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Sync fbapkg/basefbapkg.py from freiburgermsu fork #56

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Sync fbapkg/basefbapkg.py from freiburgermsu fork #56

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30 changes: 10 additions & 20 deletions modelseedpy/fbapkg/basefbapkg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,16 @@
from __future__ import absolute_import

import logging
import re # !!! import is never used
from optlang.symbolics import Zero, add # !!! add is never used
import json as _json # !!! import is never used
import re
from optlang.symbolics import Zero, add
import json as _json
from cobra.core import (
Gene,
Metabolite,
Model,
Reaction,
) # !!! none of these imports are used
)
from modelseedpy.fbapkg.mspackagemanager import MSPackageManager
from modelseedpy.core.msmodelutl import MSModelUtil
from modelseedpy.core.exceptions import FeasibilityError

logger = logging.getLogger(__name__)

Expand All @@ -30,9 +28,9 @@ class BaseFBAPkg:
Base class for FBA packages
"""

def __init__(
self, model, name, variable_types={}, constraint_types={}, reaction_types={}
):
def __init__(self, model, name, variable_types={}, constraint_types={}, reaction_types={}):
# Deferred import to avoid circular dependency
from modelseedpy.core.msmodelutl import MSModelUtil
if isinstance(model, MSModelUtil):
self.model = model.model
self.modelutl = model
Expand All @@ -47,12 +45,7 @@ def __init__(
self.pkgmgr = MSPackageManager.get_pkg_mgr(model, 1)
self.pkgmgr.addpkgobj(self)

self.constraints, self.variables, self.parameters, self.new_reactions = (
{},
{},
{},
{},
)
self.constraints, self.variables, self.parameters, self.new_reactions = {}, {}, {}, {}
self.variable_types = variable_types
self.constraint_types = constraint_types

Expand Down Expand Up @@ -92,9 +85,7 @@ def clear(self):
self.constraints[obj_type] = {}
self.model.remove_cons_vars(cobra_objs)

def build_variable(
self, obj_type, lower_bound, upper_bound, vartype, cobra_obj=None
):
def build_variable(self, obj_type, lower_bound, upper_bound, vartype, cobra_obj=None):
name = None
if self.variable_types[obj_type] == "none":
count = len(self.variables[obj_type])
Expand Down Expand Up @@ -124,8 +115,7 @@ def build_constraint(
if name in self.constraints[obj_type]:
self.model.remove_cons_vars(self.constraints[obj_type][name])
self.constraints[obj_type][name] = self.model.problem.Constraint(
Zero, lb=lower_bound, ub=upper_bound, name=name + "_" + obj_type
)
Zero, lb=lower_bound, ub=upper_bound, name=name + "_" + obj_type)
self.model.add_cons_vars(self.constraints[obj_type][name])
self.model.solver.update()
if len(coef) > 0:
Expand Down
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