[BUG] Raise ContainerAlreadyContains when running optimizations

[thuwilliamwyx]

Is there an existing issue for this?

• I have searched the existing issues

Problem description

我在尝试测试我的模型，但我发现当我在一个ipynb中多次优化时，从第二个开始就会提示ContainerAlreadyContains: Container '<optlang.container.Container object at 0x000002286E0D5DC0>' already contains an object with name 'bio1'.只有重启整个ipynb才可以。

Code sample

Code run:

import cobra
import sys
sys.path.append(r'./script/')


ecModel_file="./model/eciLC858_v3.0.json"
model = cobra.io.json.load_json_model(ecModel_file)
cobra.flux_analysis.pfba(model)

Traceback:

---------------------------------------------------------------------------
ContainerAlreadyContains                  Traceback (most recent call last)
Cell In[2], [line 8](vscode-notebook-cell:?execution_count=2&line=8)
      [6](vscode-notebook-cell:?execution_count=2&line=6) ecModel_file="./model/eciLC858_v3.0.json"
      [7](vscode-notebook-cell:?execution_count=2&line=7) model = cobra.io.json.load_json_model(ecModel_file)
----> [8](vscode-notebook-cell:?execution_count=2&line=8) cobra.flux_analysis.pfba(model)

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\cobra\flux_analysis\parsimonious.py:70, in pfba(model, fraction_of_optimum, objective, reactions)
     [68](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/flux_analysis/parsimonious.py:68)     add_pfba(m, objective=objective, fraction_of_optimum=fraction_of_optimum)
     [69](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/flux_analysis/parsimonious.py:69)     m.slim_optimize(error_value=None)
---> [70](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/flux_analysis/parsimonious.py:70)     solution = get_solution(m, reactions=reactions)
     [71](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/flux_analysis/parsimonious.py:71) return solution

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\cobra\core\model.py:1246, in Model.__exit__(self, type, value, traceback)
   [1244](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/core/model.py:1244) """Pop the top context manager and trigger the undo functions"""
   [1245](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/core/model.py:1245) context = self._contexts.pop()
-> [1246](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/core/model.py:1246) context.reset()

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\cobra\util\context.py:42, in HistoryManager.reset(self)
     [40](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/util/context.py:40) while self._history:
     [41](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/util/context.py:41)     entry = self._history.pop()
---> [42](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/util/context.py:42)     entry()

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\cobra\util\solver.py:204, in set_objective.<locals>.reset()
    [203](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/util/solver.py:203) def reset():
--> [204](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/util/solver.py:204)     model.solver.objective = reverse_value
    [205](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/cobra/util/solver.py:205)     model.solver.objective.direction = reverse_value.direction

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\optlang\glpk_interface.py:623, in Model.objective(self, value)
    [621](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:621)         if variable._index is not None:
    [622](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:622)             glp_set_obj_coef(self.problem, variable._index, 0.)
--> [623](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:623) super(Model, self.__class__).objective.fset(self, value)
    [624](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:624) self.update()
    [626](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:626) offset, coef_dict, _ = parse_optimization_expression(value, linear=True)

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\optlang\interface.py:1194, in Model.objective(self, value)
   [1192](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1192)     if isinstance(atom, Variable) and (atom.problem is None or atom.problem != self):
   [1193](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1193)         self._pending_modifications.add_var.append(atom)
-> [1194](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1194) self.update()
   [1195](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1195) if self._objective is not None:
   [1196](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1196)     self._objective.problem = None

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\optlang\interface.py:1422, in Model.update(self, callback)
   [1420](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1420) add_var = self._pending_modifications.add_var
   [1421](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1421) if len(add_var) > 0:
-> [1422](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1422)     self._add_variables(add_var)
   [1423](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1423)     self._pending_modifications.add_var = []
   [1424](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1424) callback()

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\optlang\glpk_interface.py:732, in Model._add_variables(self, variables)
    [730](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:730)     self._glpk_set_col_bounds(variable)
    [731](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:731)     glp_set_col_kind(self.problem, variable._index, _VTYPE_TO_GLPK_VTYPE[variable.type])
--> [732](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/glpk_interface.py:732) super(Model, self)._add_variables(variables)

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\optlang\interface.py:1491, in Model._add_variables(self, variables)
   [1489](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1489) def _add_variables(self, variables):
   [1490](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1490)     for variable in variables:
-> [1491](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1491)         self._variables.append(variable)
   [1492](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1492)         self._variables_to_constraints_mapping[variable.name] = set([])
   [1493](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/interface.py:1493)         variable.problem = self

File c:\ProgramData\Anaconda3\envs\ECMpy2\lib\site-packages\optlang\container.py:172, in Container.append(self, value)
    [170](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/container.py:170) name = value.name
    [171](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/container.py:171) if name in self._dict:
--> [172](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/container.py:172)     raise ContainerAlreadyContains("Container '%s' already contains an object with name '%s'." % (self, value.name))
    [173](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/container.py:173) self._indices[name] = len(self)
    [174](file:///C:/ProgramData/Anaconda3/envs/ECMpy2/lib/site-packages/optlang/container.py:174) self._object_list.append(value)

ContainerAlreadyContains: Container '<optlang.container.Container object at 0x0000021F93DA5CA0>' already contains an object with name 'bio1'.

Environment

Anything else?

No response

[cdiener]

Hi, thanks for the report. Can you fill out the rest of the issue template, espcially the environment part so we can check which versions that affects?

Please paste the output of running depinfo --markdown cobra in your environment between the details tags below.

[cdiener]

Also do you have an example with a publically available model? I could not find the one from your bug report to reproduce (eciLC858_v3.0).