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"""Test functionalities of OptGPSampler."""
import os
from typing import TYPE_CHECKING, Callable
import numpy as np
import pytest
from cobra.sampling import OptGPSampler
if TYPE_CHECKING:
from cobra import Model
from cobra.sampling import ACHRSampler
@pytest.fixture(scope="function")
def optgp(model: "Model") -> OptGPSampler:
"""Return OptGPSampler instance for tests."""
sampler = OptGPSampler(model, processes=1, thinning=1)
assert (sampler.n_warmup > 0) and (sampler.n_warmup <= 2 * len(model.variables))
assert all(sampler.validate(sampler.warmup) == "v")
return sampler
@pytest.mark.skipif("SKIP_MP" in os.environ, reason="unsafe for parallel execution")
def test_optgp_init_benchmark(model: "Model", benchmark: Callable) -> None:
"""Benchmark inital OptGP sampling."""
benchmark(lambda: OptGPSampler(model, processes=2))
def test_optgp_sample_benchmark(optgp: "Model", benchmark: Callable) -> None:
"""Benchmark OptGP sampling."""
benchmark(optgp.sample, 1)
def test_sampling(optgp: OptGPSampler) -> None:
"""Test sampling."""
s = optgp.sample(10)
assert all(optgp.validate(s) == "v")
def test_batch_sampling(optgp: OptGPSampler) -> None:
"""Test batch sampling."""
for b in optgp.batch(5, 4):
assert all(optgp.validate(b) == "v")
def test_variables_samples(achr: "ACHRSampler", optgp: OptGPSampler) -> None:
"""Test variable samples."""
vnames = np.array([v.name for v in achr.model.variables])
s = optgp.sample(10, fluxes=False)
assert s.shape == (10, optgp.warmup.shape[1])
assert (s.columns == vnames).all()
assert (optgp.validate(s) == "v").all()
def test_reproject(optgp: OptGPSampler) -> None:
"""Test reprojection of sampling."""
s = optgp.sample(10, fluxes=False).values
proj = np.apply_along_axis(optgp._reproject, 1, s)
assert all(optgp.validate(proj) == "v")
s = np.random.rand(10, optgp.warmup.shape[1])
proj = np.apply_along_axis(optgp._reproject, 1, s)
assert all(optgp.validate(proj) == "v")
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