Function copy has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def copy(self, other, parameters=None, parameter_names=None,
             posterior_only=False, **kwargs):
        """Copies data in this file to another file.
 
        The samples and stats to copy may be down selected using the given

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Function compute_acfs has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def compute_acfs(cls, fp, start_index=None, end_index=None,
                     per_walker=False, walkers=None, parameters=None):
        """Computes the autocorrleation function of the model params in the
        given file.
 
 

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Function run has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, niterations):
        """This function should run the sampler.
        """
 
        if not self._lastsample:

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Function test_create_axes_grid has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def test_create_axes_grid(nodiag):
    parameters = ['mass1', 'mass2', 'tc']
    if nodiag:
        combinations = itertools.combinations
        ndim = len(parameters) - 1

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Function _read_fields has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def _read_fields(fp, fields_group, fields, array_class,
                     thin_start=None, thin_interval=None, thin_end=None,
                     iteration=None, walkers=None, flatten=True):
        """Base function for reading samples and model stats. See
        `read_samples` and `read_model_stats` for details.

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Function gelman_rubin has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def gelman_rubin(chains, auto_burn_in=True):
    """ Calculates the univariate Gelman-Rubin convergence statistic
    which compares the evolution of multiple chains in a Markov-Chain Monte
    Carlo process and computes their difference to determine their convergence.
    The between-chain and within-chain variances are computed for each sampling

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Function prior_eval has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def prior_eval(self):
        """ Returns the joint distribution class initialized with a set of
        pre-defined distributions for each parameters.
        """
        parameters, values = zip(*self.parameters.items())

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Function create_marginalized_hist has 13 arguments (exceeds 10 allowed). Consider refactoring.

Open

def create_marginalized_hist(ax, values, label, percentiles=None,

Function get_slice has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def get_slice(self, thin_start=None, thin_interval=None, thin_end=None):
        """Formats a slice using the given arguments that can be used to
        retrieve a thinned array from an InferenceFile.
 
        Parameters

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Function __init__ has 12 arguments (exceeds 10 allowed). Consider refactoring.

Open

    def __init__(self, variable_params, data, waveform_generator,

Function set_marginal_histogram_title has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def set_marginal_histogram_title(ax, fmt, color, label=None, rotated=False):
    """ Sets the title of the marginal histograms.
 
    Parameters
    ----------

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Function remove_common_offset has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def remove_common_offset(arr):
    """Given an array of data, removes a common offset > 1000, returning the
    removed value.
    """
    offset = 0

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Function read_samples has 11 arguments (exceeds 10 allowed). Consider refactoring.

Open

    def read_samples(cls, fp, parameters,

Function read_label has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def read_label(self, parameter, error_on_none=False):
        """Returns the label for the parameter.
 
        Parameters
        -----------

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Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, variable_params, data, waveform_generator,
                 f_lower, psds=None, f_upper=None, norm=None,
                 **kwargs):
        # set up the boiler-plate attributes; note: we'll compute the
        # log evidence later

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Function write_data has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def write_data(self, strain_dict=None, stilde_dict=None,
                   psd_dict=None, low_frequency_cutoff_dict=None,
                   group=None):
        """Writes the strain/stilde/psd.
 
 

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Function compute_acls has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def compute_acls(cls, fp, start_index=None, end_index=None):
        """Computes the autocorrleation length for all model params and
        temperatures in the given file.
 
        Parameter values are averaged over all walkers at each iteration and

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Function get_file_type has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

def get_file_type(filename):
    """ Returns I/O object to use for file.
 
    Parameters
    ----------

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Function injections_from_cli has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

def injections_from_cli(opts):
    """Gets injection parameters from the inference file(s).
 
    Parameters
    ----------

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Function from_config has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def from_config(cls, cp, data, delta_f=None, delta_t=None,
                    gates=None, recalibration=None, **kwargs):
        """Initializes an instance of this class from the given config file.
 
        Parameters

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