Merge branch 'test_samplers' into 'master'

add samplers to tests

See merge request Monash/bilby!236

.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:

bilby/core/sampler/emcee.py

-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

bilby/core/sampler/pymc3.py

-from __future__ import absolute_import
+from __future__ import absolute_import, print_function
 
 from collections import OrderedDict
 import inspect

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()