Source code for test_boundary_types

"""Test functionalities of boundary type detection functions."""

import pytest

from cobra.core import Metabolite, Model, Reaction
from cobra.medium import (

[docs]def test_find_external_compartment_single(model: Model) -> None: """Test external compartment identification.""" # by name assert find_external_compartment(model) == "e" # from boundary counts for m in model.metabolites: if m.compartment == "e": m.compartment = "outside" for r in model.reactions: r._compartments = None assert find_external_compartment(model) == "outside" # names are always right model.exchanges[0].reactants[0].compartment = "extracellular" assert find_external_compartment(model) == "extracellular"
[docs]def test_find_external_compartment_multi(model: Model) -> None: """Test multiple external compartment identification.""" for r in model.reactions: r._compartments = None model.exchanges[0].reactants[0].compartment = "extracellular" # still works due to different boundary numbers assert find_external_compartment(model) == "e" model.exchanges[1].reactants[0].compartment = "extra cellular" model.remove_reactions(model.exchanges) # Now fails because same boundary count with pytest.raises(RuntimeError): find_external_compartment(model)
[docs]def test_no_names_or_boundary_reactions(empty_model: Model) -> None: """Test absence of name or boundary reactions.""" with pytest.raises(RuntimeError): find_external_compartment(empty_model)
[docs]def test_find_boundary_types_exchange(model: Model) -> None: """Test boundary type identification for exchanges.""" ex = model.exchanges assert all("EX_") for r in ex) ex = find_boundary_types(model, "exchange", "e") assert all("EX_") for r in ex)
[docs]def test_find_boundary_types_demand(model: Model) -> None: """Test boundary type identification for demands.""" dm = Reaction("demand") model.add_reaction(dm) dm.build_reaction_from_string("atp_c ->") dm = model.demands assert len(dm) == 1 assert "demand" in [ for r in dm]
[docs]def test_find_boundary_types_sink(model: Model) -> None: """Test boundary type identification for sinks.""" sn = Reaction("sink") model.add_reaction(sn) sn.build_reaction_from_string("atp_c <->") sn.bounds = -1000, 1000 sn = model.sinks assert len(sn) == 1 assert "sink" in [ for r in sn]
[docs]def test_no_boundary_reactions(empty_model: Model) -> None: """Test proper identification of no boundary reactions.""" assert find_boundary_types(empty_model, "e", None) == []
[docs]def test_is_boundary_type(model: Model) -> None: """Test correct identification of boundary types for reactions.""" assert not is_boundary_type(model.reactions.ATPM, "exchange", "e") model.reactions.ATPM.annotation["sbo"] = "SBO:0000627" assert is_boundary_type(model.reactions.ATPM, "exchange", "bla") model.reactions.ATPM.annotation["sbo"] = "SBO:0000632" assert not is_boundary_type(model.reactions.ATPM, "exchange", "e")
[docs]def test_bad_exchange(model: Model) -> None: """Test bad exchange reaction identification.""" with pytest.raises(ValueError): m = Metabolite("baddy", compartment="nonsense") model.add_boundary(m, type="exchange") m = Metabolite("goody", compartment="e") rxn = model.add_boundary(m, type="exchange") assert isinstance(rxn, Reaction)