Maboss

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)

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.

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

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)

- Added MaBoSS server support
- Added UpdatePopulation support
- Added first draft of Ensemble simulations
- Optimization of results extraction method
- Added a StoredResult class to load saved simulation results
- Added automatic testing and coverage via Travis.org and Coveralls
- Added optional error bars to figures
- Added optional proba cutoff for states & nodes trajectories