Commit 20061581 authored by Gregory Ashton's avatar Gregory Ashton
Browse files

Rewrite of the ptemcee sampler

1) Introduce "nsamples" functionality
2) Improve the evidence estimates
3) Improve result caching and exit behaviour
parent daddc5cb
This diff is collapsed.
[flake8]
exclude = .git,docs,build,dist,test,*__init__.py
max-line-length = 120
ignore = E129 W503 W504 W605
ignore = E129 W503 W504 W605 E203
[tool:pytest]
addopts =
......
......@@ -387,33 +387,19 @@ class TestPTEmcee(unittest.TestCase):
del self.sampler
def test_default_kwargs(self):
expected = dict(ntemps=2, nwalkers=500,
Tmax=None, betas=None,
threads=1, pool=None, a=2.0,
loglargs=[], logpargs=[],
loglkwargs={}, logpkwargs={},
adaptation_lag=10000, adaptation_time=100,
random=None, iterations=100, thin=1,
storechain=True, adapt=True,
swap_ratios=False,
)
expected = dict(ntemps=20, nwalkers=200, Tmax=None, betas=None, a=2.0,
adaptation_lag=10000, adaptation_time=100, random=None,
adapt=True, swap_ratios=False,)
self.assertDictEqual(expected, self.sampler.kwargs)
def test_translate_kwargs(self):
expected = dict(ntemps=2, nwalkers=150,
Tmax=None, betas=None,
threads=1, pool=None, a=2.0,
loglargs=[], logpargs=[],
loglkwargs={}, logpkwargs={},
adaptation_lag=10000, adaptation_time=100,
random=None, iterations=100, thin=1,
storechain=True, adapt=True,
swap_ratios=False,
)
expected = dict(ntemps=20, nwalkers=200, Tmax=None, betas=None, a=2.0,
adaptation_lag=10000, adaptation_time=100, random=None,
adapt=True, swap_ratios=False,)
for equiv in bilby.core.sampler.base_sampler.MCMCSampler.nwalkers_equiv_kwargs:
new_kwargs = self.sampler.kwargs.copy()
del new_kwargs['nwalkers']
new_kwargs[equiv] = 150
new_kwargs[equiv] = 200
self.sampler.kwargs = new_kwargs
self.assertDictEqual(expected, self.sampler.kwargs)
......@@ -578,7 +564,8 @@ class TestRunningSamplers(unittest.TestCase):
def test_run_ptemcee(self):
_ = bilby.run_sampler(
likelihood=self.likelihood, priors=self.priors, sampler='ptemcee',
nsteps=1000, nwalkers=10, ntemps=10, save=False)
nsamples=100, nwalkers=50, burn_in_act=1, ntemps=1,
frac_threshold=0.5, save=False)
def test_run_pymc3(self):
_ = bilby.run_sampler(
......
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