{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/832","repository_url":"https://api.github.com/repos/markovmodel/PyEMMA","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/832/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/832/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/832/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/832","id":159916260,"number":832,"title":"estimate_hidden_markov_model not working","user":{"login":"giopina","id":12557366,"avatar_url":"https://avatars.githubusercontent.com/u/12557366?v=3","gravatar_id":"","url":"https://api.github.com/users/giopina","html_url":"https://github.com/giopina","followers_url":"https://api.github.com/users/giopina/followers","following_url":"https://api.github.com/users/giopina/following{/other_user}","gists_url":"https://api.github.com/users/giopina/gists{/gist_id}","starred_url":"https://api.github.com/users/giopina/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giopina/subscriptions","organizations_url":"https://api.github.com/users/giopina/orgs","repos_url":"https://api.github.com/users/giopina/repos","events_url":"https://api.github.com/users/giopina/events{/privacy}","received_events_url":"https://api.github.com/users/giopina/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-06-13T10:12:45Z","updated_at":"2016-06-13T11:30:55Z","closed_at":null,"body":"After upgrading to the latest pyemma version  pyemma.msm.estimate_hidden_markov_model() is not working anymore. The same error is encoutered when using the method coarse_grain() on an msm object.\r\n\r\nThis is the error the program gives when calling msm.estimate_hidden_markov_model(dtrajs,4,100)\r\n\r\n---------------------------------------------------------------------------\r\nAttributeError                            Traceback (most recent call last)\r\n<ipython-input-20-b43ba4297b80> in <module>()\r\n----> 1 msm.estimate_hidden_markov_model(ctrajs,4,100)\r\n\r\n/home/mi/giopina/miniconda/lib/python2.7/site-packages/pyEMMA-2.2-py2.7-linux-x86_64.egg/pyemma/msm/api.pyc in estimate_hidden_markov_model(dtrajs, nstates, lag, reversible, stationary, connectivity, mincount_connectivity, separate, observe_nonempty, stride, dt_traj, accuracy, maxit)\r\n   1034                               accuracy=accuracy, maxit=maxit)\r\n   1035     # run estimation\r\n-> 1036     return hmsm_estimator.estimate(dtrajs)\r\n   1037 \r\n   1038 \r\n\r\n/home/mi/giopina/miniconda/lib/python2.7/site-packages/pyEMMA-2.2-py2.7-linux-x86_64.egg/pyemma/_base/estimator.pyc in estimate(self, X, **params)\r\n    346         if params:\r\n    347             self.set_params(**params)\r\n--> 348         self._model = self._estimate(X)\r\n    349         self._estimated = True\r\n    350         return self\r\n\r\n/home/mi/giopina/miniconda/lib/python2.7/site-packages/pyEMMA-2.2-py2.7-linux-x86_64.egg/pyemma/msm/estimators/maximum_likelihood_hmsm.pyc in _estimate(self, dtrajs)\r\n    191 \r\n    192         # LAG AND STRIDE DATA\r\n--> 193         dtrajs_lagged_strided = bhmm.lag_observations(dtrajs, self.lag, stride=self.stride)\r\n    194 \r\n    195         # OBSERVATION SET\r\n\r\nAttributeError: 'module' object has no attribute 'lag_observations'\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/225555968","html_url":"https://github.com/markovmodel/PyEMMA/issues/832#issuecomment-225555968","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/832","id":225555968,"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":"2016-06-13T11:30:54Z","updated_at":"2016-06-13T11:30:54Z","body":"I checked the latest devel version, and it's passing all tests:\n\n     https://travis-ci.org/markovmodel/PyEMMA/builds/135857326\n\nThis feature is definitely tested and the function ``lag_observations`` \nis part of bhmm since a while ago. My guess is that you had an older \nbhmm version on your machine and for some reason the updating didn't \nwork properly or there are multiple competing installations of this \npackage and the wrong version gets imported. I suggest to remove your \nbhmm install, make sure that none is left, and fetch a new version.\n\nMy impression is that many errors on the user side are based on version \ninconsistencies between dependencies. Since these can be installed in \nvarious ways it is not really under our control to ensure consistent \nversioning on the user side. We are working on a better way to do this \nin the near future.\n\n@clonker, do you have time to discuss this this week?\n\n\nAm 13/06/16 um 12:12 schrieb giopina:\n>\n> After upgrading to the latest pyemma version \n> pyemma.msm.estimate_hidden_markov_model() is not working anymore. The \n> same error is encoutered when using the method coarse_grain() on an \n> msm object.\n>\n> This is the error the program gives when calling \n> msm.estimate_hidden_markov_model(dtrajs,4,100)\n>\n> ------------------------------------------------------------------------\n>\n> AttributeError Traceback (most recent call last)\n> in ()\n> ----> 1 msm.estimate_hidden_markov_model(ctrajs,4,100)\n>\n> /home/mi/giopina/miniconda/lib/python2.7/site-packages/pyEMMA-2.2-py2.7-linux-x86_64.egg/pyemma/msm/api.pyc \n> in estimate_hidden_markov_model(dtrajs, nstates, lag, reversible, \n> stationary, connectivity, mincount_connectivity, separate, \n> observe_nonempty, stride, dt_traj, accuracy, maxit)\n> 1034 accuracy=accuracy, maxit=maxit)\n> 1035 # run estimation\n> -> 1036 return hmsm_estimator.estimate(dtrajs)\n> 1037\n> 1038\n>\n> /home/mi/giopina/miniconda/lib/python2.7/site-packages/pyEMMA-2.2-py2.7-linux-x86_64.egg/pyemma/_base/estimator.pyc \n> in estimate(self, X, *params)\n> 346 if params:\n> 347 self.set_params(*params)\n> --> 348 self._model = self._estimate(X)\n> 349 self._estimated = True\n> 350 return self\n>\n> /home/mi/giopina/miniconda/lib/python2.7/site-packages/pyEMMA-2.2-py2.7-linux-x86_64.egg/pyemma/msm/estimators/maximum_likelihood_hmsm.pyc \n> in _estimate(self, dtrajs)\n> 191\n> 192 # LAG AND STRIDE DATA\n> --> 193 dtrajs_lagged_strided = bhmm.lag_observations(dtrajs, \n> self.lag, stride=self.stride)\n> 194\n> 195 # OBSERVATION SET\n>\n> AttributeError: 'module' object has no attribute 'lag_observations'\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub \n> <https://github.com/markovmodel/PyEMMA/issues/832>, or mute the thread \n> <https://github.com/notifications/unsubscribe/AGMeQlaDWivFJtwBIEwb_r1DNRgRhA1jks5qLS0dgaJpZM4I0LkQ>.\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"}}
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