{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/878","repository_url":"https://api.github.com/repos/MDAnalysis/mdanalysis","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/878/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/878/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/878/events","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/878","id":159842921,"number":878,"title":"unpickling doesn't work intuitive","user":{"login":"kain88-de","id":4302678,"avatar_url":"https://avatars.githubusercontent.com/u/4302678?v=3","gravatar_id":"","url":"https://api.github.com/users/kain88-de","html_url":"https://github.com/kain88-de","followers_url":"https://api.github.com/users/kain88-de/followers","following_url":"https://api.github.com/users/kain88-de/following{/other_user}","gists_url":"https://api.github.com/users/kain88-de/gists{/gist_id}","starred_url":"https://api.github.com/users/kain88-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kain88-de/subscriptions","organizations_url":"https://api.github.com/users/kain88-de/orgs","repos_url":"https://api.github.com/users/kain88-de/repos","events_url":"https://api.github.com/users/kain88-de/events{/privacy}","received_events_url":"https://api.github.com/users/kain88-de/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Component-Core","name":"Component-Core","color":"ff0000"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Component-Selections","name":"Component-Selections","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/9","html_url":"https://github.com/MDAnalysis/mdanalysis/milestones/0.16.0","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/9/labels","id":1716502,"number":9,"title":"0.16.0","description":"","creator":{"login":"richardjgowers","id":9249543,"avatar_url":"https://avatars.githubusercontent.com/u/9249543?v=3","gravatar_id":"","url":"https://api.github.com/users/richardjgowers","html_url":"https://github.com/richardjgowers","followers_url":"https://api.github.com/users/richardjgowers/followers","following_url":"https://api.github.com/users/richardjgowers/following{/other_user}","gists_url":"https://api.github.com/users/richardjgowers/gists{/gist_id}","starred_url":"https://api.github.com/users/richardjgowers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardjgowers/subscriptions","organizations_url":"https://api.github.com/users/richardjgowers/orgs","repos_url":"https://api.github.com/users/richardjgowers/repos","events_url":"https://api.github.com/users/richardjgowers/events{/privacy}","received_events_url":"https://api.github.com/users/richardjgowers/received_events","type":"User","site_admin":false},"open_issues":16,"closed_issues":7,"state":"open","created_at":"2016-04-19T08:42:42Z","updated_at":"2016-06-12T19:28:16Z","due_on":null,"closed_at":null},"comments":3,"created_at":"2016-06-12T19:17:55Z","updated_at":"2016-06-12T19:38:14Z","closed_at":null,"body":"### Expected behaviour\r\n\r\nI can just unpickle a universe without recreating it first. Unpickling should create a whole new universe object. we already save the filename of the topology. If we also save the trajectory filename this could be done.\r\n\r\n### Actual behaviour\r\n\r\ntells me I can't unpickle it. There isn't a suitable loaded universe. \r\nThis weird behavior requires us to keep weak references to universes that aren't deleted.\r\nSo making this work out of box without loading universes separately would fix the too many files open errors we see on oxs.\r\n\r\n### Code to reproduce the behaviour\r\n\r\n``` python\r\nimport pickle\r\n\r\nwith open('filename') as f:\r\n    u = pickle.load(f)\r\n```\r\n\r\n### Currently version of MDAnalysis:\r\n(run `python -c \"import MDAnalysis as mda; print(mda.__version__)\"`)\r\n\r\n0.15.0"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/225456034","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/878#issuecomment-225456034","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/878","id":225456034,"user":{"login":"mnmelo","id":11721337,"avatar_url":"https://avatars.githubusercontent.com/u/11721337?v=3","gravatar_id":"","url":"https://api.github.com/users/mnmelo","html_url":"https://github.com/mnmelo","followers_url":"https://api.github.com/users/mnmelo/followers","following_url":"https://api.github.com/users/mnmelo/following{/other_user}","gists_url":"https://api.github.com/users/mnmelo/gists{/gist_id}","starred_url":"https://api.github.com/users/mnmelo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mnmelo/subscriptions","organizations_url":"https://api.github.com/users/mnmelo/orgs","repos_url":"https://api.github.com/users/mnmelo/repos","events_url":"https://api.github.com/users/mnmelo/events{/privacy}","received_events_url":"https://api.github.com/users/mnmelo/received_events","type":"User","site_admin":false},"created_at":"2016-06-12T19:38:14Z","updated_at":"2016-06-12T19:38:14Z","body":"I think the problem here is that the universe being unpickled isn't deemed appropriate to unpickle the underlying AtomGroups onto (`u.atoms`), as it doesn't really exist at the time.\n\nAdditionally, we want to make sure that those AtomGroups unpickle specifically onto the universe being unpickled (in case a compatible universe already exists)."}}
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