[SOLVED] Error using np.arange() in t_span with solve_ivp error in Scipy 1.8.0 but not 1.5.0

Issue

For the following input

neuron_dict = {'param_set': sb.morris_lecar_defaults(V_3 = 11.96), 'time_range': (0, 10000, 0.0001), 'initial_cond': (-3.06560496e+01,  7.33832272e-03,  8.35251563e-01), 'stretch': 4.2, 'track_event': sb.voltage_passes_threshold ,'location': np.array([20,0,100])}

sb.ivp_solver(sb.morris_lecar, time_range = neuron_dict['time_range'], initial_cond = neuron_dict['initial_cond'], params = neuron_dict['param_set'], track_event = neuron_dict['track_event'])

def ivp_solver(system_of_equations: callable,  time_range: tuple, initial_cond: tuple,params: callable = morris_lecar_defaults(), track_event: callable = voltage_passes_threshold,  numerical_method = 'BDF', rtol = 1e-8) -> object:
    track_event.direction = 1
    sol = solve_ivp(system_of_equations, time_range, initial_cond, args=(params,), events= track_event, t_eval= np.arange(time_range[0], time_range[1], time_range[2]), method = numerical_method, rtol = rtol)
    return sol

solve_ivp fails with the following output for Scipy version 1.8.0 with traceback:

Traceback (most recent call last):
  File "...MEA_foward_model.py", line 438, in <module>
    main()
  File "...MEA_foward_model.py", line 430, in main
    near_synchronous_dual_bursting_example()
  File "...MEA_foward_model.py", line 377, in near_synchronous_dual_bursting_example
    ts, voltages, currents, time_events, y_events = integrate_neurons(neurons_list)
  File "...MEA_foward_model.py", line 185, in integrate_neurons
    sol = sb.ivp_solver(sb.morris_lecar, time_range = neuron_dict['time_range'], initial_cond = neuron_dict['initial_cond'], params = neuron_dict['param_set'], track_event = neuron_dict['track_event'])
  File "...\Square_bursting_oscillations.py", line 106, in ivp_solver
    sol = solve_ivp(system_of_equations, time_range, initial_cond, args=(params,), events= track_event, t_eval= np.arange(time_range[0], time_range[1], time_range[2]), method = numerical_method, rtol = rtol)
  File "C:\Anaconda\envs\test\lib\site-packages\scipy\integrate\_ivp\ivp.py", line 512, in solve_ivp
    t0, tf = map(float, t_span)
ValueError: too many values to unpack (expected 2)

but in Scipy version 1.5.0 (my base interpreter) it runs without issue. Looking at the line highlighted in the traceback in ivp.py:
Scipy 1.8.0: t0, tf = map(float, t_span) vs Scipy 1.5.0: t0, tf = float(t_span[0]), float(t_span[1])

not sure if this has any bearing on the reason why it failed but it is odd that Scipy 1.8.0 doesn’t accept the same input. I would like to use np.arange(start, finish, interval) for my integration, is there any reason why this is failing?

Solution

According to the docs

t_span
2-tuple of floats
Interval of integration (t0, tf). The solver starts with t=t0 and 
   integrates until it reaches t=tf.

For a 2 element tuple, these are the same:

t0, tf = map(float, t_span)
t0, tf = float(t_span[0]), float(t_span[1])

But the first raises this error when t_span is longer than 2. The second just ignores the additional values. It’s the t0,tf=... unpacking that enforces the 2-element requirement.

Maybe you want to give t_eval the longer arange, and t_span just the end points.

Answered By – hpaulj

Answer Checked By – Mildred Charles (BugsFixing Admin)

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