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v0.8.0: New Variable/Parameter naming system

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@Richert Richert released this 25 Jun 04:29
· 38 commits to master since this release
  • added mapping functionalities that allow to use the pyrates-based names for variables and parameters in the model rather than the auto naming style
  • implemented the changes with the ODESystem.run and ODESystem.extract methods
  • dataframes return by ODESystem.run now contain the pyrates-like variable names in the column header
  • ODESystem.__init__ now takes a couple of new arguments: The "eq_file" is a positional argument that ties an ODESystem instance to a single fortran equation file. "params" and "state_vars" allow to provide the parameter and state variable names that can be used instead of the indexing style of auto.
  • the parameter and state-variable names that can be provided to the ODESystem.__init__ method can be directly obtained from the CircuitTemplate.get_run_func that is also used by the ODESystem.from_yaml method.