{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/34","labels_url":"https://api.github.com/repos/choderalab/perses/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/34/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/34/events","html_url":"https://github.com/choderalab/perses/issues/34","id":116956990,"number":34,"title":"run_example.py dies with recursion error","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-11-14T22:45:14Z","updated_at":"2015-11-14T23:12:57Z","closed_at":null,"body":"```\r\n[LSKI1497:perses.choderalab/examples/rjmc] choderaj% python run_example.py \r\nLOG: \r\nWarning: run_antechamber has been moved to openmoltools.amber.\r\nLOG: antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2 -s 2 -c bcc\r\n...\r\n  File \"/Users/choderaj/anaconda/lib/python2.7/site-packages/perses-0.1-py2.7.egg/perses/rjmc/topology_proposal.py\", line 131, in metadata\r\n    return self.metadata\r\nRuntimeError: maximum recursion depth exceeded while calling a Python object\r\n```"},"comment":{"url":"https://api.github.com/repos/choderalab/perses/issues/comments/156756338","html_url":"https://github.com/choderalab/perses/issues/34#issuecomment-156756338","issue_url":"https://api.github.com/repos/choderalab/perses/issues/34","id":156756338,"user":{"login":"pgrinaway","id":4674712,"avatar_url":"https://avatars.githubusercontent.com/u/4674712?v=3","gravatar_id":"","url":"https://api.github.com/users/pgrinaway","html_url":"https://github.com/pgrinaway","followers_url":"https://api.github.com/users/pgrinaway/followers","following_url":"https://api.github.com/users/pgrinaway/following{/other_user}","gists_url":"https://api.github.com/users/pgrinaway/gists{/gist_id}","starred_url":"https://api.github.com/users/pgrinaway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgrinaway/subscriptions","organizations_url":"https://api.github.com/users/pgrinaway/orgs","repos_url":"https://api.github.com/users/pgrinaway/repos","events_url":"https://api.github.com/users/pgrinaway/events{/privacy}","received_events_url":"https://api.github.com/users/pgrinaway/received_events","type":"User","site_admin":false},"created_at":"2015-11-14T23:12:57Z","updated_at":"2015-11-14T23:12:57Z","body":"> Make run_example.py into a nosetest perses/tests/test_sampler.py so we can make sure it works\r\n\r\nWe should do this, but given the API changes and the fact that we'll be creating a new set of `Sampler` classes, I was going to deprecate the current `run_example.py`, as you point out in 3. This is something that I was going to do next.\r\n\r\n> Use branches of choderalab/perses for PRs so nosetests on travis will work.\r\n\r\nOk. I can switch to that, but I think this should be a temporary measure. Eventually, I think the code should either no longer require closed-source software (more time-consuming, and a low-priority task), or should use pre-generated files in the tests, which avoids the requirement for closed-source software in tests.\r\n"}}