copulas 0.10.1__tar.gz → 0.12.1__tar.gz

{copulas-0.10.1 → copulas-0.12.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: copulas
-Version: 0.10.1
+Version: 0.12.1
 Summary: Create tabular synthetic data using copulas-based modeling.
 Author-email: "DataCebo, Inc." <info@sdv.dev>
 License: BSL-1.1
@@ -19,27 +19,36 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
-Requires-Python: <3.12,>=3.8
+Requires-Python: <3.14,>=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy<2,>=1.20.0; python_version < "3.10"
-Requires-Dist: numpy<2,>=1.23.3; python_version >= "3.10"
-Requires-Dist: pandas>=1.1.3; python_version < "3.10"
-Requires-Dist: pandas>=1.3.4; python_version >= "3.10" and python_version < "3.11"
-Requires-Dist: pandas>=1.5.0; python_version >= "3.11"
-Requires-Dist: plotly<6,>=5.10.0
-Requires-Dist: scipy<2,>=1.5.4; python_version < "3.10"
-Requires-Dist: scipy<2,>=1.9.2; python_version >= "3.10"
+Requires-Dist: numpy>=1.21.0; python_version < "3.10"
+Requires-Dist: numpy>=1.23.3; python_version >= "3.10" and python_version < "3.12"
+Requires-Dist: numpy>=1.26.0; python_version >= "3.12" and python_version < "3.13"
+Requires-Dist: numpy>=2.1.0; python_version >= "3.13"
+Requires-Dist: pandas>=1.4.0; python_version < "3.11"
+Requires-Dist: pandas>=1.5.0; python_version >= "3.11" and python_version < "3.12"
+Requires-Dist: pandas>=2.1.1; python_version >= "3.12" and python_version < "3.13"
+Requires-Dist: pandas>=2.2.3; python_version >= "3.13"
+Requires-Dist: plotly>=5.10.0; python_version < "3.13"
+Requires-Dist: plotly>=5.12.0; python_version >= "3.13"
+Requires-Dist: scipy>=1.7.3; python_version < "3.10"
+Requires-Dist: scipy>=1.9.2; python_version >= "3.10" and python_version < "3.12"
+Requires-Dist: scipy>=1.12.0; python_version >= "3.12" and python_version < "3.13"
+Requires-Dist: scipy>=1.14.1; python_version >= "3.13"
 Provides-Extra: tutorials
 Requires-Dist: markupsafe<=2.0.1; extra == "tutorials"
-Requires-Dist: scikit-learn<1.2,>=0.24; extra == "tutorials"
+Requires-Dist: scikit-learn>=0.24; python_version < "3.12" and extra == "tutorials"
+Requires-Dist: scikit-learn>=1.3.1; python_version >= "3.12" and extra == "tutorials"
 Requires-Dist: jupyter<2,>=1.0.0; extra == "tutorials"
 Provides-Extra: test
 Requires-Dist: copulas[tutorials]; extra == "test"
 Requires-Dist: pytest<7,>=6.2.5; extra == "test"
 Requires-Dist: pytest-cov<3,>=2.6.0; extra == "test"
-Requires-Dist: pytest-rerunfailures<10,>=9.0.0; extra == "test"
+Requires-Dist: pytest-rerunfailures<15,>=10.3; extra == "test"
 Requires-Dist: rundoc<0.5,>=0.4.3; extra == "test"
 Requires-Dist: tomli<3,>=2.0.0; extra == "test"
 Provides-Extra: dev
@@ -47,42 +56,25 @@ Requires-Dist: copulas[test,tutorials]; extra == "dev"
 Requires-Dist: pip>=9.0.1; extra == "dev"
 Requires-Dist: build<2,>=1.0.0; extra == "dev"
 Requires-Dist: bump-my-version<1,>=0.18.3; extra == "dev"
-Requires-Dist: watchdog<0.11,>=0.8.3; extra == "dev"
+Requires-Dist: watchdog<5,>=1.0.1; extra == "dev"
 Requires-Dist: m2r<0.3,>=0.2.0; extra == "dev"
 Requires-Dist: nbsphinx<0.7,>=0.5.0; extra == "dev"
 Requires-Dist: Sphinx<3,>=1.7.1; extra == "dev"
 Requires-Dist: sphinx_rtd_theme<0.5,>=0.2.4; extra == "dev"
-Requires-Dist: Jinja2<3,>=2; extra == "dev"
-Requires-Dist: flake8<4,>=3.7.7; extra == "dev"
-Requires-Dist: isort<5,>=4.3.4; extra == "dev"
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-Requires-Dist: autoflake<2,>=1.1; extra == "dev"
-Requires-Dist: autopep8<1.6,>=1.4.3; extra == "dev"
+Requires-Dist: sphinxcontrib_applehelp<1.0.8; extra == "dev"
+Requires-Dist: sphinxcontrib-devhelp<1.0.6; extra == "dev"
+Requires-Dist: sphinxcontrib-htmlhelp<2.0.5; extra == "dev"
+Requires-Dist: sphinxcontrib_serializinghtml<1.1.10; extra == "dev"
+Requires-Dist: sphinxcontrib_qthelp<1.0.7; extra == "dev"
+Requires-Dist: alabaster<0.7.13; extra == "dev"
+Requires-Dist: Jinja2<3,>=2; python_version < "3.12" and extra == "dev"
+Requires-Dist: Jinja2<4,>=2; python_version >= "3.12" and extra == "dev"
+Requires-Dist: ruff<1,>=0.3.2; extra == "dev"
 Requires-Dist: twine<4,>=1.10.0; extra == "dev"
 Requires-Dist: wheel>=0.30.0; extra == "dev"
 Requires-Dist: coverage<6,>=4.5.1; extra == "dev"
 Requires-Dist: tox<4,>=2.9.1; extra == "dev"
 Requires-Dist: invoke; extra == "dev"
-Requires-Dist: doc8<0.9,>=0.8.0; extra == "dev"
 Requires-Dist: urllib3<1.26,>=1.20; extra == "dev"
 Requires-Dist: tabulate<0.9,>=0.8.3; extra == "dev"
 Requires-Dist: boto3<1.10,>=1.7.47; extra == "dev"

copulas-0.12.1/copulas/__init__.py

@@ -0,0 +1,91 @@
+"""Top-level package for Copulas."""
+
+__author__ = 'DataCebo, Inc.'
+__email__ = 'info@sdv.dev'
+__version__ = '0.12.1'
+
+import sys
+import warnings
+from copy import deepcopy
+from importlib.metadata import entry_points
+from operator import attrgetter
+from types import ModuleType
+
+
+def _get_addon_target(addon_path_name):
+    """Find the target object for the add-on.
+
+    Args:
+        addon_path_name (str):
+            The add-on's name. The add-on's name should be the full path of valid Python
+            identifiers (i.e. importable.module:object.attr).
+
+    Returns:
+        tuple:
+            * object:
+                The base module or object the add-on should be added to.
+            * str:
+                The name the add-on should be added to under the module or object.
+    """
+    module_path, _, object_path = addon_path_name.partition(':')
+    module_path = module_path.split('.')
+
+    if module_path[0] != __name__:
+        msg = f"expected base module to be '{__name__}', found '{module_path[0]}'"
+        raise AttributeError(msg)
+
+    target_base = sys.modules[__name__]
+    for submodule in module_path[1:-1]:
+        target_base = getattr(target_base, submodule)
+
+    addon_name = module_path[-1]
+    if object_path:
+        if len(module_path) > 1 and not hasattr(target_base, module_path[-1]):
+            msg = f"cannot add '{object_path}' to unknown submodule '{'.'.join(module_path)}'"
+            raise AttributeError(msg)
+
+        if len(module_path) > 1:
+            target_base = getattr(target_base, module_path[-1])
+
+        split_object = object_path.split('.')
+        addon_name = split_object[-1]
+
+        if len(split_object) > 1:
+            target_base = attrgetter('.'.join(split_object[:-1]))(target_base)
+
+    return target_base, addon_name
+
+
+def _find_addons():
+    """Find and load all copulas add-ons."""
+    group = 'copulas_modules'
+    try:
+        eps = entry_points(group=group)
+    except TypeError:
+        # Load-time selection requires Python >= 3.10 or importlib_metadata >= 3.6
+        eps = entry_points().get(group, [])
+
+    for entry_point in eps:
+        try:
+            addon = entry_point.load()
+        except Exception as e:  # pylint: disable=broad-exception-caught
+            msg = f'Failed to load "{entry_point.name}" from "{entry_point.value}" with error:\n{e}'
+            warnings.warn(msg)
+            continue
+
+        try:
+            addon_target, addon_name = _get_addon_target(entry_point.name)
+        except AttributeError as error:
+            msg = f"Failed to set '{entry_point.name}': {error}."
+            warnings.warn(msg)
+            continue
+
+        if isinstance(addon, ModuleType):
+            addon_module_name = f'{addon_target.__name__}.{addon_name}'
+            if addon_module_name not in sys.modules:
+                sys.modules[addon_module_name] = addon
+
+        setattr(addon_target, addon_name, addon)
+
+
+_find_addons()

{copulas-0.10.1 → copulas-0.12.1}/copulas/bivariate/__init__.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from copulas import EPSILON
+from copulas.utils import EPSILON
 from copulas.bivariate.base import Bivariate, CopulaTypes
 from copulas.bivariate.clayton import Clayton
 from copulas.bivariate.frank import Frank
@@ -47,7 +47,6 @@ def _compute_empirical(X):
         right = sum(np.logical_and(U >= base[k], V >= base[k])) / N
 
         if left > 0:
-
             z_left.append(base[k])
             L.append(left / base[k] ** 2)
 
@@ -151,7 +150,8 @@ def select_copula(X):
 
     left_tail, empirical_left_aut, right_tail, empirical_right_aut = _compute_empirical(X)
     candidate_left_auts, candidate_right_auts = _compute_candidates(
-        copula_candidates, left_tail, right_tail)
+        copula_candidates, left_tail, right_tail
+    )
 
     empirical_aut = np.concatenate((empirical_left_aut, empirical_right_aut))
     candidate_auts = [

{copulas-0.10.1 → copulas-0.12.1}/copulas/bivariate/base.py

@@ -8,8 +8,9 @@ import numpy as np
 from scipy import stats
 from scipy.optimize import brentq
 
-from copulas import EPSILON, NotFittedError, random_state, validate_random_state
 from copulas.bivariate.utils import split_matrix
+from copulas.errors import NotFittedError
+from copulas.utils import EPSILON, random_state, validate_random_state
 
 
 class CopulaTypes(Enum):
@@ -96,7 +97,7 @@ class Bivariate(object):
             return super(Bivariate, cls).__new__(cls)
 
         if not isinstance(copula_type, CopulaTypes):
-            if (isinstance(copula_type, str) and copula_type.upper() in CopulaTypes.__members__):
+            if isinstance(copula_type, str) and copula_type.upper() in CopulaTypes.__members__:
                 copula_type = CopulaTypes[copula_type.upper()]
             else:
                 raise ValueError(f'Invalid copula type {copula_type}')
@@ -192,11 +193,7 @@ class Bivariate(object):
             dict: Parameters of the copula.
 
         """
-        return {
-            'copula_type': self.copula_type.name,
-            'theta': self.theta,
-            'tau': self.tau
-        }
+        return {'copula_type': self.copula_type.name, 'theta': self.theta, 'tau': self.tau}
 
     @classmethod
     def from_dict(cls, copula_dict):
@@ -297,6 +294,7 @@ class Bivariate(object):
         self.check_fit()
         result = []
         for _y, _v in zip(y, V):
+
             def f(u):
                 return self.partial_derivative_scalar(u, _v) - _y
 
@@ -330,7 +328,7 @@ class Bivariate(object):
             np.ndarray
 
         """
-        delta = (-2 * (X[:, 1] > 0.5) + 1)
+        delta = -2 * (X[:, 1] > 0.5) + 1
         delta = 0.0001 * delta
         X_prime = X.copy()
         X_prime[:, 1] += delta
@@ -411,10 +409,11 @@ class Bivariate(object):
 
         """
         from copulas.bivariate import select_copula  # noqa
+
         warnings.warn(
             '`Bivariate.select_copula` has been deprecated and will be removed in a later '
             'release. Please use `copulas.bivariate.select_copula` instead',
-            DeprecationWarning
+            DeprecationWarning,
         )
         return select_copula(X)
 

{copulas-0.10.1 → copulas-0.12.1}/copulas/bivariate/clayton.py

@@ -84,9 +84,10 @@ class Clayton(Bivariate):
             cdfs = [
                 np.power(
                     np.power(U[i], -self.theta) + np.power(V[i], -self.theta) - 1,
-                    -1.0 / self.theta
+                    -1.0 / self.theta,
                 )
-                if (U[i] > 0 and V[i] > 0) else 0
+                if (U[i] > 0 and V[i] > 0)
+                else 0
                 for i in range(len(U))
             ]
 

{copulas-0.10.1 → copulas-0.12.1}/copulas/bivariate/frank.py

@@ -6,9 +6,9 @@ import numpy as np
 import scipy.integrate as integrate
 from scipy.optimize import least_squares
 
-from copulas import EPSILON
 from copulas.bivariate.base import Bivariate, CopulaTypes
 from copulas.bivariate.utils import split_matrix
+from copulas.utils import EPSILON
 
 MIN_FLOAT_LOG = np.log(sys.float_info.min)
 MAX_FLOAT_LOG = np.log(sys.float_info.max)
@@ -162,6 +162,7 @@ class Frank(Bivariate):
 
     def _tau_to_theta(self, alpha):
         """Relationship between tau and theta as a solvable equation."""
+
         def debye(t):
             return t / (np.exp(t) - 1)
 

{copulas-0.10.1 → copulas-0.12.1}/copulas/datasets.py

@@ -4,7 +4,7 @@ import numpy as np
 import pandas as pd
 from scipy import stats
 
-from copulas import set_random_state, validate_random_state
+from copulas.utils import set_random_state, validate_random_state
 
 
 def _dummy_fn(state):
@@ -33,10 +33,7 @@ def sample_bivariate_age_income(size=1000, seed=42):
         income += np.random.normal(loc=np.log(age) / 100, scale=10, size=size)
         income[np.random.randint(0, 10, size=size) == 0] /= 1000
 
-    return pd.DataFrame({
-        'age': age,
-        'income': income
-    })
+    return pd.DataFrame({'age': age, 'income': income})
 
 
 def sample_trivariate_xyz(size=1000, seed=42):
@@ -61,11 +58,7 @@ def sample_trivariate_xyz(size=1000, seed=42):
     with set_random_state(validate_random_state(seed), _dummy_fn):
         x = stats.beta.rvs(a=0.1, b=0.1, size=size)
         y = stats.beta.rvs(a=0.1, b=0.5, size=size)
-        return pd.DataFrame({
-            'x': x,
-            'y': y,
-            'z': np.random.normal(size=size) + y * 10
-        })
+        return pd.DataFrame({'x': x, 'y': y, 'z': np.random.normal(size=size) + y * 10})
 
 
 def sample_univariate_bernoulli(size=1000, seed=42):

copulas-0.12.1/copulas/errors.py

@@ -0,0 +1,5 @@
+"""Copulas Exceptions."""
+
+
+class NotFittedError(Exception):
+    """NotFittedError class."""

{copulas-0.10.1 → copulas-0.12.1}/copulas/multivariate/__init__.py

@@ -5,10 +5,4 @@ from copulas.multivariate.gaussian import GaussianMultivariate
 from copulas.multivariate.tree import Tree, TreeTypes
 from copulas.multivariate.vine import VineCopula
 
-__all__ = (
-    'Multivariate',
-    'GaussianMultivariate',
-    'VineCopula',
-    'Tree',
-    'TreeTypes'
-)
+__all__ = ('Multivariate', 'GaussianMultivariate', 'VineCopula', 'Tree', 'TreeTypes')

{copulas-0.10.1 → copulas-0.12.1}/copulas/multivariate/base.py

@@ -4,7 +4,8 @@ import pickle
 
 import numpy as np
 
-from copulas import NotFittedError, get_instance, validate_random_state
+from copulas.errors import NotFittedError
+from copulas.utils import get_instance, validate_random_state
 
 
 class Multivariate(object):

{copulas-0.10.1 → copulas-0.12.1}/copulas/multivariate/gaussian.py

@@ -7,11 +7,17 @@ import numpy as np
 import pandas as pd
 from scipy import stats
 
-from copulas import (
-    EPSILON, check_valid_values, get_instance, get_qualified_name, random_state, store_args,
-    validate_random_state)
 from copulas.multivariate.base import Multivariate
 from copulas.univariate import GaussianUnivariate, Univariate
+from copulas.utils import (
+    EPSILON,
+    check_valid_values,
+    get_instance,
+    get_qualified_name,
+    random_state,
+    store_args,
+    validate_random_state,
+)
 
 LOGGER = logging.getLogger(__name__)
 DEFAULT_DISTRIBUTION = Univariate
@@ -64,26 +70,6 @@ class GaussianMultivariate(Multivariate):
 
         return stats.norm.ppf(np.column_stack(U))
 
-    def _get_correlation(self, X):
-        """Compute correlation matrix with transformed data.
-
-        Args:
-            X (numpy.ndarray):
-                Data for which the correlation needs to be computed.
-
-        Returns:
-            numpy.ndarray:
-                computed correlation matrix.
-        """
-        result = self._transform_to_normal(X)
-        correlation = pd.DataFrame(data=result).corr().to_numpy()
-        correlation = np.nan_to_num(correlation, nan=0.0)
-        # If singular, add some noise to the diagonal
-        if np.linalg.cond(correlation) > 1.0 / sys.float_info.epsilon:
-            correlation = correlation + np.identity(correlation.shape[0]) * EPSILON
-
-        return pd.DataFrame(correlation, index=self.columns, columns=self.columns)
-
     @check_valid_values
     def fit(self, X):
         """Compute the distribution for each variable and then its correlation matrix.
@@ -94,42 +80,88 @@ class GaussianMultivariate(Multivariate):
         """
         LOGGER.info('Fitting %s', self)
 
+        # Validate the input data
+        X = self._validate_input(X)
+        columns, univariates = self._fit_columns(X)
+
+        self.columns = columns
+        self.univariates = univariates
+
+        LOGGER.debug('Computing correlation.')
+        self.correlation = self._get_correlation(X)
+        self.fitted = True
+        LOGGER.debug('GaussianMultivariate fitted successfully')
+
+    def _validate_input(self, X):
+        """Validate the input data."""
         if not isinstance(X, pd.DataFrame):
             X = pd.DataFrame(X)
 
+        return X
+
+    def _fit_columns(self, X):
+        """Fit each column to its distribution."""
         columns = []
         univariates = []
         for column_name, column in X.items():
-            if isinstance(self.distribution, dict):
-                distribution = self.distribution.get(column_name, DEFAULT_DISTRIBUTION)
-            else:
-                distribution = self.distribution
-
+            distribution = self._get_distribution_for_column(column_name)
             LOGGER.debug('Fitting column %s to %s', column_name, distribution)
 
-            univariate = get_instance(distribution)
-            try:
-                univariate.fit(column)
-            except BaseException:
-                log_message = (
-                    f'Unable to fit to a {distribution} distribution for column {column_name}. '
-                    'Using a Gaussian distribution instead.'
-                )
-                LOGGER.info(log_message)
-                univariate = GaussianUnivariate()
-                univariate.fit(column)
-
+            univariate = self._fit_column(column, distribution, column_name)
             columns.append(column_name)
             univariates.append(univariate)
 
-        self.columns = columns
-        self.univariates = univariates
+        return columns, univariates
+
+    def _get_distribution_for_column(self, column_name):
+        """Retrieve the distribution for a given column name."""
+        if isinstance(self.distribution, dict):
+            return self.distribution.get(column_name, DEFAULT_DISTRIBUTION)
+
+        return self.distribution
+
+    def _fit_column(self, column, distribution, column_name):
+        """Fit a single column to its distribution with exception handling."""
+        univariate = get_instance(distribution)
+        try:
+            univariate.fit(column)
+        except Exception as error:
+            univariate = self._fit_with_fallback_distribution(
+                column, distribution, column_name, error
+            )
+
+        return univariate
+
+    def _fit_with_fallback_distribution(self, column, distribution, column_name, error):
+        """Fall back to fitting a Gaussian distribution and log the error."""
+        log_message = (
+            f'Unable to fit to a {distribution} distribution for column {column_name}. '
+            'Using a Gaussian distribution instead.'
+        )
+        LOGGER.info(log_message)
+        univariate = GaussianUnivariate()
+        univariate.fit(column)
+        return univariate
 
-        LOGGER.debug('Computing correlation')
-        self.correlation = self._get_correlation(X)
-        self.fitted = True
+    def _get_correlation(self, X):
+        """Compute correlation matrix with transformed data.
 
-        LOGGER.debug('GaussianMultivariate fitted successfully')
+        Args:
+            X (numpy.ndarray):
+                Data for which the correlation needs to be computed.
+
+        Returns:
+            numpy.ndarray:
+                computed correlation matrix.
+        """
+        result = self._transform_to_normal(X)
+        correlation = pd.DataFrame(data=result).corr().to_numpy()
+        correlation = np.nan_to_num(correlation, nan=0.0)
+        # If singular, add some noise to the diagonal
+        if np.linalg.cond(correlation) > 1.0 / sys.float_info.epsilon:
+            correlation = correlation + np.identity(correlation.shape[0]) * EPSILON
+
+        return pd.DataFrame(correlation, index=self.columns, columns=self.columns)
 
     def probability_density(self, X):
         """Compute the probability density for each point in X.
@@ -149,8 +181,7 @@ class GaussianMultivariate(Multivariate):
         self.check_fit()
         transformed = self._transform_to_normal(X)
 
-        return stats.multivariate_normal.pdf(
-            transformed, cov=self.correlation, allow_singular=True)
+        return stats.multivariate_normal.pdf(transformed, cov=self.correlation, allow_singular=True)
 
     def cumulative_distribution(self, X):
         """Compute the cumulative distribution value for each point in X.

{copulas-0.10.1 → copulas-0.12.1}/copulas/multivariate/tree.py

@@ -6,9 +6,9 @@ from enum import Enum
 import numpy as np
 import scipy
 
-from copulas import EPSILON, get_qualified_name
 from copulas.bivariate.base import Bivariate
 from copulas.multivariate.base import Multivariate
+from copulas.utils import EPSILON, get_qualified_name
 
 LOGGER = logging.getLogger(__name__)
 
@@ -98,7 +98,7 @@ class Tree(Multivariate):
         """
         # first column is the variable of interest
         tau_y = self.tau_matrix[:, y]
-        tau_y[y] = np.NaN
+        tau_y[y] = np.nan
 
         temp = np.empty([self.n_nodes, 3])
         temp[:, 0] = np.arange(self.n_nodes)
@@ -131,7 +131,7 @@ class Tree(Multivariate):
                     left_parent, right_parent = edge.parents
                     left_u, right_u = Edge.get_conditional_uni(left_parent, right_parent)
 
-                tau[i, j], pvalue = scipy.stats.kendalltau(left_u, right_u)
+                tau[i, j], _pvalue = scipy.stats.kendalltau(left_u, right_u)
 
         return tau
 
@@ -212,8 +212,7 @@ class Tree(Multivariate):
         """Produce printable representation of the class."""
         template = 'L:{} R:{} D:{} Copula:{} Theta:{}'
         return '\n'.join([
-            template.format(edge.L, edge.R, edge.D, edge.name, edge.theta)
-            for edge in self.edges
+            template.format(edge.L, edge.R, edge.D, edge.name, edge.theta) for edge in self.edges
         ])
 
     def _serialize_previous_tree(self):
@@ -237,11 +236,7 @@ class Tree(Multivariate):
                 Parameters of this Tree.
         """
         fitted = self.fitted
-        result = {
-            'tree_type': self.tree_type,
-            'type': get_qualified_name(self),
-            'fitted': fitted
-        }
+        result = {'tree_type': self.tree_type, 'type': get_qualified_name(self), 'fitted': fitted}
 
         if not fitted:
             return result
@@ -451,7 +446,7 @@ def get_tree(tree_type):
             Instance of a Tree of the specified type.
     """
     if not isinstance(tree_type, TreeTypes):
-        if (isinstance(tree_type, str) and tree_type.upper() in TreeTypes.__members__):
+        if isinstance(tree_type, str) and tree_type.upper() in TreeTypes.__members__:
             tree_type = TreeTypes[tree_type.upper()]
         else:
             raise ValueError(f'Invalid tree type {tree_type}')
@@ -657,7 +652,7 @@ class Edge(object):
             'theta': self.theta,
             'tau': self.tau,
             'U': U,
-            'likelihood': self.likelihood
+            'likelihood': self.likelihood,
         }
 
     @classmethod
@@ -674,8 +669,11 @@ class Edge(object):
                 Instance of the edge defined on the parameters.
         """
         instance = cls(
-            edge_dict['index'], edge_dict['L'], edge_dict['R'],
-            edge_dict['name'], edge_dict['theta']
+            edge_dict['index'],
+            edge_dict['L'],
+            edge_dict['R'],
+            edge_dict['name'],
+            edge_dict['theta'],
         )
         instance.U = np.array(edge_dict['U'])
         parents = edge_dict['parents']