Merge pull request #1147 from marscher/covartools_cpp

Covartools cpp
markovmodel · Aug 23, 2017 · 5b0bbbb · 5b0bbbb
2 parents 887420a + 0b806cd
commit 5b0bbbb
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,10 +5,9 @@ project (pyemma)
 add_subdirectory(pybind11)
 
 
-pybind11_add_module(regspace_clustering pyemma/coordinates/clustering/src/clustering_module.cpp
+pybind11_add_module(regspace_clustering pyemma/_ext/variational/estimators/covar_c/covartools.cpp
         )
 
-include_directories(pyemma/coordinates/clustering/include
-/home/mi/marscher/miniconda/lib/python3.6/site-packages/mdtraj/core/lib/
+include_directories(pyemma/_ext/variational/covar_c/
 
         )
diff --git a/doc/source/CHANGELOG.rst b/doc/source/CHANGELOG.rst
@@ -27,7 +27,9 @@ your Python installation to at least version 3.5.
 - msm: fix setting of dt_model for BayesianMSM. This bug led to wrongly scaled time units for mean first passage times,
   correlation and relaxation times as well for timescales for this estimator. #1116
 - coordinates: Added the covariance property of time-lagged to CovarianceLagged. #1125
-- coordinates: clustering code modernized in C++ with pybind11 interface. #
+- coordinates: clustering code modernized in C++ with pybind11 interface. #1142
+- variational: covartools code modernized in C++ with pybind11 interface. #1147
+
 
 2.4 (05-19-2017)
 ----------------

diff --git a/pyemma/_ext/variational/estimators/covar_c/_covartools.c b/pyemma/_ext/variational/estimators/covar_c/_covartools.c