# -*- coding: utf-8 -*-
"""Test functionalities of OptGPSampler."""
from __future__ import absolute_import
import numpy as np
import pytest
from cobra.sampling import OptGPSampler
@pytest.fixture(scope="function")
[docs]def optgp(model):
"""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
[docs]def test_optgp_init_benchmark(model, benchmark):
"""Benchmark inital OptGP sampling."""
benchmark(lambda: OptGPSampler(model, processes=2))
[docs]def test_optgp_sample_benchmark(optgp, benchmark):
"""Benchmark OptGP sampling."""
benchmark(optgp.sample, 1)
[docs]def test_sampling(optgp):
"""Test sampling."""
s = optgp.sample(10)
assert all(optgp.validate(s) == "v")
[docs]def test_batch_sampling(optgp):
"""Test batch sampling."""
for b in optgp.batch(5, 4):
assert all(optgp.validate(b) == "v")
[docs]def test_variables_samples(achr, optgp):
"""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()
[docs]def test_reproject(optgp):
"""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")