v0.1.0 prepared for release.

[blakeaw]

Changed

• Starting semantic versioning of the model code at v0.1.0.
• Made the parm.util.pre_equilibration function private by renaming to parm.util._pre_equilibration.
• The main PARM model parm.parm is now imported in the package __init__.py so that it can be imported like from parm import model.
• Moved the pysb dependency in setup.py to the install_requires list.

Added

• Additional sections (Install, License, etc.) and information in the README, as well as shields/badges towards the top of the README.
• New wrapper function for pre-equilibration in the util module, parm.util.pre_equilibrate that calls the _pre_equilibration function but also does addtional steps to automate the process of setting 2AT to zero concentration and adjusting the baseline cytosolic calcium concentration used for the FRET ratio. This function also has a simpler output that contains an updated parameter vector and the initial concentrations that can be directly passed to the run_model function.
• New utility function parm.util.calcium_homeostasis_reverse_rate_coupling that adjusts a parameter vector to account for coupling of the reverse rates of the calcium homeostasis reactions to the forward rates. This function can be used adjust the parameters when sampling values of the reverse rate parameters for those reactions: for example, during model training.
• New default parameter vector, default_param_values created in the package __init__.py for the main parm.parm model which can be imported like from parm import default_param_values.
• New dictionary of parameter vector masks for fancy indexing, parameter_masks, created for the main parm.parm model which can imported like from parm import parameter_masks.
• Utility function parm.util.get_parameter_vector that takes a PySB model and returns a vector of the parameter values.
• Utiltiy function parm.util.get_parameter_mask that takes a PySB model and parameter name and returns a boolean mask to fancy index the corresponding paramter value vector for that particular parameter.
• Utility function parm.util.set_tat_initial_nM that takes a parameter value vector and an initial concentration of 2AT in nM and updates the parameter vector with the desired 2AT concentration.

Fixed

• Converted the extras_require argument in the setup.py to be dictionary instead of a list, now with just the optional Cython dependency. Note that the pysb dependency was moved into the install_requires list.
• Commented out the long_description in setup.py because it was causing error when trying to read the README file.