MSMExplorer 1.1.0

We're pleased to announce the release of MSMExplorer v1.1.0. This
includes a number of new plots and minor improvements.

New Features

- Added a new function ``plot_stackdist`` that plots stacked distributions
  (a.k.a joy plots) of data (#102).

- 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).

- Added a new function ``plot_trace2d`` that plots the time evolution of a 2D numpy array
  using a colorbar to map the time (#108).

- Added a new function ``plot_decomp_grid`` that projects a 1D decomposition
onto a 2D grid (#115).

Improvements

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

• Add plot_implied_timescales example to the Fs-Peptide-Example.ipynb notebook. Also added some minor
  clarifications and explanations (#107).

MSMExplorer 1.0.0

We're pleased to announce the release of MSMExplorer v1.0.0. The focus of this
release are documentation improvements and minor bug fixes.

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).

MSMExplorer 0.3

We're pleased to announce the release of MSMExplorer v0.3.0. The focus of this
release are API improvements and minor bug fixes.

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).

MSMExplorer 0.2

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).

MSMExplorer 0.1

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