----------------------
We're pleased to announce the release of MSMBuilder v3.3.0. The focus of this
release is a completely re-written module for constructing HMMs as well as bug
fixes and incremental improvements.
API Changes
~~~~~~~~~~~
- ``FeatureUnion`` is an estimator that deprecates the functionality of
``UnionDataset``. Passing a list of paths to ``dataset()`` will no longer
automatically yield a ``UnionDataset``. This behavior is still available by
specifying ``fmt="dir-npy-union"``, but is deprecated (611).
- The command line flag for featurizers ``--out`` (deprecated in 3.2) now saves
the featurizer as a pickle file (546). Please use ``--transformed`` for the
old behavior. This is consistent with other command-line commands.
- The default number of timescales in ``MarkovStateModel`` is now one less than
the number of states (was 10). This addresses some bugs with
``implied_timescales`` and PCCA(+) (603).
New Features
~~~~~~~~~~~~
- ``GaussianHMM`` and ``VonMisesHMM`` is rewritten to feature higher code reuse
and code quality (583, 582, 584, 572, 570).
- ``KDTree`` can find n nearest points to e.g. a cluster center (599).
- ``Slicer`` featurizer can slice feature arrays as part of a pipeline
(567).
Improvements
~~~~~~~~~~~~
- ``PCCAPlus`` is compatible with scipy 0.16 (620).
- Documentation improvements (618, 608, 604, 602)
- Test improvements, especially for Windows (593, 590, 588, 579, 578,
577, 576)
- Bug fix: ``MarkovStateModel.sample()`` produced trajectories of incorrect
length. This function is still deprecated (556).
- Bug fix: The muller example dataset did not respect users' specifications for
initial coordinates (631).
- ``MarkovStateModel.draw_samples`` failed if discrete trajectories did not
contain every possible state (638). Function can now accept a single
trajectory, as well as a list of them.
- ``SuperposeFeaturizer`` now respects the topology argument when loading the
reference trajectory (555).