cli_bilby/bilby_result.py

@@ -41,6 +41,10 @@ def setup_command_line_args():
                         help="Convert all results.", default=False)
     parser.add_argument("-m", "--merge", action='store_true',
                         help="Merge the set of runs, output saved using the outdir and label")
+    parser.add_argument("-e", "--extension", type=str, choices=["json", "hdf5"],
+                        default=True, help="Use given extension for the merged output file.")
+    parser.add_argument("-g", "--gzip", action="store_true",
+                        help="Gzip the merged output results file if using JSON format.")
     parser.add_argument("-o", "--outdir", type=str, default=None,
                         help="Output directory.")
     parser.add_argument("-l", "--label", type=str, default=None,
@@ -131,4 +135,6 @@ def main():
             result.label = args.label
         if args.outdir is not None:
             result.outdir = args.outdir
-        result.save_to_file()
+
+        extension = args.extension
+        result.save_to_file(gzip=args.gzip, extension=extension)

examples/gw_examples/injection_examples/fast_tutorial.py

@@ -42,6 +42,7 @@ waveform_arguments = dict(waveform_approximant='IMRPhenomPv2',
 waveform_generator = bilby.gw.WaveformGenerator(
     duration=duration, sampling_frequency=sampling_frequency,
     frequency_domain_source_model=bilby.gw.source.lal_binary_black_hole,
+    parameter_conversion=bilby.gw.conversion.convert_to_lal_binary_black_hole_parameters,
     waveform_arguments=waveform_arguments)
 
 # Set up interferometers.  In this case we'll use two interferometers

setup.py

@@ -39,7 +39,7 @@ def write_version_file(version):
     except Exception as e:
         print("Unable to obtain git version information, exception: {}"
               .format(e))
-        git_status = ''
+        git_status = 'release'
 
     version_file = '.version'
     if os.path.isfile(version_file) is False:
@@ -64,7 +64,7 @@ def readfile(filename):
     return filecontents
 
 
-VERSION = '0.6.8'
+VERSION = '0.6.9'
 version_file = write_version_file(VERSION)
 long_description = get_long_description()
 

test/gw_prior_test.py

 from __future__ import division, absolute_import
 from collections import OrderedDict
 import unittest
+import glob
 import os
 import sys
 import pickle
@@ -25,7 +26,7 @@ class TestBBHPriorDict(unittest.TestCase):
         )
         self.filename = os.path.join(
             os.path.dirname(os.path.realpath(__file__)),
-            "prior_files/binary_black_holes.prior",
+            "prior_files/precessing_spins_binary_black_holes.prior",
         )
         self.bbh_prior_dict = bilby.gw.prior.BBHPriorDict(filename=self.filename)
         for key, value in self.bbh_prior_dict.items():
@@ -101,8 +102,8 @@ class TestBBHPriorDict(unittest.TestCase):
             self.assertTrue(self.bbh_prior_dict.test_redundancy(prior))
 
     def test_correct_not_redundant_priors_masses(self):
-        del self.bbh_prior_dict["mass_2"]
-        for prior in ["mass_2", "chirp_mass", "total_mass", "symmetric_mass_ratio"]:
+        del self.bbh_prior_dict["chirp_mass"]
+        for prior in ["chirp_mass", "total_mass", "symmetric_mass_ratio"]:
             self.assertFalse(self.bbh_prior_dict.test_redundancy(prior))
 
     def test_correct_not_redundant_priors_spin_magnitudes(self):
@@ -140,9 +141,9 @@ class TestBBHPriorDict(unittest.TestCase):
     def test_test_has_redundant_priors(self):
         self.assertFalse(self.bbh_prior_dict.test_has_redundant_keys())
         for prior in [
-            "chirp_mass",
+            "mass_1",
+            "mass_2",
             "total_mass",
-            "mass_ratio",
             "symmetric_mass_ratio",
             "cos_tilt_1",
             "cos_tilt_2",
@@ -266,26 +267,27 @@ class TestPackagedPriors(unittest.TestCase):
     """ Test that the prepackaged priors load """
 
     def test_aligned(self):
-        filename = "aligned_spin_binary_black_holes.prior"
+        filename = "aligned_spins_binary_black_holes.prior"
         prior_dict = bilby.gw.prior.BBHPriorDict(filename=filename)
         self.assertTrue("chi_1" in prior_dict)
         self.assertTrue("chi_2" in prior_dict)
 
-    def test_precessing(self):
-        filename = "precessing_binary_neutron_stars.prior"
-        prior_dict = bilby.gw.prior.BBHPriorDict(filename=filename)
-        self.assertTrue("lambda_1" in prior_dict)
-        self.assertTrue("lambda_2" in prior_dict)
-
     def test_binary_black_holes(self):
-        filename = "binary_black_holes.prior"
+        filename = "precessing_spins_binary_black_holes.prior"
         prior_dict = bilby.gw.prior.BBHPriorDict(filename=filename)
         self.assertTrue("a_1" in prior_dict)
 
-    def test_binary_neutron_stars(self):
-        filename = "binary_neutron_stars.prior"
-        prior_dict = bilby.gw.prior.BNSPriorDict(filename=filename)
-        self.assertTrue("lambda_1" in prior_dict)
+    def test_all(self):
+        prior_files = glob.glob(bilby.gw.prior.DEFAULT_PRIOR_DIR + "/*prior")
+        for ff in prior_files:
+            print("Checking prior file {}".format(ff))
+            prior_dict = bilby.gw.prior.BBHPriorDict(filename=ff)
+            self.assertTrue("chirp_mass" in prior_dict)
+            self.assertTrue("mass_ratio" in prior_dict)
+            if "precessing" in ff:
+                self.assertTrue("a_1" in prior_dict)
+            elif "aligned" in ff:
+                self.assertTrue("chi_1" in prior_dict)
 
 
 class TestBNSPriorDict(unittest.TestCase):
@@ -296,7 +298,7 @@ class TestBNSPriorDict(unittest.TestCase):
         )
         self.filename = os.path.join(
             os.path.dirname(os.path.realpath(__file__)),
-            "prior_files/binary_neutron_stars.prior",
+            "prior_files/aligned_spins_waveform_tides_on.prior",
         )
         self.bns_prior_dict = bilby.gw.prior.BNSPriorDict(filename=self.filename)
         for key, value in self.bns_prior_dict.items():
@@ -369,8 +371,8 @@ class TestBNSPriorDict(unittest.TestCase):
             self.assertTrue(self.bns_prior_dict.test_redundancy(prior))
 
     def test_correct_not_redundant_priors_masses(self):
-        del self.bns_prior_dict["mass_2"]
-        for prior in ["mass_2", "chirp_mass", "total_mass", "symmetric_mass_ratio"]:
+        del self.bns_prior_dict["chirp_mass"]
+        for prior in ["chirp_mass", "total_mass", "symmetric_mass_ratio"]:
             self.assertFalse(self.bns_prior_dict.test_redundancy(prior))
 
     def test_correct_not_redundant_priors_spin_magnitudes(self):
@@ -398,9 +400,9 @@ class TestBNSPriorDict(unittest.TestCase):
     def test_test_has_redundant_priors(self):
         self.assertFalse(self.bns_prior_dict.test_has_redundant_keys())
         for prior in [
-            "chirp_mass",
+            "mass_1",
+            "mass_2",
             "total_mass",
-            "mass_ratio",
             "symmetric_mass_ratio",
             "cos_theta_jn",
             "comoving_distance",

test/prior_files/aligned_spins_waveform_tides_on.prior

+chirp_mass = Uniform(name='chirp_mass', minimum=3.56, maximum=3.68)
+mass_ratio = Uniform(name='mass_ratio', minimum=0.05, maximum=1)
+mass_1 = Constraint(name='mass_1', minimum=1.00, maximum=22.0)
+mass_2 = Constraint(name='mass_2', minimum=1.00, maximum=2.95)
+chi_1 = bilby.gw.prior.AlignedSpin(name='chi_1', a_prior=Uniform(minimum=0, maximum=0.5))
+chi_2 = bilby.gw.prior.AlignedSpin(name='chi_2', a_prior=Uniform(minimum=0, maximum=0.05))
+luminosity_distance = bilby.core.prior.PowerLaw(alpha=2, name='luminosity_distance', minimum=1, maximum=750, unit='Mpc')
+ra = Uniform(minimum=0, maximum=2 * np.pi, name='ra',  boundary='periodic')
+dec = Cosine(name='dec')
+theta_jn = Sine(name='theta_jn')
+psi = Uniform(name='psi', minimum=0, maximum=np.pi, boundary='periodic')
+phase = Uniform(name='phase', minimum=0, maximum=2 * np.pi, boundary='periodic')
+lambda_1 = Uniform(name='lambda_2', minimum=0, maximum=5000)
+lambda_2 = Uniform(name='lambda_2', minimum=0, maximum=5000)

test/prior_files/binary_neutron_stars.prior

-# These are the default priors we use for BNS systems.
-# Note that you may wish to use more specific mass and distance parameters.
-# These commands are all known to bilby.gw.prior.
-# Lines beginning "#" are ignored.
-mass_1 = Uniform(name='mass_1', minimum=1, maximum=2, unit='$M_{\odot}$', boundary=None)
-mass_2 = Uniform(name='mass_2', minimum=1, maximum=2, unit='$M_{\odot}$', boundary=None)
-mass_ratio = Constraint(name='mass_ratio', minimum=0.125, maximum=1)
-# chirp_mass = Uniform(name='chirp_mass', minimum=0.87, maximum=1.74, unit='$M_{\odot}$', boundary=None)
-# total_mass = Uniform(name='total_mass', minimum=2, maximum=4, unit='$M_{\odot}$', boundary=None)
-# mass_ratio = Uniform(name='mass_ratio', minimum=0.5, maximum=1, boundary=None)
-# symmetric_mass_ratio = Uniform(name='symmetric_mass_ratio', minimum=0.22, maximum=0.25, boundary=None)
-chi_1 = bilby.gw.prior.AlignedSpin(a_prior=Uniform(0, 0.05), z_prior=Uniform(-1, 1), name='chi_1', latex_label='$\\chi_1$', boundary='reflective')
-chi_2 = bilby.gw.prior.AlignedSpin(a_prior=Uniform(0, 0.05), z_prior=Uniform(-1, 1), name='chi_2', latex_label='$\\chi_2$', boundary='reflective')
-luminosity_distance = bilby.gw.prior.UniformSourceFrame(name='luminosity_distance', minimum=10, maximum=500, unit='Mpc', boundary=None)
-dec = Cosine(name='dec', boundary='reflective')
-ra = Uniform(name='ra', minimum=0, maximum=2 * np.pi, boundary='periodic')
-theta_jn = Sine(name='theta_jn', boundary='reflective')
-# cos_theta_jn = Uniform(name='cos_theta_jn', minimum=-1, maximum=1, boundary=None)
-psi = Uniform(name='psi', minimum=0, maximum=np.pi, boundary='periodic')
-phase = Uniform(name='phase', minimum=0, maximum=2 * np.pi, boundary='periodic')
-lambda_1 = Uniform(name='lambda_1', minimum=0, maximum=3000, boundary=None)
-lambda_2 = Uniform(name='lambda_2', minimum=0, maximum=3000, boundary=None)
-# lambda_tilde = Uniform(name='lambda_tilde', minimum=0, maximum=5000, boundary=None)
-# delta_lambda = Uniform(name='delta_lambda', minimum=-5000, maximum=5000, boundary=None)

test/prior_files/binary_black_holes.prior → test/prior_files/precessing_spins_binary_black_holes.prior

@@ -2,25 +2,19 @@
 # Note that you may wish to use more specific mass and distance parameters.
 # These commands are all known to bilby.gw.prior.
 # Lines beginning "#" are ignored.
-mass_1 = Uniform(name='mass_1', minimum=5, maximum=100, unit='$M_{\odot}$', boundary=None)
-mass_2 = Uniform(name='mass_2', minimum=5, maximum=100, unit='$M_{\odot}$', boundary=None)
-mass_ratio = Constraint(name='mass_ratio', minimum=0.125, maximum=1)
-# chirp_mass = Uniform(name='chirp_mass', minimum=25, maximum=100, unit='$M_{\odot}$', boundary=None)
-# total_mass = Uniform(name='total_mass', minimum=10, maximum=200, unit='$M_{\odot}$', boundary=None)
-# mass_ratio = Uniform(name='mass_ratio', minimum=0.125, maximum=1, boundary=None)
-# symmetric_mass_ratio =  Uniform(name='symmetric_mass_ratio', minimum=8 / 81, maximum=0.25, boundary=None)
-a_1 = Uniform(name='a_1', minimum=0, maximum=0.8, boundary='reflective')
-a_2 = Uniform(name='a_2', minimum=0, maximum=0.8, boundary='reflective')
-tilt_1 = Sine(name='tilt_1', boundary='reflective')
-tilt_2 = Sine(name='tilt_2', boundary='reflective')
-# cos_tilt_1 = Uniform(name='cos_tilt_1', minimum=-1, maximum=1, boundary=None)
-# cos_tilt_2 = Uniform(name='cos_tilt_2', minimum=-1, maximum=1, boundary=None)
+mass_1 = Constraint(name='mass_1', minimum=5, maximum=100)
+mass_2 = Constraint(name='mass_2', minimum=5, maximum=100)
+mass_ratio = Uniform(name='mass_ratio', minimum=0.125, maximum=1)
+chirp_mass = Uniform(name='chirp_mass', minimum=25, maximum=100)
+a_1 = Uniform(name='a_1', minimum=0, maximum=0.99)
+a_2 = Uniform(name='a_2', minimum=0, maximum=0.99)
+tilt_1 = Sine(name='tilt_1')
+tilt_2 = Sine(name='tilt_2')
 phi_12 = Uniform(name='phi_12', minimum=0, maximum=2 * np.pi, boundary='periodic')
 phi_jl = Uniform(name='phi_jl', minimum=0, maximum=2 * np.pi, boundary='periodic')
-luminosity_distance = bilby.gw.prior.UniformSourceFrame(name='luminosity_distance', minimum=1e2, maximum=5e3, unit='Mpc', boundary=None)
-dec = Cosine(name='dec', boundary='reflective')
+luminosity_distance = bilby.gw.prior.UniformSourceFrame(name='luminosity_distance', minimum=1e2, maximum=5e3)
+dec = Cosine(name='dec')
 ra = Uniform(name='ra', minimum=0, maximum=2 * np.pi, boundary='periodic')
-theta_jn = Sine(name='theta_jn', boundary='reflective')
-# cos_theta_jn = Uniform(name='cos_theta_jn', minimum=-1, maximum=1, boundary=None)
+theta_jn = Sine(name='theta_jn')
 psi = Uniform(name='psi', minimum=0, maximum=np.pi, boundary='periodic')
 phase = Uniform(name='phase', minimum=0, maximum=2 * np.pi, boundary='periodic')

test/prior_test.py

@@ -911,7 +911,7 @@ class TestPriorDict(unittest.TestCase):
         self.prior_set_from_dict = bilby.core.prior.PriorDict(dictionary=self.priors)
         self.default_prior_file = os.path.join(
             os.path.dirname(os.path.realpath(__file__)),
-            "prior_files/binary_black_holes.prior",
+            "prior_files/precessing_spins_binary_black_holes.prior",
         )
         self.prior_set_from_file = bilby.core.prior.PriorDict(
             filename=self.default_prior_file
@@ -946,21 +946,23 @@ class TestPriorDict(unittest.TestCase):
 
     def test_read_from_file(self):
         expected = dict(
-            mass_1=bilby.core.prior.Uniform(
+            mass_1=bilby.core.prior.Constraint(
                 name="mass_1",
                 minimum=5,
                 maximum=100,
-                unit="$M_{\\odot}$",
-                boundary=None,
             ),
-            mass_2=bilby.core.prior.Uniform(
+            mass_2=bilby.core.prior.Constraint(
                 name="mass_2",
                 minimum=5,
                 maximum=100,
-                unit="$M_{\\odot}$",
-                boundary=None,
             ),
-            mass_ratio=bilby.core.prior.Constraint(
+            chirp_mass=bilby.core.prior.Uniform(
+                name="chirp_mass",
+                minimum=25,
+                maximum=100,
+                latex_label="$\mathcal{M}$",
+            ),
+            mass_ratio=bilby.core.prior.Uniform(
                 name="mass_ratio",
                 minimum=0.125,
                 maximum=1,
@@ -968,13 +970,13 @@ class TestPriorDict(unittest.TestCase):
                 unit=None,
             ),
             a_1=bilby.core.prior.Uniform(
-                name="a_1", minimum=0, maximum=0.8, boundary="reflective"
+                name="a_1", minimum=0, maximum=0.99
             ),
             a_2=bilby.core.prior.Uniform(
-                name="a_2", minimum=0, maximum=0.8, boundary="reflective"
+                name="a_2", minimum=0, maximum=0.99
             ),
-            tilt_1=bilby.core.prior.Sine(name="tilt_1", boundary="reflective"),
-            tilt_2=bilby.core.prior.Sine(name="tilt_2", boundary="reflective"),
+            tilt_1=bilby.core.prior.Sine(name="tilt_1"),
+            tilt_2=bilby.core.prior.Sine(name="tilt_2"),
             phi_12=bilby.core.prior.Uniform(
                 name="phi_12", minimum=0, maximum=2 * np.pi, boundary="periodic"
             ),
@@ -988,11 +990,11 @@ class TestPriorDict(unittest.TestCase):
                 unit="Mpc",
                 boundary=None,
             ),
-            dec=bilby.core.prior.Cosine(name="dec", boundary="reflective"),
+            dec=bilby.core.prior.Cosine(name="dec"),
             ra=bilby.core.prior.Uniform(
                 name="ra", minimum=0, maximum=2 * np.pi, boundary="periodic"
             ),
-            theta_jn=bilby.core.prior.Sine(name="theta_jn", boundary="reflective"),
+            theta_jn=bilby.core.prior.Sine(name="theta_jn"),
             psi=bilby.core.prior.Uniform(
                 name="psi", minimum=0, maximum=np.pi, boundary="periodic"
             ),
@@ -1054,21 +1056,23 @@ class TestPriorDict(unittest.TestCase):
         prior_set = bilby.core.prior.PriorDict(dictionary=self.default_prior_file)
         expected = bilby.core.prior.PriorDict(
             dict(
-                mass_1=bilby.core.prior.Uniform(
+                mass_1=bilby.core.prior.Constraint(
                     name="mass_1",
                     minimum=5,
                     maximum=100,
-                    unit="$M_{\\odot}$",
-                    boundary=None,
                 ),
-                mass_2=bilby.core.prior.Uniform(
+                mass_2=bilby.core.prior.Constraint(
                     name="mass_2",
                     minimum=5,
                     maximum=100,
-                    unit="$M_{\\odot}$",
-                    boundary=None,
                 ),
-                mass_ratio=bilby.core.prior.Constraint(
+                chirp_mass=bilby.core.prior.Uniform(
+                    name="chirp_mass",
+                    minimum=25,
+                    maximum=100,
+                    latex_label="$\mathcal{M}$",
+                ),
+                mass_ratio=bilby.core.prior.Uniform(
                     name="mass_ratio",
                     minimum=0.125,
                     maximum=1,
@@ -1076,13 +1080,13 @@ class TestPriorDict(unittest.TestCase):
                     unit=None,
                 ),
                 a_1=bilby.core.prior.Uniform(
-                    name="a_1", minimum=0, maximum=0.8, boundary="reflective"
+                    name="a_1", minimum=0, maximum=0.99,
                 ),
                 a_2=bilby.core.prior.Uniform(
-                    name="a_2", minimum=0, maximum=0.8, boundary="reflective"
+                    name="a_2", minimum=0, maximum=0.99,
                 ),
-                tilt_1=bilby.core.prior.Sine(name="tilt_1", boundary="reflective"),
-                tilt_2=bilby.core.prior.Sine(name="tilt_2", boundary="reflective"),
+                tilt_1=bilby.core.prior.Sine(name="tilt_1"),
+                tilt_2=bilby.core.prior.Sine(name="tilt_2"),
                 phi_12=bilby.core.prior.Uniform(
                     name="phi_12", minimum=0, maximum=2 * np.pi, boundary="periodic"
                 ),
@@ -1096,11 +1100,11 @@ class TestPriorDict(unittest.TestCase):
                     unit="Mpc",
                     boundary=None,
                 ),
-                dec=bilby.core.prior.Cosine(name="dec", boundary="reflective"),
+                dec=bilby.core.prior.Cosine(name="dec"),
                 ra=bilby.core.prior.Uniform(
                     name="ra", minimum=0, maximum=2 * np.pi, boundary="periodic"
                 ),
-                theta_jn=bilby.core.prior.Sine(name="theta_jn", boundary="reflective"),
+                theta_jn=bilby.core.prior.Sine(name="theta_jn"),
                 psi=bilby.core.prior.Uniform(
                     name="psi", minimum=0, maximum=np.pi, boundary="periodic"
                 ),
@@ -1248,7 +1252,7 @@ class TestFillPrior(unittest.TestCase):
         self.priors = bilby.core.prior.PriorDict(dictionary=self.priors)
         self.default_prior_file = os.path.join(
             os.path.dirname(os.path.realpath(__file__)),
-            "prior_files/binary_black_holes.prior",
+            "prior_files/precessing_spins_binary_black_holes.prior",
         )
         self.priors.fill_priors(self.likelihood, self.default_prior_file)
 
@@ -1288,7 +1292,7 @@ class TestCreateDefaultPrior(unittest.TestCase):
     def test_bbh_params(self):
         prior_file = os.path.join(
             os.path.dirname(os.path.realpath(__file__)),
-            "prior_files/binary_black_holes.prior",
+            "prior_files/precessing_spins_binary_black_holes.prior",
         )
         prior_set = bilby.core.prior.PriorDict(filename=prior_file)
         for prior in prior_set:
@@ -1302,7 +1306,7 @@ class TestCreateDefaultPrior(unittest.TestCase):
     def test_unknown_prior(self):
         prior_file = os.path.join(
             os.path.dirname(os.path.realpath(__file__)),
-            "prior_files/binary_black_holes.prior",
+            "prior_files/precessing_spins_binary_black_holes.prior",
         )
         self.assertIsNone(
             bilby.core.prior.create_default_prior(

test/sampler_test.py

@@ -767,7 +767,8 @@ class TestPymultinest(unittest.TestCase):
                         n_iter_before_update=100, null_log_evidence=-1e90,
                         max_modes=100, mode_tolerance=-1e90, seed=-1,
                         context=0, write_output=True, log_zero=-1e100,
-                        max_iter=0, init_MPI=False, dump_callback=None)
+                        max_iter=0, init_MPI=False, dump_callback='dumper')
+        self.sampler.kwargs['dump_callback'] = 'dumper'  # Check like the dynesty print_func
         self.assertListEqual([1, 0], self.sampler.kwargs['wrapped_params'])  # Check this separately
         self.sampler.kwargs['wrapped_params'] = None  # The dict comparison can't handle lists
         self.assertDictEqual(expected, self.sampler.kwargs)
@@ -782,7 +783,7 @@ class TestPymultinest(unittest.TestCase):
                         n_iter_before_update=100, null_log_evidence=-1e90,
                         max_modes=100, mode_tolerance=-1e90, seed=-1,
                         context=0, write_output=True, log_zero=-1e100,
-                        max_iter=0, init_MPI=False, dump_callback=None)
+                        max_iter=0, init_MPI=False, dump_callback='dumper')
 
         for equiv in bilby.core.sampler.base_sampler.NestedSampler.npoints_equiv_kwargs:
             new_kwargs = self.sampler.kwargs.copy()
@@ -790,6 +791,7 @@ class TestPymultinest(unittest.TestCase):
             new_kwargs[
                 "wrapped_params"
             ] = None  # The dict comparison can't handle lists
+            new_kwargs['dump_callback'] = 'dumper'  # Check this like Dynesty print_func
             new_kwargs[equiv] = 123
             self.sampler.kwargs = new_kwargs
             self.assertDictEqual(expected, self.sampler.kwargs)