From edefa404f49f0508a8973f2293e95a0f3d0d3457 Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Thu, 7 Nov 2019 15:01:29 -0600
Subject: [PATCH] Collection of fixes to resolve issues with testing
---
.gitlab-ci.yml | 10 ----------
bilby/core/sampler/emcee.py | 22 +++++++++++++++-------
test/gw_utils_test.py | 6 +++---
3 files changed, 18 insertions(+), 20 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fc710b579..54485557f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -44,15 +44,6 @@ basic-3.7:
<<: *test-python
image: python:3.7
-# test example on python 2
-python-2.7:
- stage: test
- image: bilbydev/bilby-test-suite-python27
- script:
- - python -m pip install .
- # Run tests without finding coverage
- - pytest --ignore=test/utils_py3_test.py
-
# test example on python 3
python-3.7:
stage: test
@@ -97,7 +88,6 @@ pages:
stage: deploy
dependencies:
- python-3.7
- - python-2.7
script:
- mkdir public/
- mv htmlcov/ public/
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index c2fc9a6f5..12d795d33 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -57,6 +57,8 @@ class Emcee(MCMCSampler):
pos0=None, nburn=None, burn_in_fraction=0.25, resume=True,
burn_in_act=3, **kwargs):
import emcee
+ self.emcee = emcee
+
if LooseVersion(emcee.__version__) > LooseVersion('2.2.1'):
self.prerelease = True
else:
@@ -93,8 +95,8 @@ class Emcee(MCMCSampler):
@property
def sampler_function_kwargs(self):
- import emcee
- keys = ['lnprob0', 'rstate0', 'blobs0', 'iterations', 'thin', 'storechain', 'mh_proposal']
+ keys = ['lnprob0', 'rstate0', 'blobs0', 'iterations', 'thin',
+ 'storechain', 'mh_proposal']
# updated function keywords for emcee > v2.2.1
updatekeys = {'p0': 'initial_state',
@@ -107,7 +109,8 @@ class Emcee(MCMCSampler):
if self.prerelease:
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__))
+ "in emcee v{}, and will be ignored.".format(
+ self.emcee.__version__))
del function_kwargs['mh_proposal']
for key in updatekeys:
@@ -259,8 +262,7 @@ class Emcee(MCMCSampler):
sys.exit()
def _initialise_sampler(self):
- import emcee
- self._sampler = emcee.EnsembleSampler(**self.sampler_init_kwargs)
+ self._sampler = self.emcee.EnsembleSampler(**self.sampler_init_kwargs)
self._init_chain_file()
@property
@@ -307,7 +309,10 @@ class Emcee(MCMCSampler):
This is used when loading in a sampler from a pickle file to figure out
how much of the run has already been completed
"""
- return len(self.sampler.blobs)
+ try:
+ return len(self.sampler.blobs)
+ except AttributeError:
+ return 0
def _draw_pos0_from_prior(self):
return np.array(
@@ -344,7 +349,10 @@ class Emcee(MCMCSampler):
iterations = sampler_function_kwargs.pop('iterations')
iterations -= self._previous_iterations
- sampler_function_kwargs['p0'] = self.pos0
+ if self.prerelease:
+ sampler_function_kwargs['initial_state'] = self.pos0
+ else:
+ sampler_function_kwargs['p0'] = self.pos0
# main iteration loop
for sample in tqdm(
diff --git a/test/gw_utils_test.py b/test/gw_utils_test.py
index b8d1838ca..e9b7b6262 100644
--- a/test/gw_utils_test.py
+++ b/test/gw_utils_test.py
@@ -124,7 +124,7 @@ class TestGWUtils(unittest.TestCase):
strain = gwutils.read_frame_file(
filename, start_time=None, end_time=None, channel=channel)
self.assertEqual(strain.channel.name, channel)
- self.assertTrue(np.all(strain.value==data))
+ self.assertTrue(np.all(strain.value==data[:-1]))
# Check reading with time limits
start_cut = 2
@@ -138,12 +138,12 @@ class TestGWUtils(unittest.TestCase):
# Check reading with unknown channels
strain = gwutils.read_frame_file(
filename, start_time=None, end_time=None)
- self.assertTrue(np.all(strain.value==data))
+ self.assertTrue(np.all(strain.value==data[:-1]))
# Check reading with incorrect channel
strain = gwutils.read_frame_file(
filename, start_time=None, end_time=None, channel='WRONG')
- self.assertTrue(np.all(strain.value==data))
+ self.assertTrue(np.all(strain.value==data[:-1]))
ts = gwpy.timeseries.TimeSeries(data=data, times=times, t0=0)
ts.name = 'NOT-A-KNOWN-CHANNEL'
--
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