Skip to content
This repository has been archived by the owner on Sep 11, 2023. It is now read-only.

error in notebook 07 #1610

Open
hima111997 opened this issue Jul 16, 2023 · 0 comments
Open

error in notebook 07 #1610

hima111997 opened this issue Jul 16, 2023 · 0 comments

Comments

@hima111997
Copy link

in notebook 07, this line :
hmm_4 = pyemma.msm.bayesian_hidden_markov_model(cluster.dtrajs, nstates=4, lag=1, dt_traj='1 ps', nsamples=50)
produces this error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[5], line 1
----> 1 hmm_4 = pyemma.msm.bayesian_hidden_markov_model(cluster.dtrajs, nstates=4, lag=1, dt_traj='1 ps', nsamples=50)

File ~/miniconda3/envs/emma/lib/python3.11/site-packages/pyemma/msm/api.py:1375, in bayesian_hidden_markov_model(dtrajs, nstates, lag, nsamples, reversible, stationary, connectivity, mincount_connectivity, separate, observe_nonempty, stride, conf, dt_traj, store_hidden, show_progress)
   1217 r""" Bayesian Hidden Markov model estimate using Gibbs sampling of the posterior
   1218 
   1219 Returns a :class:`BayesianHMSM` that contains
   (...)
   1368 
   1369 """
   1370 bhmsm_estimator = _Bayes_HMSM(lag=lag, nstates=nstates, stride=stride, nsamples=nsamples, reversible=reversible,
   1371                               stationary=stationary,
   1372                               connectivity=connectivity, mincount_connectivity=mincount_connectivity,
   1373                               separate=separate, observe_nonempty=observe_nonempty,
   1374                               dt_traj=dt_traj, conf=conf, store_hidden=store_hidden, show_progress=show_progress)
-> 1375 return bhmsm_estimator.estimate(dtrajs)

File ~/miniconda3/envs/emma/lib/python3.11/site-packages/pyemma/_base/estimator.py:418, in Estimator.estimate(self, X, **params)
    416 if params:
    417     self.set_params(**params)
--> 418 self._model = self._estimate(X)
    419 # ensure _estimate returned something
    420 assert self._model is not None

File ~/miniconda3/envs/emma/lib/python3.11/site-packages/pyemma/msm/estimators/bayesian_hmsm.py:313, in BayesianHMSM._estimate(self, dtrajs)
    304 else:
    305     estimator = BayesianHMM.default(dtrajs, n_hidden_states=self.nstates, lagtime=self.lag,
    306                                     n_samples=self.nsamples, stride=self.stride,
    307                                     initial_distribution_prior=self.p0_prior,
   (...)
    310                                     stationary=self.stationary,
    311                                     prior_submodel=True, separate=self.separate)
--> 313 estimator.fit(dtrajs, n_burn_in=0, n_thin=1, progress=progress)
    314 model = estimator.fetch_model()
    315 if self.show_progress:

File ~/miniconda3/envs/emma/lib/python3.11/site-packages/deeptime/base.py:417, in _ImmutableInputData.__call__(self, *args, **kwargs)
    415 # here we invoke the immutable setting context manager.
    416 with self:
--> 417     return self.fit_method(*args, **kwargs)

File ~/miniconda3/envs/emma/lib/python3.11/site-packages/deeptime/markov/hmm/_bayesian_hmm.py:610, in BayesianHMM.fit(self, data, n_burn_in, n_thin, progress, **kwargs)
    608 # Collect data.
    609 models = []
--> 610 for _ in progress(range(self.n_samples), desc="Drawing samples", leave=False):
    611     # Run a number of Gibbs sampling updates to generate each sample.
    612     for _ in range(n_thin):
    613         self._update(sample_model, dtrajs_lagged_strided, temp_alpha, transition_matrix_prior,
    614                      initial_distribution_prior)

TypeError: ProgressCallback.__init__() got an unexpected keyword argument 'desc'

How to solve it?

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant