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Sequences, Collections, and Alignments, oh my!","description":"Clean up `Alignment` API and better integrate alignment algorithms with sequence objects and collections.","creator":{"login":"ebolyen","id":3976804,"avatar_url":"https://avatars.githubusercontent.com/u/3976804?v=3","gravatar_id":"","url":"https://api.github.com/users/ebolyen","html_url":"https://github.com/ebolyen","followers_url":"https://api.github.com/users/ebolyen/followers","following_url":"https://api.github.com/users/ebolyen/following{/other_user}","gists_url":"https://api.github.com/users/ebolyen/gists{/gist_id}","starred_url":"https://api.github.com/users/ebolyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ebolyen/subscriptions","organizations_url":"https://api.github.com/users/ebolyen/orgs","repos_url":"https://api.github.com/users/ebolyen/repos","events_url":"https://api.github.com/users/ebolyen/events{/privacy}","received_events_url":"https://api.github.com/users/ebolyen/received_events","type":"User","site_admin":false},"open_issues":28,"closed_issues":20,"state":"open","created_at":"2015-02-12T15:40:43Z","updated_at":"2015-03-11T20:48:48Z","due_on":"2015-04-01T07:00:00Z","closed_at":null},"comments":11,"created_at":"2015-03-11T01:37:44Z","updated_at":"2015-03-11T20:48:48Z","closed_at":"2015-03-11T20:48:48Z","body":"After the changes I made to the testing procedures, particularly using nose's ``run_exit`` method, running tests within an interactive python session causes the session to exit, and running from within ``IPython`` throws the following exception:\r\n\r\n```\r\nRan 177 tests in 0.070s\r\n\r\nOK\r\nAn exception has occurred, use %tb to see the full traceback.\r\n\r\nSystemExit: False\r\n\r\nTo exit: use 'exit', 'quit', or Ctrl-D.\r\n```\r\n\r\nLooks like I'll need to detect whether we're running interactively."}}