From b5b225a0ab7e3f4aa53f47f412fa7dce54f3f517 Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Mon, 16 Sep 2019 19:19:54 -0500
Subject: [PATCH] Fix missing default kwarg n_effective in dynesty
---
bilby/core/sampler/dynesty.py | 31 ++++++++++++++++++++++++++-----
test/sampler_test.py | 4 ++--
2 files changed, 28 insertions(+), 7 deletions(-)
diff --git a/bilby/core/sampler/dynesty.py b/bilby/core/sampler/dynesty.py
index 4bcafd423..3bd8b55e4 100644
--- a/bilby/core/sampler/dynesty.py
+++ b/bilby/core/sampler/dynesty.py
@@ -87,7 +87,7 @@ class Dynesty(NestedSampler):
update_interval=None, print_func=None,
dlogz=0.1, maxiter=None, maxcall=None,
logl_max=np.inf, add_live=True, print_progress=True,
- save_bounds=False)
+ save_bounds=False, n_effective=None)
def __init__(self, likelihood, priors, outdir='outdir', label='label',
use_ratio=False, plot=False, skip_import_verification=False,
@@ -131,7 +131,8 @@ class Dynesty(NestedSampler):
@property
def sampler_function_kwargs(self):
keys = ['dlogz', 'print_progress', 'print_func', 'maxiter',
- 'maxcall', 'logl_max', 'add_live', 'save_bounds']
+ 'maxcall', 'logl_max', 'add_live', 'save_bounds',
+ 'n_effective']
return {key: self.kwargs[key] for key in keys}
@property
@@ -257,9 +258,29 @@ class Dynesty(NestedSampler):
return self.result
+ def _run_nested_wrapper(self, kwargs):
+ """ Wrapper function to run_nested
+
+ This wrapper catches exceptions related to different versions of
+ dynesty accepting different arguments.
+
+ Parameters
+ ----------
+ kwargs: dict
+ The dictionary of kwargs to pass to run_nested
+
+ """
+ logger.debug("Calling run_nested with sampler_function_kwargs {}"
+ .format(kwargs))
+ try:
+ self.sampler.run_nested(**kwargs)
+ except TypeError:
+ kwargs.pop("n_effective")
+ self.sampler.run_nested(**kwargs)
+
def _run_external_sampler_without_checkpointing(self):
logger.debug("Running sampler without checkpointing")
- self.sampler.run_nested(**self.sampler_function_kwargs)
+ self._run_nested_wrapper(self.sampler_function_kwargs)
return self.sampler.results
def _run_external_sampler_with_checkpointing(self):
@@ -276,7 +297,7 @@ class Dynesty(NestedSampler):
self.start_time = datetime.datetime.now()
while True:
sampler_kwargs['maxcall'] += self.n_check_point
- self.sampler.run_nested(**sampler_kwargs)
+ self._run_nested_wrapper(sampler_kwargs)
if self.sampler.ncall == old_ncall:
break
old_ncall = self.sampler.ncall
@@ -284,7 +305,7 @@ class Dynesty(NestedSampler):
self.write_current_state()
sampler_kwargs['add_live'] = True
- self.sampler.run_nested(**sampler_kwargs)
+ self._run_nested_wrapper(sampler_kwargs)
return self.sampler.results
def _remove_checkpoint(self):
diff --git a/test/sampler_test.py b/test/sampler_test.py
index 9657cb286..a7cfe5978 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -155,7 +155,7 @@ class TestDynesty(unittest.TestCase):
enlarge=None, bootstrap=None, vol_dec=0.5, vol_check=2.0,
facc=0.5, slices=5, dlogz=0.1, maxiter=None, maxcall=None,
logl_max=np.inf, add_live=True, print_progress=True, save_bounds=False,
- walks=20, update_interval=600, print_func='func')
+ walks=20, update_interval=600, print_func='func', n_effective=None)
self.sampler.kwargs['print_func'] = 'func' # set this manually as this is not testable otherwise
self.assertListEqual([0, 1], self.sampler.kwargs['periodic']) # Check this separately
self.sampler.kwargs['periodic'] = None # The dict comparison can't handle lists
@@ -173,7 +173,7 @@ class TestDynesty(unittest.TestCase):
enlarge=None, bootstrap=None, vol_dec=0.5, vol_check=2.0,
facc=0.5, slices=5, dlogz=0.1, maxiter=None, maxcall=None,
logl_max=np.inf, add_live=True, print_progress=True, save_bounds=False,
- walks=20, update_interval=600, print_func='func')
+ walks=20, update_interval=600, print_func='func', n_effective=None)
for equiv in bilby.core.sampler.base_sampler.NestedSampler.npoints_equiv_kwargs:
new_kwargs = self.sampler.kwargs.copy()
--
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