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"""Define global fixtures."""
import importlib.resources
from pathlib import Path
from pickle import load as _load
from typing import List, Tuple
import pytest
import cobra
from cobra import Metabolite, Model, Reaction, Solution
from cobra.io import read_sbml_model
from cobra.util import solver as sutil
data_dir = Path(__file__).parent / "data"
cobra_data_dir = importlib.resources.files(cobra.data)
def create_test_model(model_name: str = "salmonella") -> Model:
"""Return a cobra model for testing.
Parameters
----------
model_name: str
One of 'ecoli', 'textbook', or 'salmonella', or the
path to a pickled cobra.Model .
Returns
-------
cobra.Model
The cobra model.
Raises
------
OSError
If no file is found at the path specified by `model_name`.
"""
if model_name == "ecoli":
ecoli_sbml = str((cobra_data_dir / "iJO1366.xml.gz").resolve())
return read_sbml_model(ecoli_sbml)
elif model_name == "textbook":
textbook_sbml = str((cobra_data_dir / "textbook.xml.gz").resolve())
return read_sbml_model(textbook_sbml)
elif model_name == "mini":
mini_sbml = str((data_dir / "mini_fbc2.xml").resolve())
return read_sbml_model(mini_sbml)
elif model_name == "salmonella":
salmonella_pickle = str((data_dir / "salmonella.pickle").resolve())
model_name = salmonella_pickle
with open(model_name, mode="rb") as infile:
return _load(infile)
@pytest.fixture(scope="session")
def data_directory() -> Path:
"""Provide session-level fixture for test data directory."""
return data_dir
@pytest.fixture(scope="session")
def cobra_data_directory() -> Path:
"""Provide session-level fixture for cobra data directory."""
return Path(cobra_data_dir)
@pytest.fixture(scope="session")
def empty_once() -> Model:
"""Provide session-level fixture for empty model."""
return Model()
@pytest.fixture(scope="function")
def empty_model(empty_once: Model) -> Model:
"""Provide function-level fixture for empty model."""
return empty_once.copy()
@pytest.fixture(scope="session")
def small_model() -> Model:
"""Provide session-level fixture for textbook model."""
return create_test_model("textbook")
@pytest.fixture(scope="function")
def model(small_model: Model) -> Model:
"""Provide function-level fixture for textbook model."""
return small_model.copy()
@pytest.fixture(scope="session")
def large_once() -> Model:
"""Provide session-level fixture for ecoli model."""
return create_test_model("ecoli")
@pytest.fixture(scope="function")
def large_model(large_once: Model) -> Model:
"""Provide function-level fixture for ecoli model."""
return large_once.copy()
@pytest.fixture(scope="session")
def medium_model() -> Model:
"""Provide session-level fixture for salmonella model."""
return create_test_model("salmonella")
@pytest.fixture(scope="function")
def salmonella(medium_model: Model) -> Model:
"""Provide function-level fixture for salmonella model."""
return medium_model.copy()
@pytest.fixture(scope="function")
def solved_model(data_directory: Path) -> Tuple[Solution, Model]:
"""Provide function-level fixture for solved textbook model."""
model = create_test_model("textbook")
with (data_directory / "textbook_solution.pickle").open(mode="rb") as infile:
solution = _load(infile)
return solution, model
@pytest.fixture(scope="session")
def tiny_toy_model() -> Model:
"""Provide session-level fixture for tiny toy model."""
tiny = Model("Toy Model")
m1 = Metabolite("M1")
d1 = Reaction("ex1")
d1.add_metabolites({m1: -1})
d1.upper_bound = 0
d1.lower_bound = -1000
tiny.add_reactions([d1])
tiny.objective = "ex1"
return tiny
stable_optlang = ["glpk", "cplex", "gurobi"]
all_solvers = ["optlang-" + s for s in stable_optlang if s in sutil.solvers]
@pytest.fixture(params=all_solvers, scope="session")
def opt_solver(request: pytest.FixtureRequest) -> str:
"""Provide session-level fixture for parametrized optlang solver names."""
return request.param
@pytest.fixture(scope="function")
def metabolites(model: Model, request: pytest.FixtureRequest) -> List[Metabolite]:
"""Provide function-level fixture for metabolite set based on `request`."""
if request.param == "exchange":
return [
met
for met in model.metabolites
if met.compartment == "e" and "EX_" + met.id not in model.reactions
]
elif request.param == "demand":
return [
met
for met in model.metabolites
if met.compartment == "c" and "DM_" + met.id not in model.reactions
]
elif request.param == "sink":
return [
met
for met in model.metabolites
if met.compartment == "c" and "SK_" + met.id not in model.reactions
]
else:
raise ValueError("Unknown metabolites {}".format(request.param))
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