Solve Issue 31 - Random seed and output customization

[ftavella]

This PR solves issue #31 by implementing two major changes:

• Parameter sets can be generated in a reproducible manner via a random_seed parameter added to generate_parameter_sets (and the functions that call it)
• The output of find_pin_oscillations and find_grn_oscillations can now be customized via hyperparameters. All the available outputs are encoded in the DEFAULT_SIMULATION_OUTPUT variable

  DEFAULT_SIMULATION_OUTPUT = Dict(
  "model" => true,
  "hyperparameters" => true,
  "parameter_sets" => Dict(
      "oscillatory" => true,
      "non_oscillatory" => true
  ),
  "equilibration_result" => Dict(
      "parameter_index" => true,
      "equilibration_time" => true,
      "final_velocity" => true,
      "final_state" => true,
      "frequency" => true,
      "is_steady_state" => true
  ),
  "simulation_result" => Dict(
      "parameter_index" => true,
      "simulation_time" => true,
      "final_state" => true,
      "frequency" => true,
      "fft_power" => true,
      "amplitude" => true,
      "peak_variation" => true,
      "trough_variation" => true,
      "is_oscillatory" => true
  )
  )

  By specifying a dictionary with some of all of these keys one can customize the output. For example. If we simply want the simulation result (with some of its components), we can do the following:

  
  samples = 200
  connectivity_T0 = [0 0 -1;-1 0 0;0 -1 0]
  hyperparameters = DEFAULT_PIN_HYPERPARAMETERS
  sim_output_config = Dict(
  "simulation_result" => Dict(
      "parameter_index" => true,
      "final_state" => true,
      "frequency" => true,
      "amplitude" => true,
      "is_oscillatory" => true
  )
  )

hyperparameters["simulation_output"] = sim_output_config result = find_pin_oscillations(connectivity_T0, samples; hyperparameters=hyperparameters)