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GeomScale / dingo

A python library for metabolic networks sampling and analysis
GNU Lesser General Public License v3.0
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`generate_steady_states` fails when you edit a model's optimal percentage twice #83

Open hariszaf opened 7 months ago

hariszaf commented 7 months ago 
model = dingo.MetabolicNetwork.from_json("ext_data/e_coli_core.json")

model.set_opt_percentage(90)
sampler = dingo.PolytopeSampler(model)
sampler.generate_steady_states()

model.set_opt_percentage(20)
sampler = dingo.PolytopeSampler(model)
sampler.generate_steady_states()

would return:

phase 1: number of correlated samples = 500, effective sample size = 3, ratio of the maximum singilar value over the minimum singular value = 4548.22
phase 2: number of correlated samples = 500, effective sample size = 123, ratio of the maximum singilar value over the minimum singular value = 3.07681
phase 3: number of correlated samples = 500, effective sample size = 148, ratio of the maximum singilar value over the minimum singular value = 2.8596
phase 4: number of correlated samples = 1900, effective sample size = 754
[5]total ess 1028: number of correlated samples = 3400

[5]maximum marginal PSRF: 1.03027

UnboundLocalError                         Traceback (most recent call last)
[/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/dev.ipynb](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/dev.ipynb) Cell 26 line 8
      [6](vscode-notebook-cell:/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/dev.ipynb#X36sZmlsZQ%3D%3D?line=5) model.set_opt_percentage(20)
      [7](vscode-notebook-cell:/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/dev.ipynb#X36sZmlsZQ%3D%3D?line=6) sampler = dingo.PolytopeSampler(model)
----> [8](vscode-notebook-cell:/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/dev.ipynb#X36sZmlsZQ%3D%3D?line=7) sampler.generate_steady_states()

File [~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:161](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:161), in PolytopeSampler.generate_steady_states(self, ess, psrf, parallel_mmcs, num_threads)
    [149](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:149) def generate_steady_states(
    [150](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:150)     self, ess=1000, psrf=False, parallel_mmcs=False, num_threads=1
    [151](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:151) ):
    [152](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:152)     """A member function to sample steady states.
    [153](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:153) 
    [154](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:154)     Keyword arguments:
   (...)
    [158](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:158)     num_threads -- the number of threads to use for parallel mmcs
    [159](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:159)     """
--> [161](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:161)     self.get_polytope()
    [163](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:163)     P = HPolytope(self._A, self._b)
    [165](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:165)     if self._parameters["fast_computations"]:

File [~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:82](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:82), in PolytopeSampler.get_polytope(self)
     [66](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:66) """A member function to derive the corresponding full dimensional polytope
     [67](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:67) and a isometric linear transformation that maps the latter to the initial space.
     [68](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:68) """
     [70](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:70) if (
     [71](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:71)     self._A == []
     [72](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:72)     or self._b == []
   (...)
     [76](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:76)     or self._T_shift == []
     [77](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:77) ):
     [79](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:79)     (
     [80](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:80)         max_biomass_flux_vector,
     [81](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:81)         max_biomass_objective,
---> [82](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:82)     ) = self._metabolic_network.fba()
     [84](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:84)     if (
     [85](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:85)         self._parameters["fast_computations"]
     [86](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:86)         and self._parameters["remove_redundant_facets"]
     [87](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:87)     ):
     [89](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:89)         A, b, Aeq, beq = fast_remove_redundant_facets(
     [90](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:90)             self._metabolic_network.lb,
     [91](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:91)             self._metabolic_network.ub,
   (...)
     [94](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:94)             self._parameters["opt_percentage"],
     [95](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/PolytopeSampler.py:95)         )

File [~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:117](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:117), in MetabolicNetwork.fba(self)
    [114](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:114) """A member function to apply the FBA method on the metabolic network."""
    [116](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:116) if self._parameters["fast_computations"]:
--> [117](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:117)     return fast_fba(self._lb, self._ub, self._S, self._biomass_function)
    [118](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:118) else:
    [119](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/MetabolicNetwork.py:119)     return slow_fba(self._lb, self._ub, self._S, self._biomass_function)

File [~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:112](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:112), in fast_fba(lb, ub, S, c)
    [109](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:109)     v = model.getVars()
    [111](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:111) for i in range(n):
--> [112](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:112)     optimum_sol.append(v[i].x)
    [114](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:114) optimum_sol = np.asarray(optimum_sol)
    [116](https://file+.vscode-resource.vscode-cdn.net/home/luna.kuleuven.be/u0156635/github_repos/GeomScale/dingo/~/github_repos/GeomScale/dingo/dingo/gurobi_based_implementations.py:116) return optimum_sol, optimum_value

UnboundLocalError: local variable 'v' referenced before assignment

It seems the error is related to the https://github.com/GeomScale/dingo/blob/aaae4ae63f432da45eb0f4363a92767ba537a074/dingo/gurobi_based_implementations.py#L109 and the status == GRB.OPTIMAL that is not the case in the second edit. where the status is INF_OR_UNBD for some reason (https://www.gurobi.com/documentation/current/refman/optimization_status_codes.html)