Expressions issue

[Princeofthebow]

Hello, I have the following code

#test_model.py
from pysb import *
from pysb.pathfinder import set_path
from pysb.simulator import ScipyOdeSimulator
set_path('bng', 'C:\Program Files\BNG')

Model()
Monomer('A',['a'])
Parameter('Hcoeff',1.0)
Parameter('A0',20)
Observable('A_total', A())
Expression('kf_A', A_total*Hcoeff)

Rule('bindA', A(a=None) + A(a=None) >> A(a=1) % A(a=1), kf_A)
Initial(A(a=None),A0)

simres = ScipyOdeSimulator(model, tspan=[0,20]).run()

but unfortunately I get the following error:

AttributeError: 'str' object has no attribute 'args'

I think the code is correct. May this be a bug?

[jmuhlich]

Could you paste the full stack trace from the exception? Just the final error message is not quite enough to go on. Thanks.

[Princeofthebow]

Sure, so if I omitted it.

Traceback (most recent call last):
  File "test.py", line 17, in <module>
    simres = ScipyOdeSimulator(model, tspan=[0,20]).run()
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\simulator\scipyode.py", line 165, in __init__
    pysb.bng.generate_equations(self._model, self.cleanup, self.verbose)
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\bng.py", line 731, in generate_equations
    lines = iter(generate_network(model, cleanup=cleanup,
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\bng.py", line 672, in generate_network
    bngfile.execute()
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\bng.py", line 443, in execute
    output += self.generator.get_content()
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\generator\bng.py", line 26, in get_content
    self.generate_content()
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\generator\bng.py", line 31, in generate_content
    self.generate_parameters()
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\generator\bng.py", line 42, in generate_parameters
    exprs = self.model.expressions_constant()
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\core.py", line 1976, in expressions_constant
    cset = ComponentSet(e for e in self.expressions
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\core.py", line 2255, in __init__
    for value in iterable:
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\core.py", line 1977, in <genexpr>
    if e.is_constant_expression())
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\pysb\core.py", line 1644, in is_constant_expression
    for a in self.expr.atoms())
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\sympy\core\basic.py", line 523, in atoms
    result = {node for node in nodes if not node.args}
  File "C:\Users\Jpk\AppData\Local\Programs\Python\Python38\lib\site-packages\sympy\core\basic.py", line 523, in <setcomp>
    result = {node for node in nodes if not node.args}
AttributeError: 'str' object has no attribute 'args'

[jmuhlich]

Could you also paste the output of python -m pip freeze? I wonder if there is some dependency (like sympy) that's not up to date.

[jmuhlich]

I should add that your code looks correct and runs OK for me, so the problem is not your own code.

[JamesPino]

I believe this is the same issue as #503 ? Sympy >1.6 breakage.