{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/418","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/418/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/418/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/418/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/418","id":94941922,"number":418,"title":"Clean up pyemma.msm.util.mapping","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},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/milestones/5","html_url":"https://github.com/markovmodel/PyEMMA/milestones/v1.3","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/milestones/5/labels","id":1063219,"number":5,"title":"v1.3","description":"A number of functionality improvements are planned. Let us see how many really go into this release:\r\n\r\n* Include Hidden Markov models (discrete and Gaussian) from bhmm (via dependency, no code duplication). The discrete HMM should have an identical API like the MSM object and can go into the msm package (msm = discrete Markovian state models, including hidden and direct).\r\n* Include dTRAM from pytram package (via dependency, no code duplication). Think about how to make use of estimation / counting functionality of pyemma for TRAM. Think about how to extend the coordinates package so as to allow input generation for TRAM (e.g. we need energy trajectories). Connectivity functionalities can probably be used. MSM analysis functionality can be used. TRAM could generate a list of Markov models with the pyEMMA signature.\r\n* Incorporate Bayesian methods for MSM and HMM estimation. @franknoe has worked out a concept to unify the API with the existing maximum likelihood estimators.\r\n* Explicit sparse matrix support for msms.","creator":{"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},"open_issues":10,"closed_issues":13,"state":"open","created_at":"2015-04-11T16:21:44Z","updated_at":"2015-07-16T07:13:54Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2015-07-14T13:09:19Z","updated_at":"2015-07-17T08:11:48Z","closed_at":null,"body":"```pyemma.msm.util.mapping``` is in part deprecated and in other parts probably not at the right place. I think the whole module can be removed from pyEMMA, but let's see:\r\n\r\n* ```from_lcc_labels``` and ```to_lcc_labels```: Seems to be something that is (or should be) part of the msm object. Anyway these functions are one-lines, so do we need them? Maybe part of msmtools?\r\n* ```regroup_RAM``` and ```PCCA_disctrajs``` are deprecated and can be removed in the next release.\r\n* ```regroup_DISK``` should definitely not be in the msm package, but in some coordinate package utility module.\r\n\r\nSo I propose to:\r\n1. Anyone familiar with ```regroup_DISK``` to suggest a new home in coordinates and put it there.\r\n2. I'm currently rebasing the Chapman-Kolmogorow Test onto the new Estimator structure. This will avoid using the ```_lcc_labels``` functions.\r\n3. Once 1. and 2. are done we can remove the module.\r\n\r\nOK?"},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/122212047","html_url":"https://github.com/markovmodel/PyEMMA/issues/418#issuecomment-122212047","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/418","id":122212047,"user":{"login":"fabian-paul","id":8878525,"avatar_url":"https://avatars.githubusercontent.com/u/8878525?v=3","gravatar_id":"","url":"https://api.github.com/users/fabian-paul","html_url":"https://github.com/fabian-paul","followers_url":"https://api.github.com/users/fabian-paul/followers","following_url":"https://api.github.com/users/fabian-paul/following{/other_user}","gists_url":"https://api.github.com/users/fabian-paul/gists{/gist_id}","starred_url":"https://api.github.com/users/fabian-paul/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fabian-paul/subscriptions","organizations_url":"https://api.github.com/users/fabian-paul/orgs","repos_url":"https://api.github.com/users/fabian-paul/repos","events_url":"https://api.github.com/users/fabian-paul/events{/privacy}","received_events_url":"https://api.github.com/users/fabian-paul/received_events","type":"User","site_admin":false},"created_at":"2015-07-17T08:11:48Z","updated_at":"2015-07-17T08:11:48Z","body":"regroup_DISK is superseded by  pyemma.coordinates.save_trajs. I think I made the mistake of not labeling it as deprecated. The function should be removed in the future. Sorry for the confusion.  regroup_RAM and PCCA_disctrajs are already marked as deprecated and can be removed.\r\n"}}