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.

Nodes probtraj, BNet import, outputs

When computing the node probability trajectories, we would only return a node probability when it was non-zero. Now we uses the defined outputs of the model, ensuring all outputs would be present even if their probability is zero.

I also added a direct maboss.loadBNet(file) function, to load a bnet file as a maboss model directly (without explicitely callling biolqm).

Finally, when selecting output variables, there was no error checking that each variable was indeed a defined node. Now the library will return a failed assert if it is the case.

Allow models up to 1024 nodes

v0.7.8

Added assert to give an error for models with more than 1024 nodes

Fix biolqm dependency

There fix removes biolqm dependency, by loading the model of the ensemble using the bnet parser in minibn.
This also allows to have the formula in the proper, simplified form

Ensemble modelling

• Mostly ensemble modelling code (documentation to come)
• Bugfix for simulation palettes

Model conversion, remote files, stationary distribution, ...

UpPMaBoSS

• Parallel building of stepwise state probability distribution
• Option to filter states, via a list of nodes to include/exclude
• Building of stepwise node probability distribution (with filtering option)
• Method to create of update an external variable
• Now automatically using the number of threads defined in the cfg file to build stepwise probability distributions
• Improved tests

pyMaBoSS

• Model conversion to biolqm and minibn (maboss.to_biolqm(model), maboss.to_minibn(model))
• Support for remote files
• Workdir and Overwrite option now an argument of run() method
• Improved computation of asymptotic probability distribution
• Checking if temporary folder exists before deleting it
• Added a python version of the script MBSS_FormatTable.
• Added support for stationary distributions.
• Added command argument to load, to inform the MaBoSS executable to use for model verification.
• Fix documentation (methods who had disappeared because of classes reorg)
• Tests (probtraj, statdist)

Bugfix: model verification when number of nodes > 64

When loading a model, MaBoSS will be called to verify if it's valid.
For models with more than 64 nodes, specific MaBoSS version needs to be called.
This fix now uses the proper executable when verifying the model validity.

Removing pymaboss bnd check, using MaBoSS. (+others, bugfixes)

Features :

• Adding the option to load multiple cfg files
• Using MaBoSS executable to check formulas validity

Fixes :

• UpPMaBoSS variable parsing fix.
• UpPMaBoSS script update
• Restored overwriting results in UpPMaBoSS
• Treat istate probability as a string, to allow formulas. Remove value checks

New UpdatePopulation class structure

Important changes :

UpdatePopulation now splitted into two classes : UpdatePopulation and UpdatePopulationResults.
Ex :
model = UpdatePopulation(maboss_model, upp_file)
result = model.run()

workdir and overwrite are now parameters of the run() function.

We can also now change the number of step of the UpdatePopulation model easily (before calling run()):
model.setStepNumber(24)

Bug fix : Timestep conversion as a float

Merge pull request #7 from colomoto/fix/time_step

Forcing timestep as a float