get AssertionError when run RunModel.py

[yihangs]

Hi,

I tried to run python RunModel.py in Python 3.9, with no modification of any file in StrikePy, but got the following AssertionError:

python RunModels.py 


 ---------------------------------------
 >>> STRIKE-GOLDD toolbox for Python <<<
 --------------------------------------- 

 Analyzing the C2M model... 

 >>> The model contains:
2 states:
 [[x1]
 [x2]]
1 outputs:
 [x1]
1 known inputs:
 [u1]
0 unknown inputs:
 []
4 parameters:
 [[x3]
 [x4]
 [x5]
 [x6]]


 >>> Building the observability-identifiability matrix requires at least 5 Lie derivatives
     Calculating derivatives:  1 2 3 4 5
 >>> Observability-Identifiability matrix built with 5 Lie derivatives
     (calculated in 0.19940662384033203 seconds)
 >>> Calculating rank of matrix with size 6x6...
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
File /users/StrikePy/StrikePy/RunModels.py:13
     10 from strike_goldd import strike_goldd
     12 # Without arguments...
---> 13 strike_goldd()
     15 # Passing to it the options of the predefined model HIV...
     16 #strike_goldd('options_HIV')

File /users/StrikePy/StrikePy/strike_goldd.py:406, in strike_goldd(*args=())
    404 tic = time()
    405 rational_onx = rationalize_all_numbers(Matrix(onx))
--> 406 rango = st.generic_rank(Matrix(rational_onx))
        rational_onx = Matrix([
[                                  
...
...
3273 M1, M2, M3 = [M.subs(rnst).evalf(n=p) for p in plist]
   3275 # calculate the coeffs of the charpoly
   3276 # berkowitz-method sorts from highes to lowest -> reverse the tuples

File /users/miniconda3/envs/py39/lib/python3.9/site-packages/symbtools/core.py:3154, in rnd_number_subs_tuples(expr=Matrix([
[                                      ...+ u1_d2 + u1_d3*(-x3 - x4 + 2) + u1_d3 + u1_d4]]), seed=68434, rational=True, prime=False, minmax=None, **kwargs={})
   3151     tuples = [(reverse_dict[s], list_of_primes.pop()) for s in atoms_list]
   3153 elif rational:
-> 3154     tuples = [(reverse_dict[s], clean_numbers( rnd()*delta + min_val )) for s in atoms_list]
        atoms_list = [u1, u1_d1, u1_d2, u1_d3, u1_d4, x1, x2, x3, x4, x5, x6]
        reverse_dict = {u1: u1, u1_d1: u1_d1, u1_d2: u1_d2, u1_d3: u1_d3, u1_d4: u1_d4, x1: x1, x2: x2, x3: x3, x4: x4, x5: x5, x6: x6}
        delta = 1
        min_val = 0
   3155 else:
   3156     tuples = [(reverse_dict[s], rnd()*delta + min_val) for s in atoms_list]

File /users/miniconda3/envs/py39/lib/python3.9/site-packages/symbtools/core.py:3154, in <listcomp>(.0=<list_iterator object>)
   3151     tuples = [(reverse_dict[s], list_of_primes.pop()) for s in atoms_list]
   3153 elif rational:
-> 3154     tuples = [(reverse_dict[s], clean_numbers( rnd()*delta + min_val )) for s in atoms_list]
        reverse_dict = {u1: u1, u1_d1: u1_d1, u1_d2: u1_d2, u1_d3: u1_d3, u1_d4: u1_d4, x1: x1, x2: x2, x3: x3, x4: x4, x5: x5, x6: x6}
        delta = 1
        min_val = 0
        s = u1
   3155 else:
   3156     tuples = [(reverse_dict[s], rnd()*delta + min_val) for s in atoms_list]

File /users/miniconda3/envs/py39/lib/python3.9/site-packages/symbtools/core.py:2988, in clean_numbers(expr=0.8213521271023622727369684071163646876811981201...5000000000000000000000000000000000000000000000000, eps=1e-10)
   2986 symb_gen = sp.numbered_symbols('cde', cls = sp.Dummy)
   2987 for f in floats:
-> 2988     rat = sp_fff(f, maxden)
        maxden = 10000000000
        f = 0.8213521271023622727369684071163646876811981201171875000000000000000000000000000000000000000000000000
   2989     rats.append(rat)
   2990     dummy_symbs.append(next(symb_gen))

File /users/miniconda3/envs/py39/lib/python3.9/site-packages/symbtools/core.py:344, in sp_fff(x=0.8213521271023622727369684071163646876811981201...5000000000000000000000000000000000000000000000000, maxden=10000000000)
    342 def sp_fff(x, maxden):
    343     """ sympy_fraction from float"""
--> 344     return sp.Rational(fractionfromfloat(x, maxden))
        sp = <module 'sympy' from '/n/fs/ragr-research/users/yihangs/miniconda3/envs/py39/lib/python3.9/site-packages/sympy/__init__.py'>
        x = 0.8213521271023622727369684071163646876811981201171875000000000000000000000000000000000000000000000000
        maxden = 10000000000

File /users/miniconda3/envs/py39/lib/python3.9/site-packages/symbtools/core.py:338, in fractionfromfloat(x_=0.8213521271023622727369684071163646876811981201...5000000000000000000000000000000000000000000000000, maxden=10000000000)
    330 """
    331 fraction from float
    332 args:
    333 x
    334 maxdenominator (default = 1000)
    335 """
    337 x = float(x_)
--> 338 assert x == x_ # fails intentionally for numpy.complex
        x = 0.8213521271023623
        x_ = 0.8213521271023622727369684071163646876811981201171875000000000000000000000000000000000000000000000000
    339 return Fr.from_float(x).limit_denominator(maxden)

AssertionError: 

Could you help me figure this issue out?

Thanks!

[afvillaverde]

Hi,

Thanks for reporting this issue, we'll have a look at it as soon as possible.

Best,

Alex

[hanicola]

Hi,

I have just encountered the same problem and was wondering whether you have solved the issue?

Best,
Nicola