-------------------------
We're pleased to announce the release of MSMBuilder 3.6. This release
introduces project templating and a whole host of new ``sklearn`` estimators.
There are also some bugfixes and API hygiene improvements. We recommend all
users upgrade to MSMBuilder 3.6.
API Changes
~~~~~~~~~~~
- ``version.short_version`` is now 3.y instead of 3.y.z (gh-829).
- ``weighted_transform`` is no longer supported in tICA methods (gh-807). Please
used ``kinetic_mapping``.
- The cached filenames and formats for DoubleWell, QuadWell,
and MullerPotential example datasets have changed. The API through
``msmbuilder.example_datasets`` is still the same, but the data may
be re-generated instead of using a cached version from a previous installation
of MSMBuilder (gh-854).
- The alias for Ward clustering has been removed. Modelers should now use
``LandmarkAgglomerative(linkage='ward')`` (gh-874). Ward clustering is also
available in ``AgglomerativeClustering``, but without a prediction algorithm.
New Features
~~~~~~~~~~~~
- ``Butterworth``, ``DoubleEWMA``, ``StandardScaler``, ``RobustScaler`` are
available via the command line (gh-895).
- ``BinaryContactFeaturizer`` featurizes a trajectory into a
boolean array corresponding to whether each residue-residue
distance is below a cutoff (gh-798).
- ``LogisticContactFeaturizer`` produces a logistic transform
of residue-residue distances about a center distance (798).
- ``FactorAnalysis``, ``FastICA``, and ``KernelPCA`` are available in the
``decomposition`` module (gh-807).
- ``Butterworth``, ``EWMA``, and ``DoubleEWMA`` are available in the
``preprocessing`` module (gh-818).
- We encourage users to download the ``msmb_data`` conda package to easily
install example data. The data can be loaded through existing methods
in ``msmbuilder.example_datasets`` (gh-854, gh-867).
- An example dataset ``MinimalFsPeptide`` is available. This is a strided
version of the existing ``FsPeptide`` dataset. We use it for testing,
when a fully-converged dataset is not required (gh-867).
- Project templates! Read the new tutorial or the :ref:`io` page for
details (gh-768).
- ``LandmarkAgglomerative`` clustering now features the ``ward`` linkage
option. An algorithm for predicting cluster assignments with the
``ward`` objective function has been developed and implemented (gh-874).
Improvements
~~~~~~~~~~~~
- Remove a unicode character from ``ktica.py`` (gh-833)
- ``msmbuilder.decomposition.KernelTICA`` now includes all parameters in its
``__init__``, making it compatible with Osprey (gh-823).
- ``msmbuilder.tpt`` methods can now handle ``BayesianMarkovStateModels`` as
input. Please note that we still do not recommend using this module with
``BootStrapMarkovStateModel``.