[galaxy-commits] [galaxyproject/galaxy] af2f93: flake8 contrib/ .

10 Sep 2015

      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: af2f93b23609b367d15619471a18e3e6fd0c90e8
      https://github.com/galaxyproject/galaxy/commit/af2f93b23609b367d15619471a18e...
  Author: Nicola Soranzo <nicola.soranzo@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/df808d0c1e8c46e45adebaafbd30e...
  Author: Nicola Soranzo <nicola.soranzo@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/b1b710925a4c54f3081fc4b799630...
  Author: Martin Cech <cech.marten@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

[galaxy-commits] [galaxyproject/galaxy] af2f93: flake8 contrib/ .

GitHub