extract.py
    M lib/galaxy/workflow/schedulers/core.py
    M lib/tool_shed/dependencies/attribute_handlers.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.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/repository_types/registry.py
    M lib/tool_shed/tools/data_table_manager.py
    M lib/tool_shed/tools/tool_validator.py
    M lib/tool_shed/util/shed_util_common.py
    M lib/tool_shed/util/tool_util.py
    M lib/tool_shed/utility_containers/__init__.py
    M scripts/functional_tests.py
    M test/api/test_jobs.py
    M test/api/test_page_revisions.py
    M test/base/driver_util.py
    M test/base/testcase.py
    M test/functional/test_toolbox.py
    M test/galaxy_selenium/components.py
    M test/galaxy_selenium/data.py
    M test/galaxy_selenium/navigates_galaxy.py
    M test/manual/workflows_scaling.py
    M test/selenium_tests/test_stock_tours.py
    M test/shed_functional/base/twilltestcase.py
    M test/unit/datatypes/dataproviders/test_base_dataproviders.py
    M test/unit/datatypes/dataproviders/test_line_dataproviders.py
    M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
    M test/unit/jobs/test_job_wrapper.py
    M test/unit/jobs/test_mapper.py
    M test/unit/jobs/test_runner_local.py
    M test/unit/managers/base.py
    M test/unit/managers/test_CollectionManager.py
    M test/unit/managers/test_DatasetManager.py
    M test/unit/managers/test_HDAManager.py
    M test/unit/managers/test_HDCAManager.py
    M test/unit/managers/test_HistoryContentsManager.py
    M test/unit/managers/test_HistoryManager.py
    M test/unit/managers/test_UserManager.py
    M test/unit/shed_unit/test_installed_repository_manager.py
    M test/unit/shed_unit/test_tool_panel_manager.py
    M test/unit/test_objectstore.py
    M test/unit/tools/test_actions.py
    M test/unit/tools/test_collect_primary_datasets.py
    M test/unit/tools/test_column_parameters.py
    M test/unit/tools/test_data_parameters.py
    M test/unit/tools/test_dataset_matcher.py
    M test/unit/tools/test_evaluation.py
    M test/unit/tools/test_execution.py
    M test/unit/tools/test_history_imp_exp.py
    M test/unit/tools/test_parameter_parsing.py
    M test/unit/tools/test_parsing.py
    M test/unit/tools/test_select_parameters.py
    M test/unit/tools/test_tool_deps.py
    M test/unit/tools/test_tool_loader.py
    M test/unit/tools/test_toolbox.py
    M test/unit/tools/test_watcher.py
    M test/unit/tools_support.py
    M test/unit/visualizations/plugins/test_VisualizationPlugin.py
    M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
    M test/unit/web/framework/test_webapp.py
    M test/unit/workflows/test_modules.py
    M test/unit/workflows/test_run_parameters.py
    M test/unit/workflows/test_workflow_progress.py
    M tools/filters/gff/gff_filter_by_attribute.py
    M tools/filters/gff/gff_filter_by_feature_count.py
    M tools/phenotype_association/senatag.py
    M tox.ini

  Log Message:
  -----------
  Fix import order everywhere

- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports
  and py27-lint-imports-include-list tox envs
- Fix most E201 and E202 errors reported by flake8-import-order v0.15,
  but pin flake8-import-order to v0.14.3 until
  https://github.com/PyCQA/flake8-import-order/issues/123
  is fixed

This let us drop 2 jobs on Travis per each job.

  Commit: 7c1afa8f16b68fcb8948c760862d4beb68187118
      https://github.com/galaxyproject/galaxy/commit/7c1afa8f16b68fcb8948c760862d4...
  Author: Dannon Baker <dannon.baker@gmail.com>
  Date:   2017-11-14 (Tue, 14 Nov 2017)

  Changed paths:
    R .ci/flake8_lint_include_list.txt
    R .ci/flake8_wrapper_imports.sh
    M .travis.yml
    M lib/galaxy/app.py
    M lib/galaxy/config.py
    M lib/galaxy/dataset_collections/matching.py
    M lib/galaxy/dataset_collections/registry.py
    M lib/galaxy/dataset_collections/types/list.py
    M lib/galaxy/dataset_collections/types/paired.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/dataproviders/dataset.py
    M lib/galaxy/datatypes/display_applications/application.py
    M lib/galaxy/datatypes/graph.py
    M lib/galaxy/datatypes/interval.py
    M lib/galaxy/datatypes/registry.py
    M lib/galaxy/datatypes/sequence.py
    M lib/galaxy/datatypes/tabular.py
    M lib/galaxy/datatypes/tracks.py
    M lib/galaxy/datatypes/util/gff_util.py
    M lib/galaxy/dependencies/pipfiles/flake8/Pipfile
    M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
    M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
    M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
    R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile
    R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock
    R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt
    R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt
    M lib/galaxy/dependencies/pipfiles/update.sh
    M lib/galaxy/external_services/actions.py
    M lib/galaxy/external_services/service.py
    M lib/galaxy/forms/forms.py
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/dynamic_tool_destination.py
    M lib/galaxy/jobs/mapper.py
    M lib/galaxy/jobs/metrics/__init__.py
    M lib/galaxy/jobs/metrics/collectl/processes.py
    M lib/galaxy/jobs/metrics/instrumenters/collectl.py
    M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
    M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
    M lib/galaxy/jobs/rule_helper.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/chronos.py
    M lib/galaxy/jobs/runners/cli.py
    M lib/galaxy/jobs/runners/local.py
    M lib/galaxy/jobs/runners/state_handlers/resubmit.py
    M lib/galaxy/jobs/runners/util/__init__.py
    M lib/galaxy/jobs/splitters/multi.py
    M lib/galaxy/managers/citations.py
    M lib/galaxy/managers/configuration.py
    M lib/galaxy/managers/containers.py
    M lib/galaxy/managers/datasets.py
    M lib/galaxy/managers/folders.py
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/hdcas.py
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/history_contents.py
    M lib/galaxy/managers/library_datasets.py
    M lib/galaxy/managers/pages.py
    M lib/galaxy/managers/ratable.py
    M lib/galaxy/managers/rbac_secured.py
    M lib/galaxy/managers/roles.py
    M lib/galaxy/managers/sharable.py
    M lib/galaxy/managers/tags.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/managers/visualizations.py
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/migrate/check.py
    M lib/galaxy/objectstore/__init__.py
    M lib/galaxy/objectstore/azure_blob.py
    M lib/galaxy/objectstore/pithos.py
    M lib/galaxy/objectstore/rods.py
    M lib/galaxy/objectstore/s3.py
    M lib/galaxy/objectstore/s3_multipart_upload.py
    M lib/galaxy/openid/providers.py
    M lib/galaxy/queue_worker.py
    M lib/galaxy/queues.py
    M lib/galaxy/sample_tracking/request_types.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/metadata.py
    M lib/galaxy/tools/actions/upload.py
    M lib/galaxy/tools/cwl/parser.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/mulled/mulled_build.py
    M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
    M lib/galaxy/tools/deps/mulled/util.py
    M lib/galaxy/tools/deps/resolvers/__init__.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
    M lib/galaxy/tools/error_reports/plugins/biostars.py
    M lib/galaxy/tools/error_reports/plugins/email.py
    M lib/galaxy/tools/error_reports/plugins/github.py
    M lib/galaxy/tools/error_reports/plugins/influxdb.py
    M lib/galaxy/tools/error_reports/plugins/json.py
    M lib/galaxy/tools/error_reports/plugins/sentry.py
    M lib/galaxy/tools/lint.py
    M lib/galaxy/tools/linters/inputs.py
    M lib/galaxy/tools/locations/__init__.py
    M lib/galaxy/tools/locations/dockstore.py
    M lib/galaxy/tools/locations/http.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/dynamic_options.py
    M lib/galaxy/tools/parameters/output_collect.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/parser/factory.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/parser/yaml.py
    M lib/galaxy/tools/toolbox/__init__.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/filters/__init__.py
    M lib/galaxy/tools/toolbox/lineages/factory.py
    M lib/galaxy/tools/toolbox/lineages/interface.py
    M lib/galaxy/tools/toolbox/panel.py
    M lib/galaxy/tools/verify/__init__.py
    M lib/galaxy/tools/verify/test_data.py
    M lib/galaxy/tours/__init__.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/biostar.py
    M lib/galaxy/util/object_wrapper.py
    M lib/galaxy/util/pastescript/loadwsgi.py
    M lib/galaxy/util/properties.py
    M lib/galaxy/util/submodules.py
    M lib/galaxy/util/xml_macros.py
    M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
    M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
    M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
    M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
    M lib/galaxy/visualization/data_providers/registry.py
    M lib/galaxy/visualization/plugins/config_parser.py
    M lib/galaxy/visualization/plugins/registry.py
    M lib/galaxy/visualization/plugins/resource_parser.py
    M lib/galaxy/web/form_builder.py
    M lib/galaxy/web/framework/formbuilder.py
    M lib/galaxy/web/framework/helpers/__init__.py
    M lib/galaxy/web/framework/middleware/batch.py
    M lib/galaxy/web/framework/middleware/graphite.py
    M lib/galaxy/web/framework/middleware/profile.py
    M lib/galaxy/web/framework/middleware/remoteuser.py
    M lib/galaxy/web/framework/openid_manager.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/web/security/__init__.py
    M lib/galaxy/webapps/config_manage.py
    M lib/galaxy/webapps/galaxy/api/annotations.py
    M lib/galaxy/webapps/galaxy/api/configuration.py
    M lib/galaxy/webapps/galaxy/api/dataset_collections.py
    M lib/galaxy/webapps/galaxy/api/datasets.py
    M lib/galaxy/webapps/galaxy/api/datatypes.py
    M lib/galaxy/webapps/galaxy/api/extended_metadata.py
    M lib/galaxy/webapps/galaxy/api/folder_contents.py
    M lib/galaxy/webapps/galaxy/api/folders.py
    M lib/galaxy/webapps/galaxy/api/forms.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/api/item_tags.py
    M lib/galaxy/webapps/galaxy/api/job_files.py
    M lib/galaxy/webapps/galaxy/api/libraries.py
    M lib/galaxy/webapps/galaxy/api/library_contents.py
    M lib/galaxy/webapps/galaxy/api/metrics.py
    M lib/galaxy/webapps/galaxy/api/page_revisions.py
    M lib/galaxy/webapps/galaxy/api/pages.py
    M lib/galaxy/webapps/galaxy/api/provenance.py
    M lib/galaxy/webapps/galaxy/api/quotas.py
    M lib/galaxy/webapps/galaxy/api/remote_files.py
    M lib/galaxy/webapps/galaxy/api/search.py
    M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/toolshed.py
    M lib/galaxy/webapps/galaxy/api/visualizations.py
    M lib/galaxy/webapps/galaxy/api/webhooks.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/biostar.py
    M lib/galaxy/webapps/galaxy/controllers/library.py
    M lib/galaxy/webapps/galaxy/controllers/tag.py
    M lib/galaxy/webapps/galaxy/controllers/user.py
    M lib/galaxy/webapps/galaxy/controllers/visualization.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/reports/app.py
    M lib/galaxy/webapps/reports/controllers/history.py
    M lib/galaxy/webapps/reports/controllers/home.py
    M lib/galaxy/webapps/reports/controllers/jobs.py
    M lib/galaxy/webapps/reports/controllers/root.py
    M lib/galaxy/webapps/reports/controllers/sample_tracking.py
    M lib/galaxy/webapps/reports/controllers/users.py
    M lib/galaxy/webapps/reports/controllers/workflows.py
    M lib/galaxy/webapps/tool_shed/api/authenticate.py
    M lib/galaxy/webapps/tool_shed/api/categories.py
    M lib/galaxy/webapps/tool_shed/api/configuration.py
    M lib/galaxy/webapps/tool_shed/api/groups.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/api/tools.py
    M lib/galaxy/webapps/tool_shed/api/users.py
    M lib/galaxy/webapps/tool_shed/app.py
    M lib/galaxy/webapps/tool_shed/controllers/admin.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/controllers/user.py
    M lib/galaxy/webapps/tool_shed/search/tool_search.py
    M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
    M lib/galaxy/workflow/extract.py
    M lib/galaxy/workflow/schedulers/core.py
    M lib/tool_shed/dependencies/attribute_handlers.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.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/repository_types/registry.py
    M lib/tool_shed/tools/data_table_manager.py
    M lib/tool_shed/tools/tool_validator.py
    M lib/tool_shed/util/shed_util_common.py
    M lib/tool_shed/util/tool_util.py
    M lib/tool_shed/utility_containers/__init__.py
    M scripts/functional_tests.py
    M test/api/test_jobs.py
    M test/api/test_page_revisions.py
    M test/base/driver_util.py
    M test/base/testcase.py
    M test/functional/test_toolbox.py
    M test/galaxy_selenium/components.py
    M test/galaxy_selenium/data.py
    M test/galaxy_selenium/navigates_galaxy.py
    M test/manual/workflows_scaling.py
    M test/selenium_tests/test_stock_tours.py
    M test/shed_functional/base/twilltestcase.py
    M test/unit/datatypes/dataproviders/test_base_dataproviders.py
    M test/unit/datatypes/dataproviders/test_line_dataproviders.py
    M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
    M test/unit/jobs/test_job_wrapper.py
    M test/unit/jobs/test_mapper.py
    M test/unit/jobs/test_runner_local.py
    M test/unit/managers/base.py
    M test/unit/managers/test_CollectionManager.py
    M test/unit/managers/test_DatasetManager.py
    M test/unit/managers/test_HDAManager.py
    M test/unit/managers/test_HDCAManager.py
    M test/unit/managers/test_HistoryContentsManager.py
    M test/unit/managers/test_HistoryManager.py
    M test/unit/managers/test_UserManager.py
    M test/unit/shed_unit/test_installed_repository_manager.py
    M test/unit/shed_unit/test_tool_panel_manager.py
    M test/unit/test_objectstore.py
    M test/unit/tools/test_actions.py
    M test/unit/tools/test_collect_primary_datasets.py
    M test/unit/tools/test_column_parameters.py
    M test/unit/tools/test_data_parameters.py
    M test/unit/tools/test_dataset_matcher.py
    M test/unit/tools/test_evaluation.py
    M test/unit/tools/test_execution.py
    M test/unit/tools/test_history_imp_exp.py
    M test/unit/tools/test_parameter_parsing.py
    M test/unit/tools/test_parsing.py
    M test/unit/tools/test_select_parameters.py
    M test/unit/tools/test_tool_deps.py
    M test/unit/tools/test_tool_loader.py
    M test/unit/tools/test_toolbox.py
    M test/unit/tools/test_watcher.py
    M test/unit/tools_support.py
    M test/unit/visualizations/plugins/test_VisualizationPlugin.py
    M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
    M test/unit/web/framework/test_webapp.py
    M test/unit/workflows/test_modules.py
    M test/unit/workflows/test_run_parameters.py
    M test/unit/workflows/test_workflow_progress.py
    M tools/filters/gff/gff_filter_by_attribute.py
    M tools/filters/gff/gff_filter_by_feature_count.py
    M tools/phenotype_association/senatag.py
    M tox.ini

  Log Message:
  -----------
  Merge pull request #5005 from nsoranzo/flake8-import-order

Fix import order everywhere

Compare: https://github.com/galaxyproject/galaxy/compare/f86dd647da54...7c1afa8f16b6

[galaxy-commits] [galaxyproject/galaxy] 2cd95c: Fix import order everywhere

GitHub