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pure optlang for user commits
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uri.akavia committed Jun 29, 2022
1 parent 5e30e94 commit 9c42d8c
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Showing 5 changed files with 375 additions and 786 deletions.
1 change: 0 additions & 1 deletion src/cobra/core/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,3 @@
from cobra.core.group import Group
from cobra.core.solution import Solution, get_solution
from cobra.core.species import Species
from cobra.core.udconstraints import ConstraintComponent, UserDefinedConstraint
140 changes: 46 additions & 94 deletions src/cobra/core/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,12 @@
import logging
from copy import copy, deepcopy
from functools import partial
from typing import List
from warnings import warn

import optlang
from optlang import Constraint, Variable
from optlang.container import Container
from optlang.symbolics import Basic, Zero

from cobra.core.configuration import Configuration
Expand All @@ -17,7 +20,6 @@
from cobra.core.object import Object
from cobra.core.reaction import Reaction
from cobra.core.solution import get_solution
from cobra.core.udconstraints import UserDefinedConstraint
from cobra.medium import find_boundary_types, find_external_compartment, sbo_terms
from cobra.util.context import HistoryManager, get_context, resettable
from cobra.util.solver import (
Expand Down Expand Up @@ -100,7 +102,7 @@ def __init__(self, id_or_model=None, name=None):
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
self.groups = DictList() # A list of cobra.Groups
self.user_defined_const = DictList() # A list of UserDefinedConstraints
self.user_defined_const = Container() # A list of UserDefinedConstraints
self._const_ids = set()
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
Expand Down Expand Up @@ -409,29 +411,7 @@ def copy(self):
new_objects.append(new_object)
new_group.add_members(new_objects)

# new.user_defined_const = deepcopy(self.user_defined_const)

new.user_defined_const = DictList()
do_not_copy_by_ref = {"_model", "_constraint_comps", "_annotation"}
for const in self.user_defined_const:
new_user_defined_const = const.__class__()

for attr, value in const.__dict__.items():
if attr not in do_not_copy_by_ref:
new_user_defined_const.__dict__[attr] = copy(value)
new_user_defined_const._model = new
new_user_defined_const.annotation = deepcopy(const.annotation)

do_not_copy_by_ref = {"_annotation"}
for const_comp in const.constraint_comps:
new_const_comp = const_comp.__class__(variable=const_comp.variable)
for attr, value in const_comp.__dict__.items():
if attr not in do_not_copy_by_ref:
new_const_comp.__dict__[attr] = copy(value)
new_const_comp.annotation = deepcopy(const_comp.annotation)
new_user_defined_const.add_constraint_comps([new_const_comp])

new.user_defined_const.append(new_user_defined_const)
new.user_defined_const = deepcopy(self.user_defined_const)

try:
new._solver = deepcopy(self.solver)
Expand Down Expand Up @@ -900,7 +880,7 @@ def get_associated_groups(self, element):
# check whether the element is associated with the model
return [g for g in self.groups if element in g.members]

def add_user_defined_constraints(self, constraints: list) -> None:
def add_user_defined_constraints(self, constraints: List[Constraint]) -> None:
"""Adds User defined constraints (FBC V3) to the model
Parameters
Expand All @@ -909,95 +889,67 @@ def add_user_defined_constraints(self, constraints: list) -> None:
a list of UserDefinedConstraints
"""

if isinstance(constraints, Constraint):
logger.warning(
f"The constraints passed must be inside a list: {constraints}")
constraints = [constraints]
if not isinstance(constraints, list):
# if single UserDefinedConstraints, convert to a list
if isinstance(constraints, UserDefinedConstraint):
warn(f"The constraints passed must be inside a list: {constraints}")
constraints = [constraints]
else:
raise TypeError(
f"The constraints passed must be inside a list: {constraints}"
)
# if single Constraint, convert to a list
raise TypeError(
f"The constraints passed must be inside a list: {constraints}"
)

list_of_var_cons = []
for constraint in constraints:
if not isinstance(constraint, UserDefinedConstraint):
constraint: "Constraint"
if not isinstance(constraint, Constraint):
raise TypeError(
f"The user defined constraints passed must be of "
f"type 'UserDefinedConstraints': {constraint}"
f"type 'Constraints': {constraint}"
)

if constraint.lower_bound is None or constraint.upper_bound is None:
raise ValueError(f"Bounds must be set for the constraint: {constraint}")
variable_substituions = dict()
for variable in constraint.variables:
if self.variables.get(variable.name, None):
variable_substituions[variable] = self.variables.get(variable.name)
if variable.name in self.reactions:
variable_substituions[variable] = self.reactions.get_by_id(variable.name).flux_expression
constraint._expression = constraint.expression.xreplace(variable_substituions)

if constraint.id is None or constraint.id == "":
constraint.id = "$_internal_const_id" + str(len(self._const_ids))
self._const_ids.add(constraint.id)
constraint._model = self
cons_exp = 0 # an expression involving variables
list_of_var_cons = []
list_of_var_cons.append(constraint)
self.user_defined_const.has_key(constraint.name) or self.user_defined_const.append(constraint)
self.add_cons_vars(list_of_var_cons)

for item in constraint.constraint_comps:

# set the exponent of variable/flux
if item.variable_type == "linear":
var_pow = 1
elif item.variable_type == "quadratic":
var_pow = 2
else:
raise ValueError(f"Unexpected variable type set for item: {item}")

# checks if the reference variable is a rxn flux
# or variable
if item.variable in self.reactions:
rxn = self.reactions.get_by_id(item.variable)
var_to_add = rxn.flux_expression
else:
var_to_add = self.problem.Variable(item.variable)
if var_to_add not in self.variables:
list_of_var_cons.append(var_to_add)

# add the variable/flux to the constraint expression
cons_exp += item.coefficient * pow(var_to_add, var_pow)

# make the constraint using expression and bounds
new_constraint = self.problem.Constraint(
cons_exp,
name=constraint.id,
lb=constraint.lower_bound,
ub=constraint.upper_bound,
)

list_of_var_cons.append(new_constraint)
self.user_defined_const.append(constraint)
self.add_cons_vars(list_of_var_cons)

def remove_user_defined_constraints(self, constraints: list) -> None:
def remove_user_defined_constraints(self, constraints: List[Constraint]) -> None:
"""Remove the constraints from the model
Parameters
----------
constraints: list
a list of UserDefinedConstraints
"""
if isinstance(constraints, Constraint):
logger.warning(
f"The constraints passed must be inside a list: {constraints}")
constraints = [constraints]
if not isinstance(constraints, list):
# if single UserDefinedConstraints, convert to a list
if isinstance(constraints, UserDefinedConstraint):
warn(f"The constraints passed must be inside a list: {constraints}")
constraints = [constraints]
else:
raise TypeError(
f"The constraints passed must be inside a list: {constraints}"
)
# if single Constraint, convert to a list
raise TypeError(
f"The constraints passed must be inside a list: {constraints}"
)

cons_to_remove = []
for constraint in constraints:
if not isinstance(constraint, UserDefinedConstraint):
constraint: "Constraint"
if not isinstance(constraint, Constraint):
raise TypeError(
"The user defined constraints passed must be of "
"type 'UserDefinedConstraints': {constraint}"
f"The user defined constraints passed must be of "
f"type 'Constraint': {constraint}"
)
self._const_ids.remove(constraint.id)
cons_to_remove = self.constraints[constraint.id]
self.remove_cons_vars(cons_to_remove)
self._const_ids.remove(constraint.name)
cons_to_remove = self.constraints[constraint.name]
self.user_defined_const.__delitem__(constraint.name)
self.remove_cons_vars(cons_to_remove)

def add_cons_vars(self, what, **kwargs):
"""Add constraints and variables to the model's mathematical problem.
Expand Down
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