def test_save_load_observables_expressions():
buff = io.BytesIO()
tspan = np.linspace(0, 100, 100)
sim = ScipyOdeSimulator(tyson_oscillator.model, tspan).run()
sim.save(buff, include_obs_exprs=True)
sim2 = SimulationResult.load(buff)
assert len(sim2.observables) == len(tspan)
# Tyson oscillator doesn't have expressions
assert_raises(ValueError, lambda: sim2.expressions)
param_values = np.array([p.value for p in model.parameters])
par_set_calibrated = np.copy(param_values)
par_set_calibrated[rates_of_interest_mask] = 10**calibrated_pars
tspan = np.linspace(0, 180, 181)
n_conditions = 5000
max_arrestin = 100
arrestin_initials = np.linspace(0, max_arrestin, n_conditions)
par_clus1 = par_set_calibrated
arrestin_idx = 44
kcat_idx = [36, 37]
repeated_parameter_values = np.tile(par_clus1, (n_conditions, 1))
repeated_parameter_values[:, arrestin_idx] = arrestin_initials
np.save('arrestin_diff_IC_par0.npy', repeated_parameter_values)
tspan_eq = np.linspace(0, 2000, 200)
scipy_solver = ScipyOdeSimulator(model, tspan=tspan_eq)
pars_eq = np.copy(repeated_parameter_values)
pars_eq[:, kcat_idx] = 0
conc_eq = pre_equilibration(scipy_solver, param_values=pars_eq)[1]
sims_final = ScipyOdeSimulator(model, tspan=tspan).run(
param_values=repeated_parameter_values, initials=conc_eq)
sims_final.save('simulations_ic_scipy_181.h5')
arrestin_idx = 44
kcat_idx = [36, 37]
tspan_eq = np.linspace(0, 100, 100)
scipy_solver = ScipyOdeSimulator(model, tspan=tspan_eq)
pars_eq = np.copy(all_par_set_calibrated)
pars_eq[:, kcat_idx] = 0
conc_eq = pre_equilibration(scipy_solver, param_values=pars_eq)[1]
sims_final = ScipyOdeSimulator(model, tspan=tspan).run(param_values=all_par_set_calibrated,
initials=conc_eq)
print(sims_final.dataframe['__s27'])
sims_final.save('simulations_50000_arrestin_scipy_181.h5')
# Simulations without arrestin
jnk3_initial_idxs = [47, 48, 49]
pars_eq_noarrestin = np.copy(all_par_set_calibrated)
all_pars_noarrestin = np.copy(all_par_set_calibrated)
pars_eq_noarrestin[:, arrestin_idx] = 0
all_pars_noarrestin[:, arrestin_idx] = 0
pars_eq_noarrestin[:, jnk3_initial_idxs] = [0.592841488, 0, 0.007158512]
pars_eq_noarrestin[:, kcat_idx] = 0
conc_eq_noarrestin = pre_equilibration(scipy_solver, param_values=pars_eq_noarrestin)[1]
sims_final_noarrestin = ScipyOdeSimulator(model, tspan=tspan).run(param_values=all_pars_noarrestin,
initials=conc_eq_noarrestin)
