Update network utilities and input handling - New functionality

[ftavella]

In this PR:

• Consider edge cases on network comparison (is_same_network()) to speed up calculation
• Implement a new function (count_inputs_by_coherence()) to count the number of coherent and incoherent inputs in a network
• Functions to classify the coherence of single-edge additions to negative-feedback-only networks
  • is_negative_feedback_network()
  • calculate_node_coherence()
  • calculate_loop_length_and_type()
  • classify_single_addition()
• Function to convert connectivity string to matrix (connectivity_string_to_matrix())