Msmexplorer

-----------------------

New Features
~~~~~~~~~~~~

- Added a new function ``plot_implied_timescales`` that accepts a list of msm objects
calculated at different lag times. Returns an implied timescales plot (90).

- ``plot_free_energy`` now accepts a ``return_data`` flag that will return
the data used for the free energy plot(78).

Improvements
~~~~~~~~~~~~

- ``vmin`` in ``plot_free_energy`` is now set to ``1E-12`` unless otherwise specialized.

-----------------------

New Features
~~~~~~~~~~~~

- ``plot_free_energy`` now accepts two extra arguments, ``cbar`` and
``cbar_kwargs`` to add a colorbar and control its aesthetics (73).


Improvements
~~~~~~~~~~~~

- The ``shade`` option now works for ``plot_free_energy`` in the 1D case (76).
- Fixed an issue where adding cluster centers would break the visualization
if ``ndim`` > 2 (70).

-------------------------

API Changes
~~~~~~~~~~~

- ``side_ax`` in ``plot_trace`` is now optional if ``ax`` is provided (54)
- ``legend`` in ``plot_trace`` now defaults to True if ``label`` is provided,
otherwise false. It previously always defaulted to True (54).
- ``plot_voronoi`` accepts a new parameter ``alpha`` (55).
- ``plot_voronoi`` will not set axis limits if you specify ``ax`` (55).


Improvements
~~~~~~~~~~~~

- ``plot_msm_network`` and ``plot_tpaths`` can now handle lists as
``node_color`` and ``node_size`` (61).
- ``extract_palette`` can now handle rgb tuples and lists (61).

---------------------------

We're pleased to announce the release of MSMExplorer v0.2.0. The focus of this
release is improving plotting reproducibility and utilities. There is also a
major bugfix for ``plot_chord`` and ``plot_free_energy``. We encourage all
users to update to v0.2.0.

API Changes
~~~~~~~~~~~

- ``darkslategrey`` has been renamed to ``carbon`` (41).
- ``plot_free_energy`` now supports a ``random_state`` option (40)

New Features
~~~~~~~~~~~~

- ``example_datasets`` has been added. This allows example datasets to be
pulled from the ``msmb_data`` package (41).
- ``make_colormap`` has been added in ``msmexplorer.utils``. It creates a
linear colormap from a color palette (40).
- ``msme_colors`` has been added in ``msmexplorer.utils``. It allows any
non-native plotting functions to handle MSMExplorer color strings (40).

Improvements
~~~~~~~~~~~~

- Test coverage is greatly improved (43)
- ``plot_free_energy`` now produces correct 1-D free energy plots (43).
- ``extract_palette`` is now more robust (40).
- Improve example reproducibility (40)
- Fix path vertices problem in ``plot_chord`` (38).

------------------

This is the current development version of MSMExplorer

API Changes
~~~~~~~~~~~

New Features
~~~~~~~~~~~~

Improvements
~~~~~~~~~~~~

------------------------

This is the first stable version of MSMExplorer

New Features
~~~~~~~~~~~~

- Clustering plots: ``plot_voronoi``
- MSM plots: ``plot_pop_resids``, ``plot_msm_network``, ``plot_timescales``
- Projection plots: ``plot_free_energy``, ``plot_histogram``
- TPT plots: ``plot_tpaths``
- Misc. plots: ``plot_chord``, ``plot_trace``


.. _changelog:

Changelog
=========