def _test_overhead_timing():
# prints timing for simple Gaussian vanilla mcmc
import pstats
from cProfile import Profile
from io import StringIO
# noinspection PyUnresolvedReferences
from cobaya.samplers.mcmc import proposal # one-time numba compile out of profiling
LikeTest = _make_gaussian_like(15)
info = {
'likelihood': {
'like': LikeTest
},
'debug': False,
'sampler': {
'mcmc': {
'max_samples': 1000,
'burn_in': 0,
"learn_proposal": False,
"Rminus1_stop": 0.0001
}
}
}
prof = Profile()
prof.enable()
run(info)
prof.disable()
s = StringIO()
ps = pstats.Stats(prof, stream=s)
ps.strip_dirs()
ps.sort_stats('time')
ps.print_stats(10)
ps.sort_stats('cumtime')
ps.print_stats(10)
print(s.getvalue())
def test_prior_inherit_samegiven_differentdefinition():
test_info = deepcopy(test_info_common)
likname = list(test_info_common["likelihood"])[0]
default_info = get_default_info(likname, "likelihood")
name, prior = deepcopy(default_info["prior"]).popitem()
test_info["prior"] = {name: "this is not a prior"}
with pytest.raises(LoggedError):
run(test_info)
def test_polychord_resume(packages_path, skip_not_installed, tmpdir):
"""
Tests correct resuming of a run, especially conserving the original blocking.
To test preservation of the oversampling+blocking, we try to confuse the sampler by
requesting speed measuring at resuming, and providing speeds very different from the
real ones.
"""
nlive = 10
max_ndead = 2 * nlive
dead_points = []
def callback(sampler):
nonlocal dead_points
dead_points = sampler.dead[["a", "b"]].values.copy()
info = {
"likelihood": {
"A": {
"external": "lambda a: stats.norm.logpdf(a)",
"speed": 1
},
"B": {
"external": "lambda b: stats.norm.logpdf(b)",
"speed": 0.01
}
},
"params": {
"a": {
"prior": {
"min": 0,
"max": 1
}
},
"b": {
"prior": {
"min": 0,
"max": 1
}
}
},
"sampler": {
"polychord": {
"measure_speeds": True,
"nlive": nlive,
"max_ndead": max_ndead,
"callback_function": callback,
}
},
"output": str(tmpdir)
}
install_test_wrapper(skip_not_installed, run, info)
old_dead_points = dead_points.copy()
info["resume"] = True
run(info)
assert np.allclose(old_dead_points, dead_points)
def test_post_params():
# Tests:
# - added simple dynamical derived parameter "a+b"
# - added dynamical derived parameter that depends on *new* chi2__target
# - added new fixed input "c" + new derived-from-external-function "cprime"
# Generate original chain
info = {
"params": info_params, "sampler": info_sampler_dummy,
"likelihood": {"gaussian": sampled_pdf}}
updated_info_gaussian, sampler_gaussian = run(info)
products_gaussian = sampler_gaussian.products()
info_post = {
"post": {"suffix": "foo",
"remove": {"params": {"a_plus_b": None}},
"add": {
"likelihood": {
"target": {"external": target_pdf, "output_params": ["cprime"]}},
"params": {
"c": 1.234,
"a_minus_b": {"derived": "lambda a,b: a-b"},
"my_chi2__target": {
"derived": "lambda chi2__target: chi2__target"},
"cprime": None}}}}
info_post.update(updated_info_gaussian)
products = post(info_post, products_gaussian["sample"]).products
# Compare parameters
assert np.allclose(
products["sample"]["a"] - products["sample"]["b"],
products["sample"]["a_minus_b"])
assert np.allclose(
products["sample"]["cprime"], info_post["post"]["add"]["params"]["c"])
assert np.allclose(
products["sample"]["my_chi2__target"], products["sample"]["chi2__target"])
def test_post_prior(tmpdir):
# Generate original chain
info: InputDict = {
"output": os.path.join(tmpdir, "gaussian"), "force": True,
"params": info_params, "sampler": info_sampler,
"likelihood": {"one": None}, "prior": {"gaussian": sampled_pdf}}
info_post: InputDict = {
"output": info["output"], "force": True,
"post": {"suffix": "foo", 'skip': 0.1,
"remove": {"prior": {"gaussian": None}},
"add": {"prior": {"target": target_pdf_prior}}}}
_, sampler = run(info)
if mpi.is_main_process():
mcsamples_in = loadMCSamples(info["output"], settings={'ignore_rows': 0.1})
target_mean, target_cov = mpi.share(_get_targets(mcsamples_in))
else:
target_mean, target_cov = mpi.share()
for mem in [False, True]:
post(info_post, sample=sampler.products()["sample"] if mem else None)
# Load with GetDist and compare
if mpi.is_main_process():
mcsamples = loadMCSamples(
info_post["output"] + _post_ + info_post["post"]["suffix"])
new_mean = mcsamples.mean(["a", "b"])
new_cov = mcsamples.getCovMat().matrix
mpi.share((new_mean, new_cov))
else:
new_mean, new_cov = mpi.share()
assert np.allclose(new_mean, target_mean)
assert np.allclose(new_cov, target_cov)
def body_of_test(packages_path, like_name=None, like_info=None):
info = {
_packages_path: process_packages_path(packages_path),
kinds.sampler: {
"evaluate": None
}
}
if like_name:
info[kinds.likelihood] = {like_name: None}
elif like_info:
info[kinds.likelihood] = like_info
like_name = list(like_info)[0]
info[_params] = {"H0": fiducial_H0}
updated_info, sampler = run(info)
products = sampler.products()
# The default values for .get are for the _docs_ test
mean = updated_info[kinds.likelihood][like_name].get(
"H0_mean", fiducial_H0)
std = updated_info[kinds.likelihood][like_name].get(
"H0_std", fiducial_H0_std)
reference_value = -2 * norm.logpdf(fiducial_H0, loc=mean, scale=std)
computed_value = (
products["sample"]["chi2__" +
list(info[kinds.likelihood])[0]].values[0])
assert np.allclose(computed_value, reference_value)
def test_minimize_gaussian():
# parameters
dimension = 3
n_modes = 1
# MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
# Info of likelihood and prior
ranges = np.array([[0, 1] for _ in range(dimension)])
prefix = "a_"
info = info_random_gaussian_mixture(ranges=ranges,
n_modes=n_modes,
input_params_prefix=prefix,
derived=True)
mean = info[kinds.likelihood]["gaussian_mixture"]["means"][0]
cov = info[kinds.likelihood]["gaussian_mixture"]["covs"][0]
maxloglik = multivariate_normal.logpdf(mean, mean=mean, cov=cov)
if rank == 0:
print("Maximum of the gaussian mode to be found:")
print(mean)
info[kinds.sampler] = {"minimize": {"ignore_prior": True}}
info["debug"] = False
info["debug_file"] = None
# info["output_prefix"] = "./minigauss/"
from cobaya.run import run
updated_info, sampler = run(info)
products = sampler.products()
# Done! --> Tests
if rank == 0:
rel_error = abs(maxloglik -
-products["minimum"]["minuslogpost"]) / abs(maxloglik)
assert rel_error < 0.001
def body_of_test(modules, lik_name, theory):
if theory in skip_theories:
print('Skipping test with %s' % theory)
return
info = {
_path_install: process_modules_path(modules),
_theory: {
theory: None
},
_sampler: {
"evaluate": None
}
}
if lik_name.startswith("lambda"):
line = copy(lik_name)
lik_name = "whatever"
info[_likelihood] = {lik_name: line}
else:
info[_likelihood] = {lik_name: None}
info[_params] = {"H0": fiducial_H0}
updated_info, products = run(info)
# The default values for .get are for the _docs_ test
mean = updated_info[_likelihood][lik_name].get("H0", fiducial_H0)
std = updated_info[_likelihood][lik_name].get("H0_std", 1)
reference_value = -2 * norm.logpdf(fiducial_H0, loc=mean, scale=std)
computed_value = (
products["sample"]["chi2__" +
list(info[_likelihood].keys())[0]].values[0])
assert np.allclose(computed_value, reference_value)
def test_parameterization():
updated_info, sampler = run(info)
products = sampler.products()
sample = products["sample"]
from getdist.mcsamples import MCSamplesFromCobaya
gdsample = MCSamplesFromCobaya(updated_info, products["sample"])
for i, point in sample:
a = info[_params]["a"]
b = get_external_function(info[_params]["b"])(a, point["bprime"])
c = get_external_function(info[_params]["c"])(a, point["cprime"])
e = get_external_function(e_func)(b)
f = get_external_function(f_func)(b)
g = get_external_function(info[_params]["g"]["derived"])(x_func(
point["c"]))
h = get_external_function(info[_params]["h"])(info[_params]["i"])
j = get_external_function(info[_params]["j"])(b)
k = get_external_function(info[_params]["k"]["derived"])(f)
assert np.allclose(point[["b", "c", "e", "f", "g", "h", "j", "k"]],
[b, c, e, f, g, h, j, k])
# Test for GetDist too (except fixed ones, ignored by GetDist)
bcefffg_getdist = [
gdsample.samples[i][gdsample.paramNames.list().index(p)]
for p in ["b", "c", "e", "f", "g", "j", "k"]
]
assert np.allclose(bcefffg_getdist, [b, c, e, f, g, j, k])
def test_prior_inherit_samegiven_differentdefinition():
test_info = deepcopy(test_info_common)
likname = list(test_info_common[kinds.likelihood])[0]
default_info = get_default_info(likname, kinds.likelihood)
name, prior = deepcopy(default_info[_prior]).popitem()
test_info[_prior] = {name: "this is not a prior"}
with pytest.raises(LoggedError):
updated_info, products = run(test_info)
def test_prior_inherit_samegiven():
test_info = deepcopy(test_info_common)
likname = list(test_info_common[_likelihood].keys())[0]
default_info = get_default_info(likname, _likelihood)
name, prior = deepcopy(default_info[_prior]).popitem()
test_info[_prior] = {name: prior}
updated_info, products = run(test_info)
assert updated_info[_prior] == default_info[_prior]
def test_prior_inherit_differentgiven():
test_info = deepcopy(test_info_common)
test_info[_prior] = {"third": "lambda a1: 1"}
updated_info, products = run(test_info)
likname = list(test_info_common[_likelihood].keys())[0]
default_info = get_default_info(likname, _likelihood)
default_info[_prior].update(test_info[_prior])
assert updated_info[_prior] == default_info[_prior]
def test_prior_inherit_samegiven():
test_info = deepcopy(test_info_common)
likname = list(test_info_common["likelihood"])[0]
default_info = get_default_info(likname, "likelihood")
name, prior = deepcopy(default_info["prior"]).popitem()
test_info["prior"] = {name: prior}
updated_info, _ = run(test_info)
assert updated_info["prior"] == default_info["prior"]
def test_prior_inherit_samegiven_differentdefinition():
test_info = deepcopy(test_info_common)
likname = list(test_info_common[_likelihood].keys())[0]
default_info = get_default_info(likname, _likelihood)
name, prior = deepcopy(default_info[_prior]).popitem()
test_info[_prior] = {name: "this is not a prior"}
with pytest.raises(HandledException):
updated_info, products = run(test_info)
def test_prior_inherit_differentgiven():
test_info = deepcopy(test_info_common)
test_info["prior"] = {"third": "lambda a1: 1"}
updated_info, _ = run(test_info)
likname = list(test_info_common["likelihood"])[0]
default_info = get_default_info(likname, "likelihood")
default_info["prior"].update(test_info["prior"])
assert updated_info["prior"] == default_info["prior"]
def test_mcmc_fastdragging():
"""
In 2d, tests a slow parameter "a0" vs a fast one "a1".
Both share a gaussian lik with a high correlation.
"a0" is made slower by a mock unit likelihood.
Both likelihoods have mock derived paramters,
just for testing that they are tracked correctly along the dragging.
"""
info = {
_params:
odict([["a0", {
"prior": {
"min": -4,
"max": 4
},
"ref": 0
}], ["a1", {
"prior": {
"min": -4,
"max": 4
},
"ref": 0
}], ["b0", None], ["b1", None]]),
_likelihood: {
"slow": {
"external":
"import_module('test_mcmc_fastdragging').loglik_slow",
"speed": 0.25
},
"correlation": {
"external":
"import_module('test_mcmc_fastdragging').loglik_correlation",
"speed": 1
},
"derived": {
"external":
"import_module('test_mcmc_fastdragging').loglik_derived",
"speed": 1
}
},
_sampler: {
"mcmc": {
"max_samples": np.inf,
"burn_in": 0,
"Rminus1_stop": 0.01,
"Rminus1_cl_stop": 0.01,
"learn_proposal": True,
"covmat": np.eye(2),
"covmat_params": ["a0", "a1"],
"drag_nfast_times": 5,
"max_speed_slow": 0.5
}
}
}
info["debug"] = False
info["debug_file"] = None
info["output_prefix"] = "chains_test/"
updated_info, products = run(info)
def body_of_test(dim, tmpdir=None):
mindim = 4
assert dim > mindim, "Needs dimension>%d for the test." % mindim
initial_random_covmat = random_cov(dim * [[0, 1]])
i_s = list(range(dim))
shuffle(i_s)
n_altered = int(dim / 4)
i_proposal = i_s[:n_altered]
i_ref = i_s[n_altered:2 * n_altered]
i_prior = i_s[2 * n_altered:3 * n_altered]
removed = list(chain(*(i_proposal, i_ref, i_prior)))
i_covmat = [i for i in range(dim) if i not in removed]
for i in removed:
diag = initial_random_covmat[i, i]
initial_random_covmat[:, i] = 0
initial_random_covmat[i, :] = 0
initial_random_covmat[i, i] = diag
# Prepare info, including refs, priors and reduced covmat
prefix = "a_"
input_order = list(range(dim))
shuffle(input_order)
info = {_likelihood: {"one": {"prefix": ""}}, _params: odict()}
for i in input_order:
p = prefix + str(i)
info[_params][p] = {_prior: {_p_dist: "norm", "loc": 0, "scale": 1000}}
sigma = np.sqrt(initial_random_covmat[i, i])
if i in i_proposal:
info[_params][p][_p_proposal] = sigma
elif i in i_ref:
info[_params][prefix + str(i)][_p_ref] = {
_p_dist: "norm",
"scale": sigma
}
elif i in i_prior:
info[_params][prefix + str(i)][_prior]["scale"] = sigma
reduced_covmat = initial_random_covmat[np.ix_(i_covmat, i_covmat)]
reduced_covmat_params = [prefix + str(i) for i in i_covmat]
info[_sampler] = {"mcmc": {}}
if tmpdir:
filename = os.path.join(str(tmpdir), "mycovmat.dat")
header = " ".join(reduced_covmat_params)
np.savetxt(filename, reduced_covmat, header=header)
info[_sampler]["mcmc"]["covmat"] = str(filename)
else:
info[_sampler]["mcmc"]["covmat_params"] = reduced_covmat_params
info[_sampler]["mcmc"]["covmat"] = reduced_covmat
to_compare = initial_random_covmat[np.ix_(input_order, input_order)]
def callback(sampler):
assert np.allclose(to_compare, sampler.proposer.get_covariance())
info[_sampler]["mcmc"].update({
"callback_function": callback,
"callback_every": 1,
"max_samples": 1,
"burn_in": 0
})
updated_info, products = run(info)
def test_external():
os.chdir(base_dir)
mapping_proj = ['ell_0', 'ell_2', 'ell_4']
make_data_covariance(data_fn=data_fn,
covariance_fn=covariance_fn,
mapping_proj=mapping_proj)
info = yaml_load_file('./test_cobaya.yaml')
updated_info, sampler = run(info)
assert 'a' in updated_info['params']
assert 'sample' in sampler.products()
def test_parametrization():
updated_info, products = run(info)
sample = products["sample"]
for i, point in sample:
a = info[_params]["a"]
b = get_external_function(info[_params]["b"])(a, point["bprime"])
d = get_external_function(d_func)(a)
e = get_external_function(e_func)(b)
f = get_external_function(info[_params]["f"]["derived"])(x_func(
point["c"]))
assert np.allclose(point[[_derived_pre + p for p in ["d", "e", "f"]]],
[d, e, f])
def test_post_prior(tmpdir):
# Generate original chain
info = {
_output_prefix: os.path.join(str(tmpdir), "gaussian"),
_force: True,
_params: info_params,
kinds.sampler: info_sampler,
kinds.likelihood: {
"one": None
},
_prior: {
"gaussian": sampled_pdf
}
}
run(info)
info_post = {
_output_prefix: info[_output_prefix],
_force: True,
_post: {
_post_suffix: "foo",
_post_remove: {
_prior: {
"gaussian": None
}
},
_post_add: {
_prior: {
"target": target_pdf_prior
}
}
}
}
post(info_post)
# Load with GetDist and compare
mcsamples = loadMCSamples(info_post[_output_prefix] + _post_ +
info_post[_post][_post_suffix])
new_mean = mcsamples.mean(["a", "b"])
new_cov = mcsamples.getCovMat().matrix
assert abs(KL_norm(target["mean"], target["cov"], new_mean,
new_cov)) < 0.02
def test_post_prior(tmpdir):
# Generate original chain
info = {
"output": os.path.join(str(tmpdir), "gaussian"),
"force": True,
"params": info_params,
"sampler": info_sampler,
"likelihood": {
"one": None
},
"prior": {
"gaussian": sampled_pdf
}
}
run(info)
info_post = {
"output": info["output"],
"force": True,
"post": {
"suffix": "foo",
"remove": {
"prior": {
"gaussian": None
}
},
"add": {
"prior": {
"target": target_pdf
}
}
}
}
post(info_post)
# Load with GetDist and compare
mcsamples = loadMCSamples(info_post["output"] + "_post_" +
info_post["post"]["suffix"])
new_mean = mcsamples.mean(["a", "b"])
new_cov = mcsamples.getCovMat().matrix
assert abs(KL_norm(target["mean"], target["cov"], new_mean,
new_cov)) < 0.02
def test_inherit_label_and_bounds():
test_info = deepcopy(test_info_common)
likname = list(test_info_common[_likelihood].keys())[0]
default_info_params = get_default_info(likname, _likelihood)[_params]
test_info[_params] = deepcopy(default_info_params)
test_info[_params]["a1"].pop(_p_label, None)
# First, change one limit (so no inheritance at all)
test_info[_params]["b1"].pop("min")
new_max = 2
test_info[_params]["b1"]["max"] = new_max
updated_info, products = run(test_info)
assert updated_info[_params]["a1"] == default_info_params["a1"]
assert updated_info[_params]["b1"].get("min") is None
assert updated_info[_params]["b1"]["max"] == new_max
# Second, remove limits, so they are inherited
test_info = deepcopy(test_info_common)
test_info[_params] = deepcopy(default_info_params)
test_info[_params]["b1"].pop("min")
test_info[_params]["b1"].pop("max")
updated_info, products = run(test_info)
assert updated_info[_params]["b1"]["min"] == default_info_params["b1"]["min"]
assert updated_info[_params]["b1"]["max"] == default_info_params["b1"]["max"]
def test_post_params():
# Tests:
# - added simple dynamical derived parameter "a+b"
# - added dynamical derived parameter that depends on *new* chi2__target
# - added new fixed input "c" + new derived-from-external-function "cprime"
# Generate original chain
info = {
_params: info_params,
_sampler: info_sampler_dummy,
_likelihood: {
"gaussian": sampled_pdf
}
}
updated_info_gaussian, products_gaussian = run(info)
info_post = {
_post: {
_post_suffix: "foo",
_post_remove: {
_params: {
"a_plus_b": None
}
},
_post_add: {
_likelihood: {
"target": target_pdf
},
_params: {
"c": 1.234,
"a_minus_b": {
_p_derived: "lambda a,b: a-b"
},
"my_chi2__target": {
_p_derived: "lambda chi2__target: chi2__target"
},
"cprime": None
}
}
}
}
info_post.update(updated_info_gaussian)
updated_info, products = post(info_post, products_gaussian["sample"])
# Compare parameters
assert np.allclose(products["sample"]["a"] - products["sample"]["b"],
products["sample"]["a_minus_b"])
assert np.allclose(products["sample"]["cprime"],
info_post[_post][_post_add][_params]["c"])
assert np.allclose(products["sample"]["my_chi2__target"],
products["sample"]["chi2__target"])
def test_inherit_label_and_bounds():
test_info = deepcopy(test_info_common)
likname = list(test_info_common["likelihood"])[0]
default_info_params = get_default_info(likname, "likelihood")["params"]
test_info["params"] = deepcopy(default_info_params)
test_info["params"]["a1"].pop("latex", None)
# Remove limits, so they are inherited
test_info = deepcopy(test_info_common)
test_info["params"] = deepcopy(default_info_params)
test_info["params"]["b1"].pop("min")
test_info["params"]["b1"].pop("max")
updated_info, _ = run(test_info)
assert updated_info["params"]["b1"]["min"] == default_info_params["b1"][
"min"]
assert updated_info["params"]["b1"]["max"] == default_info_params["b1"][
"max"]
def test_inherit_label_and_bounds():
test_info = deepcopy(test_info_common)
likname = list(test_info_common[kinds.likelihood])[0]
default_info_params = get_default_info(likname, kinds.likelihood)[_params]
test_info[_params] = deepcopy(default_info_params)
test_info[_params]["a1"].pop(partag.latex, None)
# Remove limits, so they are inherited
test_info = deepcopy(test_info_common)
test_info[_params] = deepcopy(default_info_params)
test_info[_params]["b1"].pop("min")
test_info[_params]["b1"].pop("max")
updated_info, products = run(test_info)
assert updated_info[_params]["b1"]["min"] == default_info_params["b1"][
"min"]
assert updated_info[_params]["b1"]["max"] == default_info_params["b1"][
"max"]
def test_parameterization():
updated_info, products = run(info)
sample = products["sample"]
from getdist.mcsamples import loadCobayaSamples
gdsample = loadCobayaSamples(updated_info, products["sample"])
for i, point in sample:
a = info[_params]["a"]
b = get_external_function(info[_params]["b"])(a, point["bprime"])
c = get_external_function(info[_params]["c"])(a, point["cprime"])
e = get_external_function(e_func)(b)
f = get_external_function(f_func)(b)
g = get_external_function(info[_params]["g"]["derived"])(x_func(
point["c"]))
assert np.allclose(point[["b", "c", "e", "f", "g"]], [b, c, e, f, g])
bcefg_getdist = [
gdsample.samples[i][gdsample.paramNames.list().index(p)]
for p in ["b", "c", "e", "f", "g"]
]
assert np.allclose(bcefg_getdist, [b, c, e, f, g])
def sampling(setup):
"""
Sample CMB power spectra over cosmo. parameters using `cobaya` using either
minimization algorithms or MCMC methods.
"""
# Get experiment setup
experiment = setup["experiment"]
lmin, lmax = experiment["lmin"], experiment["lmax"]
simu = setup["simulation"]
Dl, cov = simu["Dl"], simu["covmat"]
# Chi2 for CMB spectra sampling
def chi2(_theory={"cl": {"tt": lmax}}):
Dl_theo = _theory.get_cl(ell_factor=True)["tt"][lmin:lmax]
chi2 = np.sum((Dl - Dl_theo)**2 / cov)
return -0.5 * chi2
# Chi2 for CMB spectra residuals sampling
from beyondCV import utils
Dl_Planck = utils.get_theory_cls(setup, lmax)[lmin:lmax]
def chi2_residuals(_theory={"cl": {"tt": lmax}}):
Dl_theo = _theory.get_cl(ell_factor=True)["tt"][lmin:lmax]
Delta_Dl_obs, Delta_Dl_theo = Dl, Dl_theo - Dl_Planck
chi2 = np.sum((Delta_Dl_obs - Delta_Dl_theo)**2 / cov)
return -0.5 * chi2
# Get cobaya setup
info = setup["cobaya"]
# Add likelihood function
survey = experiment.get("survey")
if survey in ["SOxSO", "SOxP", "PxP"]:
info["likelihood"] = {"chi2": chi2}
else:
info["likelihood"] = {"chi2": chi2_residuals}
from cobaya.run import run
return run(info)
def body_of_test(modules, data, theory):
assert modules, "I need a modules folder!"
info = {
_path_install: modules,
_theory: {
theory: None
},
_sampler: {
"evaluate": None
}
}
lik_name = "hst_" + data
info[_likelihood] = {lik_name: None}
fiducial_H0 = 70
info[_params] = {"H0": fiducial_H0}
updated_info, products = run(info)
mean = updated_info[_likelihood][lik_name]["H0"]
std = updated_info[_likelihood][lik_name]["H0_err"]
reference_value = -2 * norm.logpdf(fiducial_H0, loc=mean, scale=std)
computed_value = (
products["sample"]["chi2__" +
list(info[_likelihood].keys())[0]].values[0])
assert np.allclose(computed_value, reference_value)
def body_of_test(modules, data, theory):
assert modules, "I need a modules folder!"
info = {_path_install: modules,
_theory: {theory: None},
_sampler: {"evaluate": None}}
info[_likelihood] = {"des_1yr_"+data: None}
info[_params] = {
_theory: {
"H0": 68.81,
"ombh2": 0.0468 * 0.6881 ** 2,
"omch2": (0.295 - 0.0468) * 0.6881 ** 2 - 0.0006155,
"YHe": 0.245341,
"tau": 0.08,
"As": 2.260574e-09,
"ns": 0.9676
}}
if data in ["shear", "galaxy_galaxylensing"]:
info[_params].update(yaml_load(test_params_shear)[_params])
if data in ["clustering", "galaxy_galaxylensing"]:
info[_params].update(yaml_load(test_params_clustering)[_params])
# UPDATE WITH BOTH ANYWAY FOR NOW!!!!!
info[_params].update(yaml_load(test_params_shear)[_params])
info[_params].update(yaml_load(test_params_clustering)[_params])
reference_value = 650.872548
abs_tolerance = 0.1
if theory == "classy":
info[_params][_theory].update(baseline_cosmology_classy_extra)
abs_tolerance += 2
print("WE SHOULD NOT HAVE TO LOWER THE TOLERANCE THAT MUCH!!!")
updated_info, products = run(info)
# print products["sample"]
computed_value = products["sample"]["chi2__"+list(info[_likelihood].keys())[0]].values[0]
assert (computed_value-reference_value) < abs_tolerance
def body_of_test(dimension=1,
n_modes=1,
info_sampler={},
tmpdir="",
modules=None):
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
# Info of likelihood and prior
ranges = np.array([[-1, 1] for _ in range(dimension)])
while True:
info = info_random_gaussian_mixture(ranges=ranges,
n_modes=n_modes,
prefix="a_",
O_std_min=O_std_min,
O_std_max=O_std_max,
derived=True)
if n_modes == 1:
break
means = info["likelihood"]["gaussian_mixture"]["means"]
distances = chain(*[[np.linalg.norm(m1 - m2) for m2 in means[i + 1:]]
for i, m1 in enumerate(means)])
if min(distances) >= distance_factor * O_std_max:
break
if rank == 0:
print("Original mean of the gaussian mode:")
print(info["likelihood"]["gaussian_mixture"]["means"])
print("Original covmat of the gaussian mode:")
print(info["likelihood"]["gaussian_mixture"]["covs"])
info[_sampler] = info_sampler
if list(info_sampler.keys())[0] == "mcmc":
if "covmat" in info_sampler["mcmc"]:
info[_sampler]["mcmc"]["covmat_params"] = (list(
info["params"].keys())[:dimension])
info[_debug] = False
info[_debug_file] = None
info[_output_prefix] = getattr(tmpdir, "realpath()", lambda: tmpdir)()
if modules:
info[_path_install] = process_modules_path(modules)
# Delay to one chain to check that MPI communication of the sampler is non-blocking
# if rank == 1:
# info["likelihood"]["gaussian_mixture"]["delay"] = 0.1
updated_info, products = run(info)
# Done! --> Tests
if rank == 0:
if list(info_sampler.keys())[0] == "mcmc":
ignore_rows = 0.5
else:
ignore_rows = 0
results = loadCobayaSamples(updated_info,
products["sample"],
ignore_rows=ignore_rows,
name_tag="sample")
clusters = None
if "clusters" in products:
clusters = [
loadCobayaSamples(updated_info,
products["clusters"][i]["sample"],
name_tag="cluster %d" % (i + 1))
for i in products["clusters"]
]
# Plots!
try:
import getdist.plots as gdplots
from getdist.gaussian_mixtures import MixtureND
mixture = MixtureND(
info[_likelihood]["gaussian_mixture"]["means"],
info[_likelihood]["gaussian_mixture"]["covs"],
names=[p for p in info[_params] if "deriv" not in p],
label="truth")
g = gdplots.getSubplotPlotter()
to_plot = [mixture, results]
if clusters:
to_plot = to_plot + clusters
g.triangle_plot(to_plot, )
g.export("test.png")
except:
print("Plotting failed!")
# 1st test: KL divergence
if n_modes == 1:
cov_sample, mean_sample = results.getCov(), results.getMeans()
KL_final = KL_norm(
m1=info[_likelihood]["gaussian_mixture"]["means"][0],
S1=info[_likelihood]["gaussian_mixture"]["covs"][0],
m2=mean_sample[:dimension],
S2=cov_sample[:dimension, :dimension])
print("Final KL: ", KL_final)
assert KL_final <= KL_tolerance
# 2nd test: clusters
else:
if "clusters" in products:
assert len(products["clusters"].keys()) >= n_modes, (
"Not all clusters detected!")
for c2 in clusters:
cov_c2, mean_c2 = c2.getCov(), c2.getMeans()
KLs = [
KL_norm(m1=info[_likelihood]["gaussian_mixture"]
["means"][i_c1],
S1=info[_likelihood]["gaussian_mixture"]
["covs"][i_c1],
m2=mean_c2[:dimension],
S2=cov_c2[:dimension, :dimension])
for i_c1 in range(n_modes)
]
extra_tol = 4 * n_modes if n_modes > 1 else 1
assert min(KLs) <= KL_tolerance * extra_tol
else:
assert 0, "Could not check sample convergence: multimodal but no clusters"
# 3rd test: Evidence
if "logZ" in products:
logZprior = sum(np.log(ranges[:, 1] - ranges[:, 0]))
assert (products["logZ"] - logZ_nsigmas * products["logZstd"] <
-logZprior <
products["logZ"] + logZ_nsigmas * products["logZstd"])