Function create_multidim_plot has a Cognitive Complexity of 72 (exceeds 5 allowed). Consider refactoring.

Open

def create_multidim_plot(parameters, samples, labels=None,
                         mins=None, maxs=None, expected_parameters=None,
                         expected_parameters_color='r',
                         plot_marginal=True, plot_scatter=True,
                         marginal_percentiles=None, contour_percentiles=None,

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File emcee.py has 765 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# Copyright (C) 2016  Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.

File base.py has 749 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# Copyright (C) 2016  Christopher M. Biwer, Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.

File hdf.py has 647 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# Copyright (C) 2016 Christopher M. Biwer
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# self.option) any later version.

File option_utils.py has 630 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# Copyright (C) 2016 Collin Capano
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your

File scatter_histograms.py has 601 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# Copyright (C) 2016 Miriam Cabero Mueller, Collin Capano
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your

Function create_marginalized_hist has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

def create_marginalized_hist(ax, values, label, percentiles=None,
                             color='k', fillcolor='gray', linecolor='navy',
                             title=True, expected_value=None,
                             expected_color='red', rotated=False,
                             plot_min=None, plot_max=None):

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Function create_axes_grid has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

def create_axes_grid(parameters, labels=None, height_ratios=None,
                     width_ratios=None, no_diagonals=False):
    """Given a list of parameters, creates a figure with an axis for
    every possible combination of the parameters.
 
 

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File base.py has 567 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# Copyright (C) 2016  Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.

Function compute_acfs has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

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

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Function create_density_plot has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

def create_density_plot(xparam, yparam, samples, plot_density=True,
                        plot_contours=True, percentiles=None, cmap='viridis',
                        contour_color=None, xmin=None, xmax=None,
                        ymin=None, ymax=None, exclude_region=None,
                        fig=None, ax=None, use_kombine=False):

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Function _read_fields has a Cognitive Complexity of 20 (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, temps=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 create_multidim_plot has 27 arguments (exceeds 10 allowed). Consider refactoring.

Open

def create_multidim_plot(parameters, samples, labels=None,

Function results_from_cli has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def results_from_cli(opts, load_samples=True, **kwargs):
    """
    Loads an inference result file along with any labels associated with it
    from the command line options.
 
 

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Function write_metadata has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def write_metadata(self, fp, **kwargs):
        """Writes metadata about this sampler to the given file. Metadata is
        written to the file's `attrs`.
 
        Parameters

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Function data_from_cli has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def data_from_cli(opts):
    """Loads the data needed for a model from the given
    command-line options. Gates specifed on the command line are also applied.
 
    Parameters

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Function write_samples_group has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def write_samples_group(fp, samples_group, parameters, samples,
                            start_iteration=None, max_iterations=None):
        """Writes samples to the given file.
 
        Results are written to:

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Function write_samples_group has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def write_samples_group(fp, samples_group, parameters, samples,
                            start_iteration=None, max_iterations=None):
        """Writes samples to the given file.
 
        Results are written to:

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Function validate_checkpoint_files has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

def validate_checkpoint_files(checkpoint_file, backup_file):
    """Checks if the given checkpoint and/or backup files are valid.
 
    The checkpoint file is considered valid if:
 
 

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Function create_density_plot has 16 arguments (exceeds 10 allowed). Consider refactoring.

Open

def create_density_plot(xparam, yparam, samples, plot_density=True,