From 3c13736c312721192dad84d793d06b0a50ea1d39 Mon Sep 17 00:00:00 2001
From: Colm Talbot <colm.talbot@ligo.org>
Date: Mon, 8 Oct 2018 21:12:40 -0500
Subject: [PATCH] add samplers to tests
---
.gitlab-ci.yml | 4 +++
bilby/core/sampler/emcee.py | 2 +-
bilby/core/sampler/pymc3.py | 2 +-
test/sampler_test.py | 59 ++++++++++++++++++++++++++++++++++++-
4 files changed, 64 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 65a54eb66..f6ceb5637 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,6 +18,8 @@ python-2:
stage: test
image: bilbydev/test-suite-py2
before_script:
+ # Source the .bashrc for MultiNest
+ - source /root/.bashrc
# Install the dependencies specified in the Pipfile
- pipenv install --two --python=/opt/conda/bin/python2 --system --deploy
script:
@@ -30,6 +32,8 @@ python-3:
stage: test
image: bilbydev/test-suite-py3
before_script:
+ # Source the .bashrc for MultiNest
+ - source /root/.bashrc
# Install the dependencies specified in the Pipfile
- pipenv install --three --python=/opt/conda/bin/python --system --deploy
script:
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index a641586e2..190e8eec7 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import
+from __future__ import absolute_import, print_function
import numpy as np
from pandas import DataFrame
from ..utils import logger, get_progress_bar
diff --git a/bilby/core/sampler/pymc3.py b/bilby/core/sampler/pymc3.py
index ae7135325..a797836f2 100644
--- a/bilby/core/sampler/pymc3.py
+++ b/bilby/core/sampler/pymc3.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import
+from __future__ import absolute_import, print_function
from collections import OrderedDict
import inspect
diff --git a/test/sampler_test.py b/test/sampler_test.py
index 963813f00..d4cac1ae3 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -5,7 +5,6 @@ from bilby.core.result import Result
import unittest
from mock import MagicMock
import numpy as np
-import inspect
import os
import copy
@@ -393,5 +392,63 @@ class TestPymultinest(unittest.TestCase):
self.assertDictEqual(expected, self.sampler.kwargs)
+class TestRunningSamplers(unittest.TestCase):
+
+ def setUp(self):
+ np.random.seed(42)
+ bilby.core.utils.command_line_args.test = False
+ self.x = np.linspace(0, 1, 11)
+ self.model = lambda x, m, c: m * x + c
+ self.injection_parameters = dict(m=0.5, c=0.2)
+ self.sigma = 0.1
+ self.y = self.model(self.x, **self.injection_parameters) +\
+ np.random.normal(0, self.sigma, len(self.x))
+ self.likelihood = bilby.likelihood.GaussianLikelihood(
+ self.x, self.y, self.model, self.sigma)
+
+ self.priors = dict(
+ m=bilby.core.prior.Uniform(0, 5), c=bilby.core.prior.Uniform(-2, 2))
+
+ def tearDown(self):
+ del self.likelihood
+ del self.priors
+ bilby.core.utils.command_line_args.test = False
+
+ def test_run_cpnest(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors, sampler='cpnest',
+ nlive=100, save=False)
+
+ def test_run_dynesty(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors, sampler='dynesty',
+ nlive=100, save=False)
+
+ def test_run_emcee(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors, sampler='emcee',
+ nsteps=1000, nwalkers=10, save=False)
+
+ def test_run_nestle(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors, sampler='nestle',
+ nlive=100, save=False)
+
+ def test_run_ptemcee(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors, sampler='ptemcee',
+ nsteps=1000, nwalkers=10, ntemps=10, save=False)
+
+ def test_run_pymc3(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors, sampler='pymc3',
+ draws=50, tune=50, n_init=1000, save=False)
+
+ def test_run_pymultinest(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors,
+ sampler='pymultinest', nlive=100, save=False)
+
+
if __name__ == '__main__':
unittest.main()
--
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