From fd9ad47cbebc2544807fb6634421bab96c3462b3 Mon Sep 17 00:00:00 2001 From: "Martin K. Scherer" Date: Wed, 21 Sep 2016 17:30:25 +0200 Subject: [PATCH 1/2] [msm] determine reversible setting only from matrix if reversible is None. This restores the old behaviour. Fixes #935 --- pyemma/msm/models/msm.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pyemma/msm/models/msm.py b/pyemma/msm/models/msm.py index 1e906083d..4ad216215 100644 --- a/pyemma/msm/models/msm.py +++ b/pyemma/msm/models/msm.py @@ -137,10 +137,11 @@ def set_model_params(self, P, pi=None, reversible=None, dt_model='1 step', neig= list of this function (by mandatory or keyword arguments) """ + # we set reversible first, so it can be derived from P, if None was given. + self.reversible = reversible if P is not None: self.P = P self.pi = pi - self.reversible = reversible self.dt_model = dt_model self.neig = neig @@ -164,7 +165,8 @@ def P(self, value): raise ValueError('T is not a transition matrix.') # set states self.nstates = _np.shape(self._P)[0] - self.reversible = msmana.is_reversible(self._P, tol=1e-10) + if self.reversible is None: + self.reversible = msmana.is_reversible(self._P) from scipy.sparse import issparse self.sparse = issparse(self._P) From 47935a38f13e06e3eab4b5a6f1eacbcc32d2790f Mon Sep 17 00:00:00 2001 From: "Martin K. Scherer" Date: Wed, 21 Sep 2016 17:38:14 +0200 Subject: [PATCH 2/2] [doc] added changelog entry --- doc/source/CHANGELOG.rst | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/doc/source/CHANGELOG.rst b/doc/source/CHANGELOG.rst index 3500001c8..443a2fa28 100644 --- a/doc/source/CHANGELOG.rst +++ b/doc/source/CHANGELOG.rst @@ -1,7 +1,14 @@ Changelog ========= -2.2.4 (9-24-16) +2.2.5 (9-21-16) +--------------- + +**Fixes**: + +- msm: fixed setting of 'reversible' attribute. #935 + +2.2.4 (9-20-16) --------------- **New features**: