LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
versioneer.py
deeptime/__init__.py
deeptime/_version.py
deeptime/base.py
deeptime/base_torch.py
deeptime/metrics.py
deeptime/setup.py
deeptime.egg-info/PKG-INFO
deeptime.egg-info/SOURCES.txt
deeptime.egg-info/dependency_links.txt
deeptime.egg-info/not-zip-safe
deeptime.egg-info/requires.txt
deeptime.egg-info/top_level.txt
deeptime/basis/__init__.py
deeptime/basis/base.py
deeptime/basis/monomials.py
deeptime/basis/setup.py
deeptime/basis/src/basis_bindings.cpp
deeptime/clustering/__init__.py
deeptime/clustering/cluster_model.py
deeptime/clustering/kmeans.py
deeptime/clustering/metric.py
deeptime/clustering/regspace.py
deeptime/clustering/setup.py
deeptime/clustering/include/kmeans.h
deeptime/clustering/include/metric.h
deeptime/clustering/include/regspace.h
deeptime/clustering/include/bits/kmeans_bits.h
deeptime/clustering/include/bits/metric_base_bits.h
deeptime/clustering/src/clustering_module.cpp
deeptime/covariance/__init__.py
deeptime/covariance/covariance.py
deeptime/covariance/setup.py
deeptime/covariance/util/__init__.py
deeptime/covariance/util/moments.py
deeptime/covariance/util/running_moments.py
deeptime/covariance/util/covar_c/__init__.py
deeptime/covariance/util/covar_c/covartools.cpp
deeptime/covariance/util/covar_c/covartools.hpp
deeptime/covariance/util/covar_c/covartools.py
deeptime/covariance/util/covar_c/setup.py
deeptime/data/__init__.py
deeptime/data/bickley_simulator.py
deeptime/data/birth_death_chain_dataset.py
deeptime/data/datasets.py
deeptime/data/double_well_dataset.py
deeptime/data/drunkards_walk_simulator.py
deeptime/data/ellipsoids_dataset.py
deeptime/data/pbf_simulator.py
deeptime/data/setup.py
deeptime/data/util.py
deeptime/data/data/double_well_discrete.npz
deeptime/data/include/integrator.h
deeptime/data/include/pbf.h
deeptime/data/include/systems.h
deeptime/data/src/data_module.cpp
deeptime/decomposition/__init__.py
deeptime/decomposition/cca.py
deeptime/decomposition/dmd.py
deeptime/decomposition/koopman.py
deeptime/decomposition/kvad.py
deeptime/decomposition/kvadnet.py
deeptime/decomposition/tae.py
deeptime/decomposition/tica.py
deeptime/decomposition/vamp.py
deeptime/decomposition/vampnet.py
deeptime/kernels/__init__.py
deeptime/kernels/base.py
deeptime/kernels/kernels.py
deeptime/kernels/kernels_torch.py
deeptime/kernels/setup.py
deeptime/markov/__init__.py
deeptime/markov/_base.py
deeptime/markov/_transition_matrix.py
deeptime/markov/pcca.py
deeptime/markov/reactive_flux.py
deeptime/markov/sample.py
deeptime/markov/setup.py
deeptime/markov/transition_counting.py
deeptime/markov/util.py
deeptime/markov/_bindings/include/discrete_trajectories.h
deeptime/markov/_bindings/include/simulation.h
deeptime/markov/_bindings/src/markov_module.cpp
deeptime/markov/hmm/__init__.py
deeptime/markov/hmm/bayesian_hmm.py
deeptime/markov/hmm/hidden_markov_model.py
deeptime/markov/hmm/maximum_likelihood_hmm.py
deeptime/markov/hmm/output_model.py
deeptime/markov/hmm/setup.py
deeptime/markov/hmm/util.py
deeptime/markov/hmm/_bindings/include/OutputModelUtils.h
deeptime/markov/hmm/_bindings/include/docs.h
deeptime/markov/hmm/_bindings/include/utils.h
deeptime/markov/hmm/_bindings/src/hmm_module.cpp
deeptime/markov/hmm/init/__init__.py
deeptime/markov/hmm/init/setup.py
deeptime/markov/hmm/init/discrete/__init__.py
deeptime/markov/hmm/init/discrete/_init_discrete_impl.py
deeptime/markov/hmm/init/gaussian/__init__.py
deeptime/markov/hmm/init/gaussian/_init_gaussian_impl.py
deeptime/markov/msm/__init__.py
deeptime/markov/msm/_koopman_reweighted_msm_impl.py
deeptime/markov/msm/augmented_msm.py
deeptime/markov/msm/bayesian_msm.py
deeptime/markov/msm/koopman_reweighted_msm.py
deeptime/markov/msm/markov_state_model.py
deeptime/markov/msm/maximum_likelihood_msm.py
deeptime/markov/tools/__init__.py
deeptime/markov/tools/setup.py
deeptime/markov/tools/analysis/__init__.py
deeptime/markov/tools/analysis/api.py
deeptime/markov/tools/analysis/dense/__init__.py
deeptime/markov/tools/analysis/dense/assessment.py
deeptime/markov/tools/analysis/dense/committor.py
deeptime/markov/tools/analysis/dense/correlations.py
deeptime/markov/tools/analysis/dense/decomposition.py
deeptime/markov/tools/analysis/dense/expectations.py
deeptime/markov/tools/analysis/dense/fingerprints.py
deeptime/markov/tools/analysis/dense/hitting_probability.py
deeptime/markov/tools/analysis/dense/mean_first_passage_time.py
deeptime/markov/tools/analysis/dense/pcca.py
deeptime/markov/tools/analysis/dense/sensitivity.py
deeptime/markov/tools/analysis/dense/stationary_vector.py
deeptime/markov/tools/analysis/sparse/__init__.py
deeptime/markov/tools/analysis/sparse/assessment.py
deeptime/markov/tools/analysis/sparse/committor.py
deeptime/markov/tools/analysis/sparse/decomposition.py
deeptime/markov/tools/analysis/sparse/expectations.py
deeptime/markov/tools/analysis/sparse/fingerprints.py
deeptime/markov/tools/analysis/sparse/mean_first_passage_time.py
deeptime/markov/tools/analysis/sparse/stationary_vector.py
deeptime/markov/tools/estimation/__init__.py
deeptime/markov/tools/estimation/api.py
deeptime/markov/tools/estimation/setup.py
deeptime/markov/tools/estimation/dense/__init__.py
deeptime/markov/tools/estimation/dense/bootstrapping.py
deeptime/markov/tools/estimation/dense/covariance.py
deeptime/markov/tools/estimation/dense/mle.py
deeptime/markov/tools/estimation/dense/ratematrix.py
deeptime/markov/tools/estimation/dense/setup.py
deeptime/markov/tools/estimation/dense/transition_matrix.py
deeptime/markov/tools/estimation/dense/_bindings/include/mle_trev.h
deeptime/markov/tools/estimation/dense/_bindings/include/sampler.h
deeptime/markov/tools/estimation/dense/_bindings/src/mle_module.cpp
deeptime/markov/tools/estimation/dense/tmat_sampling/__init__.py
deeptime/markov/tools/estimation/dense/tmat_sampling/sampler_nrev.py
deeptime/markov/tools/estimation/dense/tmat_sampling/sampler_rev.py
deeptime/markov/tools/estimation/dense/tmat_sampling/sampler_revpi.py
deeptime/markov/tools/estimation/dense/tmat_sampling/setup.py
deeptime/markov/tools/estimation/dense/tmat_sampling/tmatrix_sampler.py
deeptime/markov/tools/estimation/sparse/__init__.py
deeptime/markov/tools/estimation/sparse/connectivity.py
deeptime/markov/tools/estimation/sparse/count_matrix.py
deeptime/markov/tools/estimation/sparse/effective_counts.py
deeptime/markov/tools/estimation/sparse/likelihood.py
deeptime/markov/tools/estimation/sparse/prior.py
deeptime/markov/tools/estimation/sparse/setup.py
deeptime/markov/tools/estimation/sparse/transition_matrix.py
deeptime/markov/tools/estimation/sparse/_bindings/include/mle_trev_sparse.h
deeptime/markov/tools/estimation/sparse/_bindings/src/mle_sparse_module.cpp
deeptime/markov/tools/estimation/sparse/mle/__init__.py
deeptime/markov/tools/estimation/sparse/mle/setup.py
deeptime/markov/tools/estimation/sparse/mle/newton/__init__.py
deeptime/markov/tools/estimation/sparse/mle/newton/linsolve.py
deeptime/markov/tools/estimation/sparse/mle/newton/linsolve_sparse.py
deeptime/markov/tools/estimation/sparse/mle/newton/mle_rev.py
deeptime/markov/tools/estimation/sparse/mle/newton/objective_sparse.py
deeptime/markov/tools/estimation/sparse/mle/newton/objective_sparse_ops.cpp
deeptime/markov/tools/flux/__init__.py
deeptime/markov/tools/flux/api.py
deeptime/markov/tools/flux/dense/__init__.py
deeptime/markov/tools/flux/dense/tpt.py
deeptime/markov/tools/flux/sparse/__init__.py
deeptime/markov/tools/flux/sparse/pathways.py
deeptime/markov/tools/flux/sparse/tpt.py
deeptime/markov/tools/kahandot/kahandot_module.cpp
deeptime/numeric/__init__.py
deeptime/numeric/eig_qr.c
deeptime/numeric/eig_qr.pyx
deeptime/numeric/eigen.py
deeptime/numeric/setup.py
deeptime/numeric/slepc.py
deeptime/numeric/utils.py
deeptime/sindy/__init__.py
deeptime/sindy/_sindy.py
deeptime/src/include/common.h
deeptime/src/include/distribution_utils.h
deeptime/src/include/thread_utils.h
deeptime/util/__init__.py
deeptime/util/decorators.py
deeptime/util/exceptions.py
deeptime/util/matrix.py
deeptime/util/parallel.py
deeptime/util/platform.py
deeptime/util/stats.py
deeptime/util/torch.py
deeptime/util/types.py