Build model update

[BryanRumsey]

No description provided.

[mdip226]

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/CLE_examples_convergence.ipynb)
unused:
import numpy
parameter_values=None

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/Events.ipynb)
unused:
parameter_values=None

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/KineticModelForStyrenePolymerization.ipynb)
TimeSpan class not defined throws error

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/Live Output with Python Solvers.ipynb)
unused:
parameter_values=None
typo:
"Resume Resume"

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/Model_Pre_Compilation.ipynb)
why perf counter say Time to complete 20 runs using pre compiled model and solver: 0.1910390830016695
when it took 10.3 sec
non-precompiled took 3m 19s and says 199.717

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/Negative_Timespan_Example.ipynb)
typos:
'we must swift'

---

Process Results

---

To visualize the results with the infection event at t=0 we must swift the time sub array in the results by the added simulation time.

Simulate Infection with past population data

To model population data from prior to the infection we need to modify the infect event trigger by the ent time of the add period. We do this using the variable solver to modify the infect_start parameter.

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/Run GillesPy2 Simulations in Parallel.ipynb)
dask import, maybe add a comment about installation?

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/SBML_Import_Test.ipynb)
libsbml required import?

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/hybrid_continuous_species.ipynb)
(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/hybrid_switching_example.ipynb)
match case in filename

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/AdvancedFeatures/hybrid_switching_example.ipynb)
typo: threshold

---

Run the Simulations

---

The hybrid switching condition is based on a coefficient of variance for each species. The error threshhold for this condition can be user modified by instantiating the solver, and calling the run function from it, rather than the solver.

The default value is 0.03 and is a threshold to the coefficient of variance for each species at the selected forward step (t + tau).

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/DataVisualization.ipynb)
typo: add ()

---

Run the Simulations

---

model.run creates a Results object with a list of Trajectory objects.

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/Models/ExtraModels/Dimerization.ipynb)
unused named argument
cell 6 "run" can be model.run()

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/Models/ExtraModels/Opioid_Model.ipynb)
typo: opoid to opioid

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/Models/ExtraModels/Oregonator.ipynb)
oregonator drop off at t=3.5?

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/Models/ExtraModels/SpeedComparisons/hybrid_switching_decay_model_performance.ipynb)
unused math, random
match case in filename
unused named argument

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/Models/ExtraModels/Brusselator.ipynb)
unused named argument (i think in all of the ExtraModels/StartingModels, and the ones in the examples dir)

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/examples/StartingModels/VilarOscillator/VilarOscillator.py)
maybe put this in another directory?, it's lonely in this one

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/gillespy2/solvers/cpp/example_models.py)
can't tell if this is used anywhere

(https://github.com/StochSS/GillesPy2/blob/bb8eabc583a570bbd4097705d8e4ea9ae453ed3d/test/TestingBattery.ipynb)
invalid syntax in cell 20 with the url
some unused model imports
that status bar is awesome

[mdip226]

The tests are still running but I might have to pause them for now and come back to them

[mdip226]

./test_python_solver_perf.py::TestPythonSolverPerf::test_python_solver_perf Failed with Error: A model is required to run the simulation.
  File "/usr/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
    yield
  File "/usr/lib/python3.8/unittest/case.py", line 676, in run
    self._callTestMethod(testMethod)
  File "/usr/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
    method()
  File "/home/mdip/Projects/GillesPy2/test/test_python_solver_perf.py", line 57, in test_python_solver_perf
    perf_data = python_profiler.run_profiler(model, solver)
  File "/home/mdip/Projects/GillesPy2/test/profiling/python_profiler.py", line 43, in run_profiler
    solver.run(number_of_trajectories=trajectories, t=timesteps, timeout=0)
  File "/home/mdip/Projects/GillesPy2/gillespy2/solvers/numpy/ssa_solver.py", line 90, in run
    self = NumPySSASolver(model=model)
  File "/home/mdip/Projects/GillesPy2/gillespy2/solvers/numpy/ssa_solver.py", line 38, in __init__
    raise SimulationError("A model is required to run the simulation.")
gillespy2.core.gillespyError.SimulationError: A model is required to run the simulation.

[mdip226]

one more:

./test_StochML.py::TestStochML::test_StochML_from_and_to_model Failed with Error: could not convert string to float: 'None'
  File "/usr/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
    yield
  File "/usr/lib/python3.8/unittest/case.py", line 676, in run
    self._callTestMethod(testMethod)
  File "/usr/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
    method()
  File "/home/mdip/Projects/GillesPy2/test/test_StochML.py", line 30, in test_StochML_from_and_to_model
    stochml_model = stochml.to_model('model')
  File "/home/mdip/Projects/GillesPy2/gillespy2/core/model.py", line 1331, in to_model
    model.volume = float(expr)
ValueError: could not convert string to float: 'None'

[mdip226]

i think that's it!