Reduce imports
Importing bilby is pretty horribly slow, sometimes taking O(s). This is due to the number of top-level imports we have.
Using len(sys.modules) as a proxy for the number of packages being imported when bilby imports shows that we're being pretty bad on imports. The following gives an idea of the number of things imported for a few reference modules.
import sys
print(len(sys.modules.keys()))
import numpy
print(len(sys.modules.keys()))
import lal
print(len(sys.modules.keys()))
import bilby
print(len(sys.modules.keys()))58
220
234
1714We're about an order of magnitude above numpy and lal. This is probably why it takes so long to import bilby.
There are basically two choices we can make to reduce these, one is to not link everything internally, this would be one could not just do
import bilby
bilby.gw.prior.BBHPriorDict()Specific modules would be imported individually. Given the amount of linkage between modules, I'm not sure how successful that would be.
The second choice would be to limit the packages that we import at the top level to e.g., just numpy. Removing matplotlib, gwpy, astropy would help a lot. pandas and scipy also contribute quite a bit, but are used very widely. I think tqdm and dill are relatively harmless, but we may want to also remove these from the top level. lal/lalsimulation just add one extra module each, I guess because they're SWIG wrappers, but I'd still vote for not importing them at the top level and just doing it inside the function. Built in packages don't really make a difference.
We could also define a decorator something like requires_import that checks the relevant packages can be imported, although we should check that doesn't hurt performance for things like source models.
For completeness, here's all of the imports in the package
Expand/collapse
$ grep import bilby/**.py (dev)
bilby/__init__.py:import sys
bilby/__init__.py:from . import core, gw, hyper
bilby/__init__.py:from .core import utils, likelihood, prior, result, sampler
bilby/__init__.py:from .core.sampler import run_sampler
bilby/__init__.py:from .core.likelihood import Likelihood
bilby/core/__init__.py:from . import grid, likelihood, prior, result, sampler, series, utils
bilby/core/grid.py:import numpy as np
bilby/core/grid.py:import os
bilby/core/grid.py:import json
bilby/core/grid.py:from collections import OrderedDict
bilby/core/grid.py:from .prior import Prior, PriorDict
bilby/core/grid.py:from .utils import (logtrapzexp, check_directory_exists_and_if_not_mkdir,
bilby/core/grid.py:from .utils import BilbyJsonEncoder, load_json, move_old_file
bilby/core/grid.py:from .result import FileMovedError
bilby/core/grid.py: import gzip
bilby/core/likelihood.py:import copy
bilby/core/likelihood.py:import numpy as np
bilby/core/likelihood.py:from scipy.special import gammaln, xlogy
bilby/core/likelihood.py:from scipy.stats import multivariate_normal
bilby/core/likelihood.py:from .utils import infer_parameters_from_function
bilby/core/prior/__init__.py:from .analytical import *
bilby/core/prior/__init__.py:from .base import *
bilby/core/prior/__init__.py:from .conditional import *
bilby/core/prior/__init__.py:from .dict import *
bilby/core/prior/__init__.py:from .interpolated import *
bilby/core/prior/__init__.py:from .joint import *
bilby/core/prior/__init__.py:from .slabspike import *
bilby/core/prior/analytical.py:import numpy as np
bilby/core/prior/analytical.py:from scipy.special import erfinv
bilby/core/prior/analytical.py:from scipy.special._ufuncs import xlogy, erf, log1p, stdtrit, gammaln, stdtr, \
bilby/core/prior/analytical.py:from .base import Prior
bilby/core/prior/analytical.py:from bilby.core.utils import logger
bilby/core/prior/base.py:from importlib import import_module
bilby/core/prior/base.py:import json
bilby/core/prior/base.py:import os
bilby/core/prior/base.py:import re
bilby/core/prior/base.py:import numpy as np
bilby/core/prior/base.py:import scipy.stats
bilby/core/prior/base.py:from scipy.integrate import cumtrapz
bilby/core/prior/base.py:from scipy.interpolate import interp1d
bilby/core/prior/base.py:from bilby.core.utils import infer_args_from_method, BilbyJsonEncoder, decode_bilby_json, logger, \
bilby/core/prior/base.py: kwargs[key] = getattr(import_module(module), name)
bilby/core/prior/base.py: other_cls = getattr(import_module(module), other_cls)
bilby/core/prior/conditional.py:import numpy as np
bilby/core/prior/conditional.py:from .base import Prior, PriorException
bilby/core/prior/conditional.py:from bilby.core.prior.interpolated import Interped
bilby/core/prior/conditional.py:from bilby.core.prior.analytical import DeltaFunction, PowerLaw, Uniform, LogUniform, \
bilby/core/prior/conditional.py:from bilby.core.utils import infer_args_from_method, infer_parameters_from_function
bilby/core/prior/dict.py:from importlib import import_module
bilby/core/prior/dict.py:from io import open as ioopen
bilby/core/prior/dict.py:import json
bilby/core/prior/dict.py:import os
bilby/core/prior/dict.py:from matplotlib.cbook import flatten
bilby/core/prior/dict.py:import numpy as np
bilby/core/prior/dict.py:from bilby.core.prior.analytical import DeltaFunction
bilby/core/prior/dict.py:from bilby.core.prior.base import Prior, Constraint
bilby/core/prior/dict.py:from bilby.core.prior.joint import JointPrior
bilby/core/prior/dict.py:from bilby.core.utils import logger, check_directory_exists_and_if_not_mkdir, BilbyJsonEncoder, decode_bilby_json
bilby/core/prior/dict.py: import_module(prior_dict["__module__"]),
bilby/core/prior/dict.py: logger.debug("Cannot import prior module {}.{}".format(
bilby/core/prior/dict.py: cls = getattr(import_module(module), cls, cls)
bilby/core/prior/dict.py: import_module(val.get("__module__", "none")),
bilby/core/prior/dict.py: logger.debug("Cannot import prior module {}.{}".format(
bilby/core/prior/dict.py: from .conditional import DirichletElement
bilby/core/prior/dict.py: import_module(prior_dict["__module__"]),
bilby/core/prior/dict.py: logger.debug("Cannot import prior module {}.{}".format(
bilby/core/prior/interpolated.py:import numpy as np
bilby/core/prior/interpolated.py:from scipy.integrate import cumtrapz
bilby/core/prior/interpolated.py:from scipy.interpolate import interp1d
bilby/core/prior/interpolated.py:from .base import Prior
bilby/core/prior/interpolated.py:from bilby.core.utils import logger
bilby/core/prior/joint.py:import numpy as np
bilby/core/prior/joint.py:import scipy.stats
bilby/core/prior/joint.py:from scipy.special import erfinv
bilby/core/prior/joint.py:from .base import Prior, PriorException
bilby/core/prior/joint.py:from bilby.core.utils import logger, infer_args_from_method, get_dict_with_properties
bilby/core/prior/slabspike.py:import numpy as np
bilby/core/prior/slabspike.py:from bilby.core.prior.base import Prior
bilby/core/prior/slabspike.py:from bilby.core.utils import logger
bilby/core/result.py:import inspect
bilby/core/result.py:import os
bilby/core/result.py:from collections import OrderedDict, namedtuple
bilby/core/result.py:from copy import copy
bilby/core/result.py:from distutils.version import LooseVersion
bilby/core/result.py:from importlib import import_module
bilby/core/result.py:from itertools import product
bilby/core/result.py:import corner
bilby/core/result.py:import h5py
bilby/core/result.py:import json
bilby/core/result.py:import matplotlib
bilby/core/result.py:import matplotlib.pyplot as plt
bilby/core/result.py:from matplotlib import lines as mpllines
bilby/core/result.py:import numpy as np
bilby/core/result.py:import pandas as pd
bilby/core/result.py:import scipy.stats
bilby/core/result.py:from scipy.special import logsumexp
bilby/core/result.py:from . import utils
bilby/core/result.py:from .utils import (
bilby/core/result.py:from .prior import Prior, PriorDict, DeltaFunction
bilby/core/result.py: import deepdish
bilby/core/result.py: import dill
bilby/core/result.py: cls = getattr(import_module(data['__module__']), data['__name__'])
bilby/core/result.py: import gzip
bilby/core/result.py: import dill
bilby/core/result.py: import dill
bilby/core/result.py: import arviz as az
bilby/core/sampler/__init__.py:import inspect
bilby/core/sampler/__init__.py:import sys
bilby/core/sampler/__init__.py:import datetime
bilby/core/sampler/__init__.py:from collections import OrderedDict
bilby/core/sampler/__init__.py:import bilby
bilby/core/sampler/__init__.py:from ..utils import command_line_args, logger, loaded_modules_dict
bilby/core/sampler/__init__.py:from ..prior import PriorDict, DeltaFunction
bilby/core/sampler/__init__.py:from .base_sampler import Sampler, SamplingMarginalisedParameterError
bilby/core/sampler/__init__.py:from .cpnest import Cpnest
bilby/core/sampler/__init__.py:from .dynamic_dynesty import DynamicDynesty
bilby/core/sampler/__init__.py:from .dynesty import Dynesty
bilby/core/sampler/__init__.py:from .emcee import Emcee
bilby/core/sampler/__init__.py:from .kombine import Kombine
bilby/core/sampler/__init__.py:from .nestle import Nestle
bilby/core/sampler/__init__.py:from .polychord import PyPolyChord
bilby/core/sampler/__init__.py:from .ptemcee import Ptemcee
bilby/core/sampler/__init__.py:from .ptmcmc import PTMCMCSampler
bilby/core/sampler/__init__.py:from .pymc3 import Pymc3
bilby/core/sampler/__init__.py:from .pymultinest import Pymultinest
bilby/core/sampler/__init__.py:from .ultranest import Ultranest
bilby/core/sampler/__init__.py:from .fake_sampler import FakeSampler
bilby/core/sampler/__init__.py:from .dnest4 import DNest4
bilby/core/sampler/__init__.py:from . import proposal
bilby/core/sampler/__init__.py: from . import IMPLEMENTED_SAMPLERS
bilby/core/sampler/__init__.py: from bilby.core.likelihood import ZeroLikelihood
bilby/core/sampler/base_sampler.py:import datetime
bilby/core/sampler/base_sampler.py:import distutils.dir_util
bilby/core/sampler/base_sampler.py:import numpy as np
bilby/core/sampler/base_sampler.py:import os
bilby/core/sampler/base_sampler.py:import tempfile
bilby/core/sampler/base_sampler.py:from pandas import DataFrame
bilby/core/sampler/base_sampler.py:from ..utils import logger, check_directory_exists_and_if_not_mkdir, command_line_args, Counter
bilby/core/sampler/base_sampler.py:from ..prior import Prior, PriorDict, DeltaFunction, Constraint
bilby/core/sampler/base_sampler.py:from ..result import Result, read_in_result
bilby/core/sampler/base_sampler.py: skip_import_verification: bool
bilby/core/sampler/base_sampler.py: use_ratio=False, plot=False, skip_import_verification=False,
bilby/core/sampler/base_sampler.py: if not skip_import_verification:
bilby/core/sampler/base_sampler.py: self.external_sampler = __import__(external_sampler_name)
bilby/core/sampler/base_sampler.py: import emcee
bilby/core/sampler/cpnest.py:import array
bilby/core/sampler/cpnest.py:import copy
bilby/core/sampler/cpnest.py:import numpy as np
bilby/core/sampler/cpnest.py:from pandas import DataFrame
bilby/core/sampler/cpnest.py:from .base_sampler import NestedSampler
bilby/core/sampler/cpnest.py:from .proposal import Sample, JumpProposalCycle
bilby/core/sampler/cpnest.py:from ..utils import logger, check_directory_exists_and_if_not_mkdir
bilby/core/sampler/cpnest.py: from cpnest import model as cpmodel, CPNest
bilby/core/sampler/cpnest.py: from cpnest.parameter import LivePoint
bilby/core/sampler/cpnest.py: from cpnest.nest2pos import compute_weights
bilby/core/sampler/cpnest.py: import sys
bilby/core/sampler/cpnest.py: from cpnest.proposal import ProposalCycle
bilby/core/sampler/cpnest.py: import cpnest.proposal
bilby/core/sampler/cpnest.py: import cpnest.proposal
bilby/core/sampler/dnest4.py:import os
bilby/core/sampler/dnest4.py:import shutil
bilby/core/sampler/dnest4.py:import distutils.dir_util
bilby/core/sampler/dnest4.py:import signal
bilby/core/sampler/dnest4.py:import time
bilby/core/sampler/dnest4.py:import datetime
bilby/core/sampler/dnest4.py:import sys
bilby/core/sampler/dnest4.py:import numpy as np
bilby/core/sampler/dnest4.py:import pandas as pd
bilby/core/sampler/dnest4.py:from ..utils import check_directory_exists_and_if_not_mkdir, logger
bilby/core/sampler/dnest4.py:from .base_sampler import NestedSampler
bilby/core/sampler/dnest4.py: exit_code=77, skip_import_verification=False, temporary_directory=True, **kwargs):
bilby/core/sampler/dnest4.py: use_ratio=use_ratio, plot=plot, skip_import_verification=skip_import_verification,
bilby/core/sampler/dnest4.py: import dnest4
bilby/core/sampler/dnest4.py: import dnest4
bilby/core/sampler/dynamic_dynesty.py:import os
bilby/core/sampler/dynamic_dynesty.py:import dill as pickle
bilby/core/sampler/dynamic_dynesty.py:import signal
bilby/core/sampler/dynamic_dynesty.py:import numpy as np
bilby/core/sampler/dynamic_dynesty.py:from ..utils import logger, check_directory_exists_and_if_not_mkdir
bilby/core/sampler/dynamic_dynesty.py:from .base_sampler import Sampler
bilby/core/sampler/dynamic_dynesty.py:from .dynesty import Dynesty
bilby/core/sampler/dynamic_dynesty.py: skip_import_verification: bool
bilby/core/sampler/dynamic_dynesty.py: skip_import_verification=False, check_point=True, n_check_point=None, check_point_delta_t=600,
bilby/core/sampler/dynamic_dynesty.py: plot=plot, skip_import_verification=skip_import_verification,
bilby/core/sampler/dynamic_dynesty.py: import dynesty
bilby/core/sampler/dynesty.py:import datetime
bilby/core/sampler/dynesty.py:import dill
bilby/core/sampler/dynesty.py:import os
bilby/core/sampler/dynesty.py:import sys
bilby/core/sampler/dynesty.py:import pickle
bilby/core/sampler/dynesty.py:import signal
bilby/core/sampler/dynesty.py:import time
bilby/core/sampler/dynesty.py:from tqdm.auto import tqdm
bilby/core/sampler/dynesty.py:import matplotlib.pyplot as plt
bilby/core/sampler/dynesty.py:import numpy as np
bilby/core/sampler/dynesty.py:from pandas import DataFrame
bilby/core/sampler/dynesty.py:from ..utils import (
bilby/core/sampler/dynesty.py:from .base_sampler import Sampler, NestedSampler
bilby/core/sampler/dynesty.py:from ..result import rejection_sample
bilby/core/sampler/dynesty.py:from numpy import linalg
bilby/core/sampler/dynesty.py:from dynesty.utils import unitcheck
bilby/core/sampler/dynesty.py:import warnings
bilby/core/sampler/dynesty.py: skip_import_verification: bool
bilby/core/sampler/dynesty.py: use_ratio=False, plot=False, skip_import_verification=False,
bilby/core/sampler/dynesty.py: plot=plot, skip_import_verification=skip_import_verification,
bilby/core/sampler/dynesty.py: import multiprocessing
bilby/core/sampler/dynesty.py: import dynesty
bilby/core/sampler/dynesty.py: import dynesty
bilby/core/sampler/dynesty.py: from ... import __version__ as bilby_version
bilby/core/sampler/dynesty.py: from dynesty import __version__ as dynesty_version
bilby/core/sampler/dynesty.py: from ... import __version__ as bilby_version
bilby/core/sampler/dynesty.py: from dynesty import __version__ as dynesty_version
bilby/core/sampler/dynesty.py: import dynesty.plotting as dyplot
bilby/core/sampler/dynesty.py: from dynesty import plotting as dyplot
bilby/core/sampler/dynesty.py: import dynesty
bilby/core/sampler/dynesty.py: import pandas as pd
bilby/core/sampler/emcee.py:from collections import namedtuple
bilby/core/sampler/emcee.py:import os
bilby/core/sampler/emcee.py:import signal
bilby/core/sampler/emcee.py:import shutil
bilby/core/sampler/emcee.py:from shutil import copyfile
bilby/core/sampler/emcee.py:import sys
bilby/core/sampler/emcee.py:import numpy as np
bilby/core/sampler/emcee.py:from pandas import DataFrame
bilby/core/sampler/emcee.py:from distutils.version import LooseVersion
bilby/core/sampler/emcee.py:import dill as pickle
bilby/core/sampler/emcee.py:from ..utils import logger, check_directory_exists_and_if_not_mkdir
bilby/core/sampler/emcee.py:from .base_sampler import MCMCSampler, SamplerError
bilby/core/sampler/emcee.py: use_ratio=False, plot=False, skip_import_verification=False,
bilby/core/sampler/emcee.py: import emcee
bilby/core/sampler/emcee.py: skip_import_verification=skip_import_verification, **kwargs)
bilby/core/sampler/emcee.py: import emcee
bilby/core/sampler/emcee.py: from tqdm.auto import tqdm
bilby/core/sampler/fake_sampler.py:import numpy as np
bilby/core/sampler/fake_sampler.py:from .base_sampler import Sampler
bilby/core/sampler/fake_sampler.py:from ..result import read_in_result
bilby/core/sampler/fake_sampler.py: use_ratio=False, plot=False, skip_import_verification=True,
bilby/core/sampler/kombine.py:from ..utils import logger
bilby/core/sampler/kombine.py:import numpy as np
bilby/core/sampler/kombine.py:import os
bilby/core/sampler/kombine.py:from .emcee import Emcee
bilby/core/sampler/kombine.py: use_ratio=False, plot=False, skip_import_verification=False,
bilby/core/sampler/kombine.py: use_ratio=use_ratio, plot=plot, skip_import_verification=skip_import_verification,
bilby/core/sampler/kombine.py: import kombine
bilby/core/sampler/kombine.py: from tqdm.auto import tqdm
bilby/core/sampler/nestle.py:import numpy as np
bilby/core/sampler/nestle.py:from pandas import DataFrame
bilby/core/sampler/nestle.py:from .base_sampler import NestedSampler
bilby/core/sampler/nestle.py: import nestle
bilby/core/sampler/nestle.py: import nestle
bilby/core/sampler/nestle.py: import nestle
bilby/core/sampler/polychord.py:import numpy as np
bilby/core/sampler/polychord.py:from .base_sampler import NestedSampler
bilby/core/sampler/polychord.py: import pypolychord
bilby/core/sampler/polychord.py: from pypolychord.settings import PolyChordSettings
bilby/core/sampler/proposal.py:from collections import OrderedDict
bilby/core/sampler/proposal.py:from inspect import isclass
bilby/core/sampler/proposal.py:import numpy as np
bilby/core/sampler/proposal.py:import random
bilby/core/sampler/proposal.py:from ..prior import Uniform
bilby/core/sampler/ptemcee.py:import os
bilby/core/sampler/ptemcee.py:import datetime
bilby/core/sampler/ptemcee.py:import copy
bilby/core/sampler/ptemcee.py:import signal
bilby/core/sampler/ptemcee.py:import sys
bilby/core/sampler/ptemcee.py:import time
bilby/core/sampler/ptemcee.py:import dill
bilby/core/sampler/ptemcee.py:from collections import namedtuple
bilby/core/sampler/ptemcee.py:import logging
bilby/core/sampler/ptemcee.py:import numpy as np
bilby/core/sampler/ptemcee.py:import pandas as pd
bilby/core/sampler/ptemcee.py:import matplotlib.pyplot as plt
bilby/core/sampler/ptemcee.py:import scipy.signal
bilby/core/sampler/ptemcee.py:from ..utils import logger, check_directory_exists_and_if_not_mkdir
bilby/core/sampler/ptemcee.py:from .base_sampler import SamplerError, MCMCSampler
bilby/core/sampler/ptemcee.py: skip_import_verification=False,
bilby/core/sampler/ptemcee.py: skip_import_verification=skip_import_verification,
bilby/core/sampler/ptemcee.py: from scipy.optimize import minimize
bilby/core/sampler/ptemcee.py: import ptemcee
bilby/core/sampler/ptemcee.py: import schwimmbad
bilby/core/sampler/ptemcee.py: import emcee
bilby/core/sampler/ptmcmc.py:import glob
bilby/core/sampler/ptmcmc.py:import shutil
bilby/core/sampler/ptmcmc.py:import numpy as np
bilby/core/sampler/ptmcmc.py:from .base_sampler import MCMCSampler, SamplerNotInstalledError
bilby/core/sampler/ptmcmc.py:from ..utils import logger
bilby/core/sampler/ptmcmc.py: use_ratio=False, plot=False, skip_import_verification=False,
bilby/core/sampler/ptmcmc.py: skip_import_verification=skip_import_verification,
bilby/core/sampler/ptmcmc.py: # PTMCMC is imported with Caps so need to overwrite the parent function
bilby/core/sampler/ptmcmc.py: self.external_sampler = __import__(external_sampler_name)
bilby/core/sampler/ptmcmc.py: def _import_external_sampler():
bilby/core/sampler/ptmcmc.py: from PTMCMCSampler import PTMCMCSampler
bilby/core/sampler/ptmcmc.py: PTMCMCSampler = self._import_external_sampler()
bilby/core/sampler/pymc3.py:from collections import OrderedDict
bilby/core/sampler/pymc3.py:from distutils.version import StrictVersion
bilby/core/sampler/pymc3.py:import numpy as np
bilby/core/sampler/pymc3.py:from ..utils import derivatives, infer_args_from_method
bilby/core/sampler/pymc3.py:from ..prior import DeltaFunction, Sine, Cosine, PowerLaw, MultivariateGaussian
bilby/core/sampler/pymc3.py:from .base_sampler import MCMCSampler
bilby/core/sampler/pymc3.py:from ..likelihood import GaussianLikelihood, PoissonLikelihood, ExponentialLikelihood, \
bilby/core/sampler/pymc3.py:from ...gw.likelihood import BasicGravitationalWaveTransient, GravitationalWaveTransient
bilby/core/sampler/pymc3.py: skip_import_verification=False, **kwargs):
bilby/core/sampler/pymc3.py: _, STEP_METHODS, _ = self._import_external_sampler()
bilby/core/sampler/pymc3.py: skip_import_verification=skip_import_verification, **kwargs)
bilby/core/sampler/pymc3.py: def _import_external_sampler():
bilby/core/sampler/pymc3.py: import pymc3
bilby/core/sampler/pymc3.py: from pymc3.sampling import STEP_METHODS
bilby/core/sampler/pymc3.py: from pymc3.theanof import floatX
bilby/core/sampler/pymc3.py: def _import_theano():
bilby/core/sampler/pymc3.py: import theano # noqa
bilby/core/sampler/pymc3.py: import theano.tensor as tt
bilby/core/sampler/pymc3.py: from theano.compile.ops import as_op # noqa
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: theano, tt, as_op = self._import_theano()
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: theano, tt, as_op = self._import_theano()
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: theano, tt, as_op = self._import_theano()
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: theano, tt, as_op = self._import_theano()
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: pymc3, _, _ = self._import_external_sampler()
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: pymc3, STEP_METHODS, floatX = self._import_external_sampler()
bilby/core/sampler/pymc3.py: theano, tt, as_op = self._import_theano()
bilby/core/sampler/pymultinest.py:import importlib
bilby/core/sampler/pymultinest.py:import os
bilby/core/sampler/pymultinest.py:import shutil
bilby/core/sampler/pymultinest.py:import distutils.dir_util
bilby/core/sampler/pymultinest.py:import signal
bilby/core/sampler/pymultinest.py:import time
bilby/core/sampler/pymultinest.py:import datetime
bilby/core/sampler/pymultinest.py:import sys
bilby/core/sampler/pymultinest.py:import numpy as np
bilby/core/sampler/pymultinest.py:from ..utils import check_directory_exists_and_if_not_mkdir
bilby/core/sampler/pymultinest.py:from ..utils import logger
bilby/core/sampler/pymultinest.py:from .base_sampler import NestedSampler
bilby/core/sampler/pymultinest.py: importance_nested_sampling: bool, (False)
bilby/core/sampler/pymultinest.py: If true, use importance nested sampling
bilby/core/sampler/pymultinest.py: importance_nested_sampling=False,
bilby/core/sampler/pymultinest.py: skip_import_verification=False,
bilby/core/sampler/pymultinest.py: skip_import_verification=skip_import_verification,
bilby/core/sampler/pymultinest.py: import pymultinest
bilby/core/sampler/pymultinest.py: pm_run = importlib.import_module("pymultinest.run")
bilby/core/sampler/ultranest.py:import datetime
bilby/core/sampler/ultranest.py:import distutils.dir_util
bilby/core/sampler/ultranest.py:import inspect
bilby/core/sampler/ultranest.py:import os
bilby/core/sampler/ultranest.py:import shutil
bilby/core/sampler/ultranest.py:import signal
bilby/core/sampler/ultranest.py:import time
bilby/core/sampler/ultranest.py:import numpy as np
bilby/core/sampler/ultranest.py:from pandas import DataFrame
bilby/core/sampler/ultranest.py:from ..utils import check_directory_exists_and_if_not_mkdir, logger
bilby/core/sampler/ultranest.py:from .base_sampler import NestedSampler
bilby/core/sampler/ultranest.py: skip_import_verification=False,
bilby/core/sampler/ultranest.py: skip_import_verification=skip_import_verification,
bilby/core/sampler/ultranest.py: import ultranest
bilby/core/sampler/ultranest.py: import ultranest.stepsampler
bilby/core/series.py:from . import utils
bilby/core/utils.py:from distutils.spawn import find_executable
bilby/core/utils.py:import logging
bilby/core/utils.py:import os
bilby/core/utils.py:import shutil
bilby/core/utils.py:import sys
bilby/core/utils.py:from math import fmod
bilby/core/utils.py:import argparse
bilby/core/utils.py:import inspect
bilby/core/utils.py:import functools
bilby/core/utils.py:import types
bilby/core/utils.py:import subprocess
bilby/core/utils.py:import multiprocessing
bilby/core/utils.py:from importlib import import_module
bilby/core/utils.py:import json
bilby/core/utils.py:import warnings
bilby/core/utils.py:import numpy as np
bilby/core/utils.py:from scipy.interpolate import interp2d
bilby/core/utils.py:from scipy.special import logsumexp
bilby/core/utils.py:import pandas as pd
bilby/core/utils.py:import matplotlib.pyplot as plt
bilby/core/utils.py: in both functions and methods; this is important, since the first
bilby/core/utils.py: available for any script which includes `import bilby`, but no help command
bilby/core/utils.py: # Here we import bilby, which initialses and parses the default command-line args
bilby/core/utils.py: >>> import bilby
bilby/core/utils.py: # Next, we import argparse and define a new argparse object
bilby/core/utils.py: >>> import argparse
bilby/core/utils.py: from scipy.interpolate.dfitpack import bispeu
bilby/core/utils.py: from .prior import MultivariateGaussianDist, Prior, PriorDict
bilby/core/utils.py: from ..gw.prior import HealPixMapPriorDist
bilby/core/utils.py: from astropy import cosmology as cosmo, units
bilby/core/utils.py: logger.debug("Cannot import astropy, cannot write cosmological priors")
bilby/core/utils.py: import gzip
bilby/core/utils.py: cls = getattr(import_module(dct['__module__']), dct['__name__'])
bilby/core/utils.py: cls = getattr(import_module(dct['__module__']), dct['__name__'])
bilby/core/utils.py: return getattr(import_module(dct["__module__"]), dct["__name__"], default)
bilby/core/utils.py: from astropy import cosmology as cosmo
bilby/core/utils.py: logger.debug("Cannot import astropy, cosmological priors may not be "
bilby/core/utils.py: from astropy import units
bilby/core/utils.py: logger.debug("Cannot import astropy, cosmological priors may not be "
bilby/core/utils.py: from matplotlib import rcParams
bilby/core/utils.py: from matplotlib import rcParams
bilby/core/utils.py: from .prior.dict import PriorDict
bilby/core/utils.py: import h5py
bilby/gw/__init__.py:from . import (conversion, cosmology, detector, eos, likelihood, prior,
bilby/gw/__init__.py:from .waveform_generator import WaveformGenerator
bilby/gw/__init__.py:from .likelihood import GravitationalWaveTransient
bilby/gw/__init__.py:from .detector import calibration
bilby/gw/conversion.py:import sys
bilby/gw/conversion.py:import multiprocessing
bilby/gw/conversion.py:from tqdm.auto import tqdm
bilby/gw/conversion.py:import numpy as np
bilby/gw/conversion.py:from pandas import DataFrame
bilby/gw/conversion.py:from ..core.likelihood import MarginalizedLikelihoodReconstructionError
bilby/gw/conversion.py:from ..core.utils import logger, solar_mass
bilby/gw/conversion.py:from ..core.prior import DeltaFunction
bilby/gw/conversion.py:from .utils import lalsim_SimInspiralTransformPrecessingNewInitialConditions
bilby/gw/conversion.py:from .eos.eos import SpectralDecompositionEOS, EOSFamily, IntegrateTOV
bilby/gw/conversion.py:from .cosmology import get_cosmology
bilby/gw/conversion.py: from astropy import units
bilby/gw/conversion.py: from astropy.cosmology import z_at_value
bilby/gw/cosmology.py:from ..core.utils import logger
bilby/gw/cosmology.py: from astropy import cosmology as cosmo
bilby/gw/detector/__init__.py:from ..conversion import convert_to_lal_binary_black_hole_parameters
bilby/gw/detector/__init__.py:from .calibration import *
bilby/gw/detector/__init__.py:from .interferometer import *
bilby/gw/detector/__init__.py:from .networks import *
bilby/gw/detector/__init__.py:from .psd import *
bilby/gw/detector/__init__.py:from .strain_data import *
bilby/gw/detector/__init__.py: import lal
bilby/gw/detector/__init__.py: import lalsimulation as lalsim
bilby/gw/detector/calibration.py:import numpy as np
bilby/gw/detector/calibration.py:from scipy.interpolate import interp1d
bilby/gw/detector/geometry.py:import numpy as np
bilby/gw/detector/geometry.py:from .. import utils as gwutils
bilby/gw/detector/interferometer.py:import os
bilby/gw/detector/interferometer.py:import sys
bilby/gw/detector/interferometer.py:import numpy as np
bilby/gw/detector/interferometer.py:from matplotlib import pyplot as plt
bilby/gw/detector/interferometer.py:from ...core import utils
bilby/gw/detector/interferometer.py:from ...core.utils import docstring, logger
bilby/gw/detector/interferometer.py:from .. import utils as gwutils
bilby/gw/detector/interferometer.py:from ..utils import PropertyAccessor
bilby/gw/detector/interferometer.py:from .calibration import Recalibrate
bilby/gw/detector/interferometer.py:from .geometry import InterferometerGeometry
bilby/gw/detector/interferometer.py:from .strain_data import InterferometerStrainData
bilby/gw/detector/interferometer.py: import gwpy
bilby/gw/detector/interferometer.py: import gwpy.signal
bilby/gw/detector/interferometer.py: import deepdish
bilby/gw/detector/interferometer.py: import deepdish
bilby/gw/detector/interferometer.py: import dill
bilby/gw/detector/interferometer.py: import dill
bilby/gw/detector/networks.py:import os
bilby/gw/detector/networks.py:import sys
bilby/gw/detector/networks.py:import warnings
bilby/gw/detector/networks.py:import numpy as np
bilby/gw/detector/networks.py:import math
bilby/gw/detector/networks.py:from ...core import utils
bilby/gw/detector/networks.py:from ...core.utils import logger
bilby/gw/detector/networks.py:from .. import utils as gwutils
bilby/gw/detector/networks.py:from .interferometer import Interferometer
bilby/gw/detector/networks.py:from .psd import PowerSpectralDensity
bilby/gw/detector/networks.py:from .strain_data import InterferometerStrainData
bilby/gw/detector/networks.py: import deepdish
bilby/gw/detector/networks.py: import deepdish
bilby/gw/detector/networks.py: import dill
bilby/gw/detector/networks.py: import dill
bilby/gw/detector/psd.py:import os
bilby/gw/detector/psd.py:import numpy as np
bilby/gw/detector/psd.py:from scipy.interpolate import interp1d
bilby/gw/detector/psd.py:from ...core import utils
bilby/gw/detector/psd.py:from ...core.utils import logger
bilby/gw/detector/psd.py:from .strain_data import InterferometerStrainData
bilby/gw/detector/psd.py: self.__import_amplitude_spectral_density()
bilby/gw/detector/psd.py: self.__import_power_spectral_density()
bilby/gw/detector/psd.py: def __import_amplitude_spectral_density(self):
bilby/gw/detector/psd.py: def __import_power_spectral_density(self):
bilby/gw/detector/strain_data.py:import numpy as np
bilby/gw/detector/strain_data.py:from scipy.signal.windows import tukey
bilby/gw/detector/strain_data.py:from ...core import utils
bilby/gw/detector/strain_data.py:from ...core.series import CoupledTimeAndFrequencySeries
bilby/gw/detector/strain_data.py:from ...core.utils import logger
bilby/gw/detector/strain_data.py:from .. import utils as gwutils
bilby/gw/detector/strain_data.py:from ..utils import PropertyAccessor
bilby/gw/detector/strain_data.py: import gwpy
bilby/gw/detector/strain_data.py: import gwpy.signal
bilby/gw/detector/strain_data.py: import lal
bilby/gw/detector/strain_data.py: import pycbc
bilby/gw/detector/strain_data.py: import pycbc
bilby/gw/eos/__init__.py:from .tov_solver import IntegrateTOV
bilby/gw/eos/__init__.py:from .eos import (SpectralDecompositionEOS,
bilby/gw/eos/eos.py:import os
bilby/gw/eos/eos.py:import numpy as np
bilby/gw/eos/eos.py:import matplotlib.pyplot as plt
bilby/gw/eos/eos.py:from scipy.integrate import cumtrapz, quad
bilby/gw/eos/eos.py:from scipy.interpolate import interp1d, CubicSpline
bilby/gw/eos/eos.py:from scipy.optimize import minimize_scalar
bilby/gw/eos/eos.py:from .tov_solver import IntegrateTOV
bilby/gw/eos/eos.py:from ...core import utils
bilby/gw/eos/tov_solver.py:import numpy as np
bilby/gw/eos/tov_solver.py:from scipy.integrate import solve_ivp
bilby/gw/likelihood.py:import gc
bilby/gw/likelihood.py:import os
bilby/gw/likelihood.py:import json
bilby/gw/likelihood.py:import copy
bilby/gw/likelihood.py:import numpy as np
bilby/gw/likelihood.py:import scipy.integrate as integrate
bilby/gw/likelihood.py:from scipy.interpolate import interp1d
bilby/gw/likelihood.py: from scipy.special import logsumexp
bilby/gw/likelihood.py: from scipy.misc import logsumexp
bilby/gw/likelihood.py:from scipy.special import i0e
bilby/gw/likelihood.py:from ..core.likelihood import Likelihood
bilby/gw/likelihood.py:from ..core.utils import BilbyJsonEncoder, decode_bilby_json
bilby/gw/likelihood.py:from ..core.utils import (
bilby/gw/likelihood.py:from ..core.prior import Interped, Prior, Uniform
bilby/gw/likelihood.py:from .detector import InterferometerList, get_empty_interferometer
bilby/gw/likelihood.py:from .prior import BBHPriorDict, CBCPriorDict, Cosmological
bilby/gw/likelihood.py:from .source import lal_binary_black_hole
bilby/gw/likelihood.py:from .utils import (
bilby/gw/likelihood.py:from .waveform_generator import WaveformGenerator
bilby/gw/likelihood.py:from collections import namedtuple
bilby/gw/likelihood.py: from lal import git_version, __version__
bilby/gw/likelihood.py: from lalsimulation import git_version, __version__
bilby/gw/prior.py:import os
bilby/gw/prior.py:import copy
bilby/gw/prior.py:import numpy as np
bilby/gw/prior.py:from scipy.interpolate import InterpolatedUnivariateSpline, interp1d
bilby/gw/prior.py:from scipy.integrate import cumtrapz
bilby/gw/prior.py:from scipy.special import hyp2f1
bilby/gw/prior.py:from scipy.stats import norm
bilby/gw/prior.py:from ..core.prior import (PriorDict, Uniform, Prior, DeltaFunction, Gaussian,
bilby/gw/prior.py:from ..core.utils import infer_args_from_method, logger
bilby/gw/prior.py:from .conversion import (
bilby/gw/prior.py:from .cosmology import get_cosmology
bilby/gw/prior.py: from astropy import cosmology as cosmo, units
bilby/gw/prior.py: self.hp = self._check_imports()
bilby/gw/prior.py: def _check_imports():
bilby/gw/prior.py: import healpy
bilby/gw/result.py:import json
bilby/gw/result.py:import pickle
bilby/gw/result.py:import os
bilby/gw/result.py:import matplotlib.pyplot as plt
bilby/gw/result.py:from matplotlib import rcParams
bilby/gw/result.py:import numpy as np
bilby/gw/result.py:from ..core.result import Result as CoreResult
bilby/gw/result.py:from ..core.utils import (
bilby/gw/result.py:from .utils import plot_spline_pos, spline_angle_xform, asd_from_freq_series
bilby/gw/result.py:from .detector import get_empty_interferometer, Interferometer
bilby/gw/result.py: import plotly.graph_objects as go
bilby/gw/result.py: from plotly.offline import plot
bilby/gw/result.py: from plotly.subplots import make_subplots
bilby/gw/result.py: "HTML plotting requested, but plotly cannot be imported, "
bilby/gw/result.py: from astropy.time import Time
bilby/gw/result.py: from ligo.skymap import io, version, plot, postprocess, bayestar, kde
bilby/gw/result.py: import healpy as hp
bilby/gw/sampler/__init__.py:from . import proposal
bilby/gw/sampler/proposal.py:import random
bilby/gw/sampler/proposal.py:import numpy as np
bilby/gw/sampler/proposal.py:from ...core.sampler.proposal import JumpProposal
bilby/gw/source.py:import numpy as np
bilby/gw/source.py:from ..core import utils
bilby/gw/source.py:from ..core.utils import logger
bilby/gw/source.py:from .conversion import bilby_to_lalsimulation_spins
bilby/gw/source.py:from .utils import (lalsim_GetApproximantFromString,
bilby/gw/source.py: import lal
bilby/gw/source.py: import lalsimulation as lalsim
bilby/gw/utils.py:import os
bilby/gw/utils.py:import json
bilby/gw/utils.py:from math import fmod
bilby/gw/utils.py:import numpy as np
bilby/gw/utils.py:from scipy.interpolate import interp1d
bilby/gw/utils.py:import matplotlib.pyplot as plt
bilby/gw/utils.py:from ..core.utils import (ra_dec_to_theta_phi,
bilby/gw/utils.py: from gwpy.timeseries import TimeSeries
bilby/gw/utils.py: import lal
bilby/gw/utils.py: import lalsimulation as lalsim
bilby/gw/utils.py: from ligo.gracedb.rest import GraceDb
bilby/gw/waveform_generator.py:import numpy as np
bilby/gw/waveform_generator.py:from ..core import utils
bilby/gw/waveform_generator.py:from ..core.series import CoupledTimeAndFrequencySeries
bilby/gw/waveform_generator.py:from .utils import PropertyAccessor
bilby/gw/waveform_generator.py:from .conversion import convert_to_lal_binary_black_hole_parameters
bilby/hyper/__init__.py:from . import likelihood, model
bilby/hyper/likelihood.py:import logging
bilby/hyper/likelihood.py:import numpy as np
bilby/hyper/likelihood.py:from ..core.likelihood import Likelihood
bilby/hyper/likelihood.py:from .model import Model
bilby/hyper/likelihood.py:from ..core.prior import PriorDict
bilby/hyper/model.py:from ..core.utils import infer_args_from_function_except_n_args