{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/674","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/674/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/674/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/674/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/674","id":126903949,"number":674,"title":"[coor_refactor] write performance tests and compare measures with last release ","user":{"login":"marscher","id":170287,"avatar_url":"https://avatars.githubusercontent.com/u/170287?v=3","gravatar_id":"","url":"https://api.github.com/users/marscher","html_url":"https://github.com/marscher","followers_url":"https://api.github.com/users/marscher/followers","following_url":"https://api.github.com/users/marscher/following{/other_user}","gists_url":"https://api.github.com/users/marscher/gists{/gist_id}","starred_url":"https://api.github.com/users/marscher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marscher/subscriptions","organizations_url":"https://api.github.com/users/marscher/orgs","repos_url":"https://api.github.com/users/marscher/repos","events_url":"https://api.github.com/users/marscher/events{/privacy}","received_events_url":"https://api.github.com/users/marscher/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/milestones/11","html_url":"https://github.com/markovmodel/PyEMMA/milestones/coordinates%20refactoring","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/milestones/11/labels","id":1470086,"number":11,"title":"coordinates refactoring","description":"track remaining tasks in coordinates refactoring branch","creator":{"login":"marscher","id":170287,"avatar_url":"https://avatars.githubusercontent.com/u/170287?v=3","gravatar_id":"","url":"https://api.github.com/users/marscher","html_url":"https://github.com/marscher","followers_url":"https://api.github.com/users/marscher/followers","following_url":"https://api.github.com/users/marscher/following{/other_user}","gists_url":"https://api.github.com/users/marscher/gists{/gist_id}","starred_url":"https://api.github.com/users/marscher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marscher/subscriptions","organizations_url":"https://api.github.com/users/marscher/orgs","repos_url":"https://api.github.com/users/marscher/repos","events_url":"https://api.github.com/users/marscher/events{/privacy}","received_events_url":"https://api.github.com/users/marscher/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":12,"state":"open","created_at":"2015-12-21T19:11:47Z","updated_at":"2016-01-15T16:14:53Z","due_on":"2016-01-14T23:00:00Z","closed_at":null},"comments":1,"created_at":"2016-01-15T16:14:53Z","updated_at":"2016-01-20T13:33:55Z","closed_at":null,"body":"We need to have tests for:\r\n* io operations (FeatureReader, NumPyReader, ...)\r\n* estimators (Clustering, TICA, PCA, ...)\r\n* pipelining operations (chunked vs full-file/traj mode)\r\n\r\nThe data sets should lie on a local hard disk to avoid fluctuations due to network access. All tests should be long running and deterministic (eg. use the same random seed).\r\n\r\nWhich data sets should we use (eg. they have to fit on the hard drive of the testing system)?\r\n\r\nWe can think about automatizing this via our Jenkins service as soon we have defined these things. I'll suggest to store these tests in a separate repo to easily test against multiple versions of PyEMMA."},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/173204473","html_url":"https://github.com/markovmodel/PyEMMA/issues/674#issuecomment-173204473","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/674","id":173204473,"user":{"login":"franknoe","id":6495810,"avatar_url":"https://avatars.githubusercontent.com/u/6495810?v=3","gravatar_id":"","url":"https://api.github.com/users/franknoe","html_url":"https://github.com/franknoe","followers_url":"https://api.github.com/users/franknoe/followers","following_url":"https://api.github.com/users/franknoe/following{/other_user}","gists_url":"https://api.github.com/users/franknoe/gists{/gist_id}","starred_url":"https://api.github.com/users/franknoe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/franknoe/subscriptions","organizations_url":"https://api.github.com/users/franknoe/orgs","repos_url":"https://api.github.com/users/franknoe/repos","events_url":"https://api.github.com/users/franknoe/events{/privacy}","received_events_url":"https://api.github.com/users/franknoe/received_events","type":"User","site_admin":false},"created_at":"2016-01-20T13:33:55Z","updated_at":"2016-01-20T13:33:55Z","body":"In addition: featurization, in particular distances and contacts\n\nAm 15/01/16 um 17:14 schrieb Martin K. Scherer:\n>\n> We need to have tests for:\n>\n>   * io operations (FeatureReader, NumPyReader, ...)\n>   * estimators (Clustering, TICA, PCA, ...)\n>   * pipelining operations (chunked vs full-file/traj mode)\n>\n> The data sets should lie on a local hard disk to avoid fluctuations \n> due to network access. All tests should be long running and \n> deterministic (eg. use the same random seed).\n>\n> Which data sets should we use (eg. they have to fit on the hard drive \n> of the testing system)?\n>\n> We can think about automatizing this via our Jenkins service as soon \n> we have defined these things. I'll suggest to store these tests in a \n> separate repo to easily test against multiple versions of PyEMMA.\n>\n> —\n> Reply to this email directly or view it on GitHub \n> <https://github.com/markovmodel/PyEMMA/issues/674>.\n>\n\n\n-- \n\n----------------------------------------------\nProf. Dr. Frank Noe\nHead of Computational Molecular Biology group\nFreie Universitaet Berlin\n\nPhone: (+49) (0)30 838 75354\nWeb:   research.franknoe.de\nMail:  Arnimallee 6, 14195 Berlin, Germany\n----------------------------------------------\n\n"}}