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Refactoring simulation methods into optimization.py #7

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Merged
jdtibochab merged 6 commits into from
Apr 28, 2025
Merged

Refactoring simulation methods into optimization.py #7

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273005b
Refactoring simulation methods into optimization.py
glucksfall Apr 22, 2025
b6cc25d
Locked scipy version
glucksfall Apr 22, 2025
e870302
Added _check_options allows use of pint.Quantities and sympy.Symbols …
glucksfall Apr 23, 2025
28c8e62
Fixed when a reaction is associated to a metabolite, but not otherwise
glucksfall Apr 24, 2025
9742b00
Reverted use of isinstance instead of type
glucksfall Apr 26, 2025
48394ad
Corrections to merge method
glucksfall Apr 26, 2025
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4 changes: 4 additions & 0 deletions .vscode/settings.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"python.analysis.typeCheckingMode": "basic",
"python.analysis.autoImportCompletions": true
}
12 changes: 6 additions & 6 deletions coralme/builder/troubleshooting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import sympy
import pandas
import logging
import sys

log = logging.getLogger(__name__)

def process_model(model, growth_key = sympy.Symbol('mu', positive = True), parameters = dict()):
Expand All @@ -21,7 +21,7 @@ def process_model(model, growth_key = sympy.Symbol('mu', positive = True), param

dct = {}
for met in model.metabolites:
filter1 = isinstance(met, (cobra.core.metabolite.Metabolite, coralme.core.component.Metabolite))
filter1 = type(met) == cobra.core.metabolite.Metabolite or type(met) == coralme.core.component.Metabolite
filter2 = met.id.startswith('trna')
filter3 = met.id.endswith('trna_c')

Expand All @@ -39,9 +39,9 @@ def process_model(model, growth_key = sympy.Symbol('mu', positive = True), param
# lb = lb.subs(parameters).subs(growth_key, 1.)
# if hasattr(ub, 'subs'):
# ub = ub.subs(parameters).subs(growth_key, 1.)
# if met not in rxn.metabolites:
# # Sometimes it has a ghost association, ? e.g. h_c in ATPM of Synechocystis
# continue
if met not in rxn.metabolites:
# Sometimes it has a ghost association, ? e.g. h_c in ATPM of Synechocystis
continue
# coeff = rxn.metabolites[met]
# if hasattr(coeff, 'subs'):
# coeff = coeff.subs(parameters).subs(growth_key, 1.)
Expand Down Expand Up @@ -216,7 +216,7 @@ def brute_force_check(me_model, metabolites_to_add, growth_key_and_value,solver=
"""
if solver in ['gurobi', 'cplex']:
me_model.get_solution = me_model.optimize_windows
me_model.get_feasibility =me_model.feas_windows(solver = solver)
me_model.get_feasibility = me_model.feas_windows(solver = solver)
elif solver == "qminos":
me_model.get_solution = me_model.optimize
me_model.get_feasibility = me_model.feasibility
Expand Down
1 change: 1 addition & 0 deletions coralme/core/__init__.py
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Expand Up @@ -3,3 +3,4 @@
import coralme.core.parameters
import coralme.core.processdata
import coralme.core.reaction
import coralme.core.optimization
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