CHANGELOG.md

 # All notable changes will be documented in this file
 
+## [0.6.8] 2020-05-21
+### Changes
+- Improvement to the proposal step in dynesty (!774)
+- Fix a bug in checking and making directories (!792)
+- Clean up of the default prior files (!789)
+
 ## [0.6.8] 2020-05-13
 ### Added
 - Option to sample in the sky frame (!786)

bilby/core/prior/base.py

@@ -68,6 +68,9 @@ class Prior(object):
         if sorted(self.__dict__.keys()) != sorted(other.__dict__.keys()):
             return False
         for key in self.__dict__:
+            if key == "least_recently_sampled":
+                # ignore sample drawn from prior in comparison
+                continue
             if type(self.__dict__[key]) is np.ndarray:
                 if not np.array_equal(self.__dict__[key], other.__dict__[key]):
                     return False

bilby/core/result.py

@@ -23,7 +23,8 @@ from .utils import (
     check_directory_exists_and_if_not_mkdir,
     latex_plot_format, safe_save_figure,
     BilbyJsonEncoder, load_json,
-    move_old_file, get_version_information
+    move_old_file, get_version_information,
+    decode_bilby_json,
 )
 from .prior import Prior, PriorDict, DeltaFunction
 
@@ -358,10 +359,27 @@ class Result(object):
 
         if os.path.isfile(filename):
             dictionary = deepdish.io.load(filename)
-            # Some versions of deepdish/pytables return the dictionanary as
+            # Some versions of deepdish/pytables return the dictionary as
             # a dictionary with a key 'data'
             if len(dictionary) == 1 and 'data' in dictionary:
                 dictionary = dictionary['data']
+
+            if "priors" in dictionary:
+                # parse priors from JSON string (allowing for backwards
+                # compatibility)
+                if not isinstance(dictionary["priors"], PriorDict):
+                    try:
+                        priordict = PriorDict()
+                        for key, value in dictionary["priors"].items():
+                            if key not in ["__module__", "__name__", "__prior_dict__"]:
+                                priordict[key] = decode_bilby_json(value)
+                        dictionary["priors"] = priordict
+                    except Exception as e:
+                        raise IOError(
+                            "Unable to parse priors from '{}':\n{}".format(
+                                filename, e,
+                            )
+                        )
             try:
                 if isinstance(dictionary.get('posterior', None), dict):
                     dictionary['posterior'] = pd.DataFrame(dictionary['posterior'])
@@ -609,8 +627,9 @@ class Result(object):
                     dictionary['sampler_kwargs'][key] = str(dictionary['sampler_kwargs'])
 
         try:
+            # convert priors to JSON dictionary for both JSON and hdf5 files
+            dictionary["priors"] = dictionary["priors"]._get_json_dict()
             if extension == 'json':
-                dictionary["priors"] = dictionary["priors"]._get_json_dict()
                 if gzip:
                     import gzip
                     # encode to a string
@@ -1123,15 +1142,16 @@ class Result(object):
         idxs = np.arange(nsteps)
         fig, axes = plt.subplots(nrows=ndim, figsize=(6, 3 * ndim))
         walkers = self.walkers[:, :, :]
+        parameter_labels = sanity_check_labels(self.parameter_labels)
         for i, ax in enumerate(axes):
             ax.plot(idxs[:self.nburn + 1], walkers[:, :self.nburn + 1, i].T,
                     lw=0.1, color='r')
-            ax.set_ylabel(self.parameter_labels[i])
+            ax.set_ylabel(parameter_labels[i])
 
         for i, ax in enumerate(axes):
             ax.plot(idxs[self.nburn:], walkers[:, self.nburn:, i].T, lw=0.1,
                     color='k')
-            ax.set_ylabel(self.parameter_labels[i])
+            ax.set_ylabel(parameter_labels[i])
 
         fig.tight_layout()
         outdir = self._safe_outdir_creation(kwargs.get('outdir'), self.plot_walkers)

bilby/core/sampler/base_sampler.py

@@ -430,6 +430,7 @@ class Sampler(object):
             likelihood evaluations.
 
         """
+        logger.info("Generating initial points from the prior")
         unit_cube = []
         parameters = []
         likelihood = []

bilby/core/sampler/dynesty.py

@@ -257,11 +257,11 @@ class Dynesty(NestedSampler):
         # Constructing output.
         string = []
         string.append("bound:{:d}".format(bounditer))
-        string.append("nc:{:d}".format(nc))
-        string.append("ncall:{:d}".format(ncall))
+        string.append("nc:{:3d}".format(nc))
+        string.append("ncall:{:.1e}".format(ncall))
         string.append("eff:{:0.1f}%".format(eff))
         string.append("{}={:0.2f}+/-{:0.2f}".format(key, logz, logzerr))
-        string.append("dlogz:{:0.3f}>{:0.2f}".format(delta_logz, dlogz))
+        string.append("dlogz:{:0.3f}>{:0.2g}".format(delta_logz, dlogz))
 
         self.pbar.set_postfix_str(" ".join(string), refresh=False)
         self.pbar.update(niter - self.pbar.n)
@@ -715,19 +715,20 @@ def sample_rwalk_bilby(args):
     reject = 0
     nfail = 0
     act = np.inf
-    u_list = [u]
-    v_list = [prior_transform(u)]
-    logl_list = [loglikelihood(v_list[-1])]
-    max_walk_warning = True
+    u_list = []
+    v_list = []
+    logl_list = []
 
-    while len(u_list) < nact * act:
+    ii = 0
+    while ii < nact * act:
+        ii += 1
 
         # Propose a direction on the unit n-sphere.
         drhat = rstate.randn(n)
         drhat /= linalg.norm(drhat)
 
         # Scale based on dimensionality.
-        dr = drhat * rstate.rand()**(1. / n)
+        dr = drhat * rstate.rand() ** (1.0 / n)
 
         # Transform to proposal distribution.
         du = np.dot(axes, dr)
@@ -778,16 +779,12 @@ def sample_rwalk_bilby(args):
                 old_act=old_act, maxmcmc=maxmcmc)
 
         # If we've taken too many likelihood evaluations then break
-        if accept + reject > maxmcmc and accept > 0:
-            if max_walk_warning:
-                warnings.warn(
-                    "Hit maximum number of walks {} with accept={}, reject={}, "
-                    "and nfail={} try increasing maxmcmc"
-                    .format(maxmcmc, accept, reject, nfail))
-                max_walk_warning = False
-            if accept > 0:
-                # Break if we are above maxmcmc and have at least one accepted point
-                break
+        if accept + reject > maxmcmc:
+            warnings.warn(
+                "Hit maximum number of walks {} with accept={}, reject={}, "
+                "and nfail={} try increasing maxmcmc"
+                .format(maxmcmc, accept, reject, nfail))
+            break
 
     # If the act is finite, pick randomly from within the chain
     if np.isfinite(act) and int(.5 * nact * act) < len(u_list):
@@ -795,17 +792,11 @@ def sample_rwalk_bilby(args):
         u = u_list[idx]
         v = v_list[idx]
         logl = logl_list[idx]
-    elif len(u_list) == 1:
-        logger.warning("Returning the only point in the chain")
-        u = u_list[-1]
-        v = v_list[-1]
-        logl = logl_list[-1]
     else:
-        idx = np.random.randint(int(len(u_list) / 2), len(u_list))
-        logger.warning("Returning random point in second half of the chain")
-        u = u_list[idx]
-        v = v_list[idx]
-        logl = logl_list[idx]
+        logger.debug("Unable to find a new point using walk: returning a random point")
+        u = np.random.uniform(size=n)
+        v = prior_transform(u)
+        logl = loglikelihood(v)
 
     blob = {'accept': accept, 'reject': reject, 'fail': nfail, 'scale': scale}
     kwargs["old_act"] = act

bilby/core/sampler/ptemcee.py

@@ -193,7 +193,13 @@ class Ptemcee(MCMCSampler):
         )
         self.convergence_inputs = ConvergenceInputs(**convergence_inputs_dict)
 
-        # MultiProcessing inputs
+        # Check if threads was given as an equivalent arg
+        if threads == 1:
+            for equiv in self.npool_equiv_kwargs:
+                if equiv in kwargs:
+                    threads = kwargs.pop(equiv)
+
+        # Store threads
         self.threads = threads
 
         # Misc inputs
@@ -221,10 +227,6 @@ class Ptemcee(MCMCSampler):
             for equiv in self.nwalkers_equiv_kwargs:
                 if equiv in kwargs:
                     kwargs["nwalkers"] = kwargs.pop(equiv)
-        if "threads" not in kwargs:
-            for equiv in self.npool_equiv_kwargs:
-                if equiv in kwargs:
-                    kwargs["threads"] = kwargs.pop(equiv)
 
     def get_pos0_from_prior(self):
         """ Draw the initial positions from the prior

bilby/core/sampler/pymultinest.py

@@ -2,7 +2,10 @@ import importlib
 import os
 import tempfile
 import shutil
+import distutils.dir_util
 import signal
+import time
+import datetime
 
 import numpy as np
 
@@ -115,8 +118,15 @@ class Pymultinest(NestedSampler):
         # for PyMultiNest >=2.9 the n_params kwarg cannot be None
         if self.kwargs["n_params"] is None:
             self.kwargs["n_params"] = self.ndim
+        if self.kwargs['dump_callback'] is None:
+            self.kwargs['dump_callback'] = self._dump_callback
         NestedSampler._verify_kwargs_against_default_kwargs(self)
 
+    def _dump_callback(self, *args, **kwargs):
+        if self.use_temporary_directory:
+            self._copy_temporary_directory_contents_to_proper_path()
+        self._calculate_and_save_sampling_time()
+
     def _apply_multinest_boundaries(self):
         if self.kwargs["wrapped_params"] is None:
             self.kwargs["wrapped_params"] = []
@@ -154,10 +164,6 @@ class Pymultinest(NestedSampler):
             shutil.copytree(
                 self.outputfiles_basename, self.temporary_outputfiles_basename
             )
-            if os.path.islink(self.outputfiles_basename):
-                os.unlink(self.outputfiles_basename)
-            else:
-                shutil.rmtree(self.outputfiles_basename)
 
     def write_current_state_and_exit(self, signum=None, frame=None):
         """ Write current state and exit on exit_code """
@@ -166,26 +172,35 @@ class Pymultinest(NestedSampler):
                 signum, self.exit_code
             )
         )
+        self._calculate_and_save_sampling_time()
         if self.use_temporary_directory:
             self._move_temporary_directory_to_proper_path()
         os._exit(self.exit_code)
 
-    def _move_temporary_directory_to_proper_path(self):
+    def _copy_temporary_directory_contents_to_proper_path(self):
         """
-        Move the temporary back to the proper path
-
-        Anything in the proper path at this point is removed including links
+        Copy the temporary back to the proper path.
+        Do not delete the temporary directory.
         """
         logger.info(
             "Overwriting {} with {}".format(
                 self.outputfiles_basename, self.temporary_outputfiles_basename
             )
         )
-        if os.path.islink(self.outputfiles_basename.strip("/")):
-            os.unlink(self.outputfiles_basename.strip("/"))
-        elif os.path.isdir(self.outputfiles_basename):
-            shutil.rmtree(self.outputfiles_basename, ignore_errors=True)
-        shutil.move(self.temporary_outputfiles_basename, self.outputfiles_basename)
+        if self.outputfiles_basename.endswith('/'):
+            outputfiles_basename_stripped = self.outputfiles_basename[:-1]
+        else:
+            outputfiles_basename_stripped = self.outputfiles_basename
+        distutils.dir_util.copy_tree(self.temporary_outputfiles_basename, outputfiles_basename_stripped)
+
+    def _move_temporary_directory_to_proper_path(self):
+        """
+        Copy the temporary back to the proper path
+
+        Anything in the temporary directory at this point is removed
+        """
+        self._copy_temporary_directory_contents_to_proper_path()
+        shutil.rmtree(self.temporary_outputfiles_basename)
 
     def run_sampler(self):
         import pymultinest
@@ -193,17 +208,20 @@ class Pymultinest(NestedSampler):
         self._verify_kwargs_against_default_kwargs()
 
         self._setup_run_directory()
+        self._check_and_load_sampling_time_file()
 
         # Overwrite pymultinest's signal handling function
         pm_run = importlib.import_module("pymultinest.run")
         pm_run.interrupt_handler = self.write_current_state_and_exit
 
+        self.start_time = time.time()
         out = pymultinest.solve(
             LogLikelihood=self.log_likelihood,
             Prior=self.prior_transform,
             n_dims=self.ndim,
             **self.kwargs
         )
+        self._calculate_and_save_sampling_time()
 
         self._clean_up_run_directory()
 
@@ -218,26 +236,22 @@ class Pymultinest(NestedSampler):
         self.result.log_evidence_err = out["logZerr"]
         self.calc_likelihood_count()
         self.result.outputfiles_basename = self.outputfiles_basename
+        self.result.sampling_time = datetime.timedelta(seconds=self.total_sampling_time)
         return self.result
 
     def _setup_run_directory(self):
         """
         If using a temporary directory, the output directory is moved to the
-        temporary directory and symlinked back.
+        temporary directory.
         """
         if self.use_temporary_directory:
             temporary_outputfiles_basename = tempfile.TemporaryDirectory().name
             self.temporary_outputfiles_basename = temporary_outputfiles_basename
 
             if os.path.exists(self.outputfiles_basename):
-                shutil.move(self.outputfiles_basename, self.temporary_outputfiles_basename)
+                distutils.dir_util.copy_tree(self.outputfiles_basename, self.temporary_outputfiles_basename)
             check_directory_exists_and_if_not_mkdir(temporary_outputfiles_basename)
 
-            os.symlink(
-                os.path.abspath(self.temporary_outputfiles_basename),
-                os.path.abspath(self.outputfiles_basename),
-                target_is_directory=True,
-            )
             self.kwargs["outputfiles_basename"] = self.temporary_outputfiles_basename
             logger.info("Using temporary file {}".format(temporary_outputfiles_basename))
         else:
@@ -245,6 +259,21 @@ class Pymultinest(NestedSampler):
             self.kwargs["outputfiles_basename"] = self.outputfiles_basename
             logger.info("Using output file {}".format(self.outputfiles_basename))
 
+    def _check_and_load_sampling_time_file(self):
+        self.time_file_path = self.kwargs["outputfiles_basename"] + '/sampling_time.dat'
+        if os.path.exists(self.time_file_path):
+            with open(self.time_file_path, 'r') as time_file:
+                self.total_sampling_time = float(time_file.readline())
+        else:
+            self.total_sampling_time = 0
+
+    def _calculate_and_save_sampling_time(self):
+        current_time = time.time()
+        new_sampling_time = current_time - self.start_time
+        self.total_sampling_time += new_sampling_time
+        with open(self.time_file_path, 'w') as time_file:
+            time_file.write(str(self.total_sampling_time))
+
     def _clean_up_run_directory(self):
         if self.use_temporary_directory:
             self._move_temporary_directory_to_proper_path()

bilby/core/sampler/ultranest.py

@@ -123,10 +123,11 @@ class Ultranest(NestedSampler):
         ):
             self.kwargs["wrapped_params"] = []
             for param, value in self.priors.items():
-                if value.boundary == "periodic":
-                    self.kwargs["wrapped_params"].append(1)
-                else:
-                    self.kwargs["wrapped_params"].append(0)
+                if param in self.search_parameter_keys:
+                    if value.boundary == "periodic":
+                        self.kwargs["wrapped_params"].append(1)
+                    else:
+                        self.kwargs["wrapped_params"].append(0)
 
     @property
     def outputfiles_basename(self):

bilby/core/utils.py

@@ -556,7 +556,9 @@ def check_directory_exists_and_if_not_mkdir(directory):
         Name of the directory
 
     """
-    if not os.path.exists(directory):
+    if directory == "":
+        return
+    elif not os.path.exists(directory):
         os.makedirs(directory)
         logger.debug('Making directory {}'.format(directory))
     else:

bilby/gw/prior.py

@@ -25,6 +25,9 @@ except ImportError:
                  " not be able to use some of the prebuilt functions.")
 
 
+DEFAULT_PRIOR_DIR = os.path.join(os.path.dirname(__file__), 'prior_files')
+
+
 class BilbyPriorConversionError(Exception):
     pass
 
@@ -406,17 +409,17 @@ class BBHPriorDict(CBCPriorDict):
             By default this generates many additional parameters, see
             BBHPriorDict.default_conversion_function
         """
-        basedir = os.path.join(os.path.dirname(__file__), 'prior_files')
         if dictionary is None and filename is None:
-            fname = 'binary_black_holes.prior'
             if aligned_spin:
-                fname = 'aligned_spin_' + fname
+                fname = 'aligned_spins_binary_black_holes.prior'
                 logger.info('Using aligned spin prior')
-            filename = os.path.join(basedir, fname)
+            else:
+                fname = 'precessing_spins_binary_black_holes.prior'
+            filename = os.path.join(DEFAULT_PRIOR_DIR, fname)
             logger.info('No prior given, using default BBH priors in {}.'.format(filename))
         elif filename is not None:
             if not os.path.isfile(filename):
-                filename = os.path.join(os.path.dirname(__file__), 'prior_files', filename)
+                filename = os.path.join(DEFAULT_PRIOR_DIR, filename)
         super(BBHPriorDict, self).__init__(dictionary=dictionary, filename=filename,
                                            conversion_function=conversion_function)
 
@@ -514,15 +517,15 @@ class BNSPriorDict(CBCPriorDict):
             BNSPriorDict.default_conversion_function
         """
         if aligned_spin:
-            default_file = 'binary_neutron_stars.prior'
+            default_file = 'aligned_spins_waveform_tides_on.prior'
         else:
-            default_file = 'precessing_binary_neutron_stars.prior'
+            default_file = 'precessing_spins_waveform_tides_on.prior'
         if dictionary is None and filename is None:
-            filename = os.path.join(os.path.dirname(__file__), 'prior_files', default_file)
+            filename = os.path.join(DEFAULT_PRIOR_DIR, default_file)
             logger.info('No prior given, using default BNS priors in {}.'.format(filename))
         elif filename is not None:
             if not os.path.isfile(filename):
-                filename = os.path.join(os.path.dirname(__file__), 'prior_files', filename)
+                filename = os.path.join(DEFAULT_PRIOR_DIR, filename)
         super(BNSPriorDict, self).__init__(dictionary=dictionary, filename=filename,
                                            conversion_function=conversion_function)
 
@@ -628,8 +631,7 @@ class CalibrationPriorDict(PriorDict):
             See superclass
         """
         if dictionary is None and filename is not None:
-            filename = os.path.join(os.path.dirname(__file__),
-                                    'prior_files', filename)
+            filename = os.path.join(DEFAULT_PRIOR_DIR, filename)
         super(CalibrationPriorDict, self).__init__(dictionary=dictionary, filename=filename)
         self.source = None
 

bilby/gw/prior_files/GW150914.prior

-mass_ratio = Uniform(name='mass_ratio', minimum=0.125, maximum=1, boundary='reflective')
-chirp_mass = Uniform(name='chirp_mass', minimum=25, maximum=31, unit='$M_{\odot}$', boundary='reflective')
+mass_ratio = Uniform(name='mass_ratio', minimum=0.125, maximum=1)
+chirp_mass = Uniform(name='chirp_mass', minimum=25, maximum=31)
 mass_1 = Constraint(name='mass_1', minimum=10, maximum=80)
 mass_2 = Constraint(name='mass_2', minimum=10, maximum=80)
-a_1 = Uniform(name='a_1', minimum=0, maximum=0.99, boundary='reflective')
-a_2 = Uniform(name='a_2', minimum=0, maximum=0.99, boundary='reflective')
+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', boundary='reflective')
 tilt_2 = Sine(name='tilt_2', boundary='reflective')
 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 = PowerLaw(alpha=2, name='luminosity_distance', minimum=50, maximum=2000, unit='Mpc', latex_label='$d_L$')
-dec =  Cosine(name='dec', boundary='reflective')
+dec =  Cosine(name='dec')
 ra =  Uniform(name='ra', minimum=0, maximum=2 * np.pi, boundary='periodic')
 theta_jn =  Sine(name='theta_jn', boundary='reflective')
 psi =  Uniform(name='psi', minimum=0, maximum=np.pi, boundary='periodic')

bilby/gw/prior_files/GW170817.prior

@@ -3,16 +3,16 @@
 # mass_2 = Constraint(name='mass_2', minimum=1., maximum=1.4)
 chirp_mass = Uniform(name='chirp_mass', minimum=0.87, maximum=1.74, unit='$M_{\odot}$', boundary=None)
 mass_ratio = Uniform(name='mass_ratio', minimum=0.125, maximum=1.0, boundary=None)
-a_1 = Uniform(name='a_1', minimum=0, maximum=0.05, boundary='reflective')
-a_2 = Uniform(name='a_2', minimum=0, maximum=0.05, boundary='reflective')
-tilt_1 = Sine(name='tilt_1', boundary='reflective')
-tilt_2 = Sine(name='tilt_2', boundary='reflective')
+a_1 = Uniform(name='a_1', minimum=0, maximum=0.05)
+a_2 = Uniform(name='a_2', minimum=0, maximum=0.05)
+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=10, maximum=100, unit='Mpc', boundary=None)
-dec = Cosine(name='dec', boundary='reflective')
+dec = Cosine(name='dec')
 ra = Uniform(name='ra', minimum=0, maximum=2 * np.pi, boundary='periodic')
-theta_jn = Sine(name='theta_jn', boundary='reflective')
+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 = Constraint(name='lambda_1', minimum=0, maximum=5000)

bilby/gw/prior_files/aligned_spin_binary_black_holes.prior → bilby/gw/prior_files/aligned_spins_binary_black_holes.prior

@@ -2,19 +2,15 @@
 # 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)
-chi_1 = bilby.gw.prior.AlignedSpin(name='chi_1', a_prior=Uniform(minimum=0, maximum=0.8), boundary='reflective')
-chi_2 = bilby.gw.prior.AlignedSpin(name='chi_2', a_prior=Uniform(minimum=0, maximum=0.8), boundary='reflective')
-luminosity_distance = bilby.gw.prior.UniformSourceFrame(name='luminosity_distance', minimum=1e2, maximum=5e3, unit='Mpc', boundary=None)
-dec = Cosine(name='dec', boundary='reflective')
+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)
+chi_1 = bilby.gw.prior.AlignedSpin(name='chi_1', a_prior=Uniform(minimum=0, maximum=0.99))
+chi_2 = bilby.gw.prior.AlignedSpin(name='chi_2', a_prior=Uniform(minimum=0, maximum=0.99))
+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')

bilby/gw/prior_files/aligned_spins_waveform_tides_off.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) #optional
-mass_2 = Constraint(name='mass_2', minimum=1.00, maximum=2.95) #optional
+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')
-cos_theta_jn = Uniform(name='cos_theta_jn', minimum=-1, maximum=1)
+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')

bilby/gw/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) #optional
-mass_2 = Constraint(name='mass_2', minimum=1.00, maximum=2.95) #optional
+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')
-cos_theta_jn = Uniform(name='cos_theta_jn', minimum=-1, maximum=1)
+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)

bilby/gw/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_tilde = Uniform(name='delta_lambda_tilde', minimum=-5000, maximum=5000, boundary=None)

bilby/gw/prior_files/precessing_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)
-a_1 = Uniform(name='a_1', minimum=0, maximum=0.05, boundary='reflective')
-a_2 = Uniform(name='a_2', minimum=0, maximum=0.05, 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)
-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=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_tilde = Uniform(name='delta_lambda_tilde', minimum=-5000, maximum=5000, boundary=None)

bilby/gw/prior_files/binary_black_holes.prior → bilby/gw/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')

bilby/gw/prior_files/precessing_spins_waveform_tides_off.prior

@@ -11,6 +11,6 @@ phi_jl = Uniform(name='phi_jl', minimum=0, maximum=2 * np.pi, boundary='periodic
 luminosity_distance = bilby.gw.prior.UniformComovingVolume(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')
-cos_theta_jn = Uniform(name='cos_theta_jn', minimum=-1, maximum=1)
+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')

bilby/gw/prior_files/precessing_spins_waveform_tides_on.prior

@@ -11,7 +11,7 @@ phi_jl = Uniform(name='phi_jl', minimum=0, maximum=2 * np.pi, boundary='periodic
 luminosity_distance = bilby.gw.prior.UniformComovingVolume(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')
-cos_theta_jn = Uniform(name='cos_theta_jn', minimum=-1, maximum=1)
+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)