diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index 9f028c9fc91901344434aaf434c48d190daa50cf..56e6887d188ccb78e16e614799f74cd324a7e8b9 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -2,6 +2,7 @@ from __future__ import absolute_import, print_function
import numpy as np
from pandas import DataFrame
+from distutils.version import LooseVersion
from ..utils import logger, get_progress_bar
from .base_sampler import MCMCSampler, SamplerError
@@ -38,7 +39,7 @@ class Emcee(MCMCSampler):
"""
default_kwargs = dict(nwalkers=500, a=2, args=[], kwargs={},
- postargs=None, threads=1, pool=None, live_dangerously=False,
+ postargs=None, pool=None, live_dangerously=False,
runtime_sortingfn=None, lnprob0=None, rstate0=None,
blobs0=None, iterations=100, thin=1, storechain=True, mh_proposal=None)
@@ -62,17 +63,69 @@ class Emcee(MCMCSampler):
if 'iterations' not in kwargs:
if 'nsteps' in kwargs:
kwargs['iterations'] = kwargs.pop('nsteps')
+ if 'threads' in kwargs:
+ if kwargs['threads'] != 1:
+ logger.warning("The 'threads' argument cannot be used for "
+ "parallelisation. This run will proceed "
+ "without parallelisation, but consider the use "
+ "of an appropriate Pool object passed to the "
+ "'pool' keyword.")
+ kwargs['threads'] = 1
@property
def sampler_function_kwargs(self):
+ import emcee
+
keys = ['lnprob0', 'rstate0', 'blobs0', 'iterations', 'thin', 'storechain', 'mh_proposal']
- return {key: self.kwargs[key] for key in keys}
+
+ # updated function keywords for emcee > v2.2.1
+ updatekeys = {'p0': 'initial_state',
+ 'lnprob0': 'log_prob0',
+ 'storechain': 'store'}
+
+ function_kwargs = {key: self.kwargs[key] for key in keys if key in self.kwargs}
+ function_kwargs['p0'] = self.pos0
+
+ if LooseVersion(emcee.__version__) > LooseVersion('2.2.1'):
+ if function_kwargs['mh_proposal'] is not None:
+ logger.warning("The 'mh_proposal' option is no longer used "
+ "in emcee v{}, and will be ignored.".format(emcee.__version__))
+ del function_kwargs['mh_proposal']
+
+ for key in updatekeys:
+ if updatekeys[key] not in function_kwargs:
+ function_kwargs[updatekeys[key]] = function_kwargs.pop(key)
+ else:
+ del function_kwargs[key]
+
+ return function_kwargs
@property
def sampler_init_kwargs(self):
- return {key: value
- for key, value in self.kwargs.items()
- if key not in self.sampler_function_kwargs}
+ import emcee
+
+ init_kwargs = {key: value
+ for key, value in self.kwargs.items()
+ if key not in self.sampler_function_kwargs}
+
+ init_kwargs['lnpostfn'] = self.lnpostfn
+ init_kwargs['dim'] = self.ndim
+
+ # updated init keywords for emcee > v2.2.1
+ updatekeys = {'dim': 'ndim',
+ 'lnpostfn': 'log_prob_fn'}
+
+ if LooseVersion(emcee.__version__) > LooseVersion('2.2.1'):
+ for key in updatekeys:
+ if key in init_kwargs:
+ init_kwargs[updatekeys[key]] = init_kwargs.pop(key)
+
+ oldfunckeys = ['p0', 'lnprob0', 'storechain', 'mh_proposal']
+ for key in oldfunckeys:
+ if key in init_kwargs:
+ del init_kwargs[key]
+
+ return init_kwargs
@property
def nburn(self):
@@ -104,12 +157,19 @@ class Emcee(MCMCSampler):
def nsteps(self, nsteps):
self.kwargs['iterations'] = nsteps
+ def __getstate__(self):
+ # In order to be picklable with dill, we need to discard the pool
+ # object before trying.
+ d = self.__dict__
+ d["_Sampler__kwargs"]["pool"] = None
+ return d
+
def run_sampler(self):
import emcee
tqdm = get_progress_bar()
- sampler = emcee.EnsembleSampler(dim=self.ndim, lnpostfn=self.lnpostfn, **self.sampler_init_kwargs)
+ sampler = emcee.EnsembleSampler(**self.sampler_init_kwargs)
self._set_pos0()
- for _ in tqdm(sampler.sample(p0=self.pos0, **self.sampler_function_kwargs),
+ for _ in tqdm(sampler.sample(**self.sampler_function_kwargs),
total=self.nsteps):
pass
self.result.sampler_output = np.nan
diff --git a/bilby/gw/detector.py b/bilby/gw/detector.py
index 38cda74fe96d52d5d5c52aa49fc10c6d7c801bff..599f492462a458d2393c2f0b59ac84a71a7b41db 100644
--- a/bilby/gw/detector.py
+++ b/bilby/gw/detector.py
@@ -1304,7 +1304,7 @@ class Interferometer(object):
`waveform_generator.frequency_domain_strain()`. If
`waveform_generator` is also given, the injection_polarizations will
be calculated directly and this argument can be ignored.
- waveform_generator: bilby.gw.waveform_generator
+ waveform_generator: bilby.gw.waveform_generator.WaveformGenerator
A WaveformGenerator instance using the source model to inject. If
`injection_polarizations` is given, this will be ignored.
@@ -2158,7 +2158,7 @@ def get_interferometer_with_fake_noise_and_injection(
`waveform_generator.frequency_domain_strain()`. If
`waveform_generator` is also given, the injection_polarizations will
be calculated directly and this argument can be ignored.
- waveform_generator: bilby.gw.waveform_generator
+ waveform_generator: bilby.gw.waveform_generator.WaveformGenerator
A WaveformGenerator instance using the source model to inject. If
`injection_polarizations` is given, this will be ignored.
sampling_frequency: float
diff --git a/test/sampler_test.py b/test/sampler_test.py
index cd40784c786189ae8dd640889c9330b8b0ef4dac..0ffbb2bac84f0096fa8dc7e20052b0ad1ee09b78 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -191,7 +191,7 @@ class TestEmcee(unittest.TestCase):
def test_default_kwargs(self):
expected = dict(nwalkers=500, a=2, args=[], kwargs={},
- postargs=None, threads=1, pool=None, live_dangerously=False,
+ postargs=None, pool=None, live_dangerously=False,
runtime_sortingfn=None, lnprob0=None, rstate0=None,
blobs0=None, iterations=100, thin=1, storechain=True, mh_proposal=None
)
@@ -199,7 +199,7 @@ class TestEmcee(unittest.TestCase):
def test_translate_kwargs(self):
expected = dict(nwalkers=100, a=2, args=[], kwargs={},
- postargs=None, threads=1, pool=None, live_dangerously=False,
+ postargs=None, pool=None, live_dangerously=False,
runtime_sortingfn=None, lnprob0=None, rstate0=None,
blobs0=None, iterations=100, thin=1, storechain=True, mh_proposal=None)
for equiv in bilby.core.sampler.base_sampler.MCMCSampler.nwalkers_equiv_kwargs: