v0.7.19

• fix get_initial_state with joined nodes (#48)

Restrictions in variables' names

• Remove restriction in the variables' name preventing them to contain boolean operators.
• Introduction of a list of reserved names, which can't be used (True, False, And, Or, Xor, Not, Node)
• Fix bug in plotting entropy

Fixing bug in parsing initial states

Fixed a bug in the parser for initial states, where a formula was refused if it contained spaces.

Added plotting options

• Added an optional nil_label to replace in piechart, PCA chart
• Added an argument to PCA plot to highlight a model
• Fix arrow and text size
• Added option to label PCA comparison
• Fixing comparison colors
• Saving the PCA figure as self._pcafig
• Saving the 3D figure as self._3dfig

Bugfixes

• Restore a cache of plotted figures
• Fix the figsize argument for 3D plotting
• Fix the state filtering
• Adding dtype for pandas Series (planned change in pandas default behaviour)

Ensemble features and bugfixes

• Fixed ensemble simulation copy()
• set_models_path now also work with zipped ensembles
• legend can be deactivated on piecharts
• PCA model comparison also work on state distributions
• PCA methods now allow a matplotlib axes as parameter
• PCA methods allow a cutoff_arrows to hide small arrows.
• Added a 3D plotting method for model distributions

Ensemble: add support for zipfile as input

v0.7.13

Tagging v0.7.13

Ensemble simulation improvements

• Allowing per-model mutations
• Improvements in plotting
• Filters now also work with states
• Bugfixes

Fixing two bugs in the parser

Two bugs in the parser that Gautier found :

• Refstate should allow -1 values (which ignores it)
• A node can have non-defined rates. In this case, default rates are used

First version of simulation through C library

Added a first version of the MaBoSS C library interface.
For classic simulation, and upmaboss simulations, setting cmaboss=True in the run() command will use the C library.

Also added a option to run through a optimized engine, which only returns the probability of the last states. For classic and upmaboss simulations, setting only_final_state=True in the run() command will use this new engine.