risk-network 0.0.13b4__py3-none-any.whl → 0.0.13b5__py3-none-any.whl

risk/{network/plotter/labels.py → _network/_plotter/_labels.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/labels
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_labels
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 import copy
@@ -10,10 +10,9 @@ import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 
-from risk.log import params
-from risk.network.graph.graph import Graph
-from risk.network.plotter.utils.colors import get_annotated_domain_colors, to_rgba
-from risk.network.plotter.utils.layout import calculate_bounding_box
+from ..._log import params
+from .._graph import Graph
+from ._utils import calculate_bounding_box, get_annotated_domain_colors, to_rgba
 
 TERM_DELIMITER = "::::"  # String used to separate multiple domain terms when constructing composite domain labels
 
@@ -22,7 +21,8 @@ class Labels:
     """Class to handle the annotation of network graphs with labels for different domains."""
 
     def __init__(self, graph: Graph, ax: plt.Axes):
-        """Initialize the Labeler object with a network graph and matplotlib axes.
+        """
+        Initialize the Labeler object with a network graph and matplotlib axes.
 
         Args:
             graph (Graph): Graph object containing the network data.
@@ -56,7 +56,8 @@ class Labels:
         ids_to_keep: Union[List, Tuple, np.ndarray, None] = None,
         ids_to_labels: Union[Dict[int, str], None] = None,
     ) -> None:
-        """Annotate the network graph with labels for different domains, positioned around the network for clarity.
+        """
+        Annotate the network graph with labels for different domains, positioned around the network for clarity.
 
         Args:
             scale (float, optional): Scale factor for positioning labels around the perimeter. Defaults to 1.05.
@@ -261,7 +262,8 @@ class Labels:
         arrow_base_shrink: float = 0.0,
         arrow_tip_shrink: float = 0.0,
     ) -> None:
-        """Annotate the network graph with a label for the given nodes, with one arrow pointing to each centroid of sublists of nodes.
+        """
+        Annotate the network graph with a label for the given nodes, with one arrow pointing to each centroid of sublists of nodes.
 
         Args:
             nodes (List, Tuple, or np.ndarray): List of node labels or list of lists of node labels.
@@ -349,7 +351,8 @@ class Labels:
             )
 
     def _calculate_domain_centroid(self, nodes: List) -> tuple:
-        """Calculate the most centrally located node in .
+        """
+        Calculate the most centrally located node in the domain based on the coordinates of the nodes.
 
         Args:
             nodes (List): List of node labels to include in the subnetwork.
@@ -384,7 +387,8 @@ class Labels:
         filtered_domain_terms: Dict[int, str],
         valid_indices: List[int],
     ) -> None:
-        """Process the ids_to_keep, apply filtering, and store valid domain centroids and terms.
+        """
+        Process the ids_to_keep, apply filtering, and store valid domain centroids and terms.
 
         Args:
             domain_id_to_centroid_map (Dict[int, np.ndarray]): Mapping of domain IDs to their centroids.
@@ -450,7 +454,8 @@ class Labels:
         filtered_domain_terms: Dict[int, str],
         valid_indices: List[int],
     ) -> None:
-        """Process remaining domains to fill in additional labels, respecting the remaining_labels limit.
+        """
+        Process remaining domains to fill in additional labels, respecting the remaining_labels limit.
 
         Args:
             domain_id_to_centroid_map (Dict[int, np.ndarray]): Mapping of domain IDs to their centroids.
@@ -551,7 +556,8 @@ class Labels:
         filtered_domain_terms: Dict[int, str],
         valid_indices: List[int],
     ) -> bool:
-        """Validate and process the domain terms, updating relevant dictionaries if valid.
+        """
+        Validate and process the domain terms, updating relevant dictionaries if valid.
 
         Args:
             domain_id (int): Domain ID to process.
@@ -607,7 +613,8 @@ class Labels:
         min_chars_per_line: int,
         max_chars_per_line: int,
     ) -> str:
-        """Process terms for a domain, applying word length constraints and combining words where appropriate.
+        """
+        Process terms for a domain, applying word length constraints and combining words where appropriate.
 
         Args:
             domain_id (int): Domain ID to process.
@@ -646,7 +653,8 @@ class Labels:
         ids_to_colors: Union[Dict[int, Any], None] = None,
         random_seed: int = 888,
     ) -> List:
-        """Get colors for the labels based on node annotation or a specified colormap.
+        """
+        Get colors for the labels based on node annotation or a specified colormap.
 
         Args:
             cmap (str, optional): Name of the colormap to use for generating label colors. Defaults to "gist_rainbow".
@@ -682,8 +690,9 @@ class Labels:
     def _combine_words(
         self, words: List[str], max_chars_per_line: int, max_label_lines: int
     ) -> str:
-        """Combine words to fit within the max_chars_per_line and max_label_lines constraints,
-        and separate the final output by TERM_DELIMITER for plotting.
+        """
+        Combine words to fit within the max_chars_per_line and max_label_lines constraints, and separate the
+        final output by TERM_DELIMITER for plotting.
 
         Args:
             words (List[str]): List of words to combine.
@@ -753,7 +762,8 @@ class Labels:
         radius: float,
         offset: float,
     ) -> Dict[int, Any]:
-        """Calculate and optimize label positions for clarity.
+        """
+        Calculate and optimize label positions for clarity.
 
         Args:
             filtered_domain_centroids (Dict[int, Any]): Centroids of the filtered domains.
@@ -777,7 +787,8 @@ class Labels:
     def _calculate_equidistant_positions_around_center(
         self, center: Tuple[float, float], radius: float, label_offset: float, num_domains: int
     ) -> List[np.ndarray]:
-        """Calculate positions around a center at equidistant angles.
+        """
+        Calculate positions around a center at equidistant angles.
 
         Args:
             center (Tuple[float, float]): The center point around which positions are calculated.
@@ -799,7 +810,8 @@ class Labels:
     def _optimize_label_positions(
         self, best_label_positions: Dict[int, Any], domain_centroids: Dict[int, Any]
     ) -> Dict[int, Any]:
-        """Optimize label positions around the perimeter to minimize total distance to centroids.
+        """
+        Optimize label positions around the perimeter to minimize total distance to centroids.
 
         Args:
             best_label_positions (Dict[int, Any]): Initial positions of labels around the perimeter.
@@ -838,7 +850,8 @@ class Labels:
     def _calculate_total_distance(
         self, label_positions: Dict[int, Any], domain_centroids: Dict[int, Any]
     ) -> float:
-        """Calculate the total distance from label positions to their domain centroids.
+        """
+        Calculate the total distance from label positions to their domain centroids.
 
         Args:
             label_positions (Dict[int, Any]): Positions of labels around the perimeter.
@@ -862,7 +875,8 @@ class Labels:
         j: int,
         domain_centroids: Dict[int, Any],
     ) -> float:
-        """Swap two labels and evaluate the total distance after the swap.
+        """
+        Swap two labels and evaluate the total distance after the swap.
 
         Args:
             label_positions (Dict[int, Any]): Positions of labels around the perimeter.
@@ -887,7 +901,8 @@ class Labels:
     def _apply_str_transformation(
         self, words: List[str], transformation: Union[str, Dict[str, str]]
     ) -> List[str]:
-        """Apply a user-specified case transformation to each word in the list without appending duplicates.
+        """
+        Apply a user-specified case transformation to each word in the list without appending duplicates.
 
         Args:
             words (List[str]): A list of words to transform.

risk/{network/plotter/network.py → _network/_plotter/_network.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/network
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_network
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple, Union
@@ -8,19 +8,21 @@ from typing import Any, Dict, List, Tuple, Union
 import networkx as nx
 import numpy as np
 
-from risk.log import params
-from risk.network.graph.graph import Graph
-from risk.network.plotter.utils.colors import get_domain_colors, to_rgba
+from ..._log import params
+from .._graph import Graph
+from ._utils import get_domain_colors, to_rgba
 
 
 class Network:
-    """A class for plotting network graphs with customizable options.
+    """
+    A class for plotting network graphs with customizable options.
 
     The Network class provides methods to plot network graphs with flexible node and edge properties.
     """
 
     def __init__(self, graph: Graph, ax: Any = None) -> None:
-        """Initialize the Plotter class.
+        """
+        Initialize the Plotter class.
 
         Args:
             graph (Graph): The network data and attributes to be visualized.
@@ -41,7 +43,8 @@ class Network:
         node_alpha: Union[float, None] = 1.0,
         edge_alpha: Union[float, None] = 1.0,
     ) -> None:
-        """Plot the network graph with customizable node colors, sizes, edge widths, and node edge widths.
+        """
+        Plot the network graph with customizable node colors, sizes, edge widths, and node edge widths.
 
         Args:
             node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
@@ -124,7 +127,8 @@ class Network:
         node_alpha: Union[float, None] = None,
         edge_alpha: Union[float, None] = None,
     ) -> None:
-        """Plot a subnetwork of selected nodes with customizable node and edge attributes.
+        """
+        Plot a subnetwork of selected nodes with customizable node and edge attributes.
 
         Args:
             nodes (List, Tuple, or np.ndarray): List of node labels to include in the subnetwork. Accepts nested lists.
@@ -211,7 +215,8 @@ class Network:
         ids_to_colors: Union[Dict[int, Any], None] = None,
         random_seed: int = 888,
     ) -> np.ndarray:
-        """Adjust the colors of nodes in the network graph based on significance.
+        """
+        Adjust the colors of nodes in the network graph based on significance.
 
         Args:
             cmap (str, optional): Colormap to use for coloring the nodes. Defaults to "gist_rainbow".
@@ -270,7 +275,8 @@ class Network:
     def get_annotated_node_sizes(
         self, significant_size: int = 50, nonsignificant_size: int = 25
     ) -> np.ndarray:
-        """Adjust the sizes of nodes in the network graph based on whether they are significant or not.
+        """
+        Adjust the sizes of nodes in the network graph based on whether they are significant or not.
 
         Args:
             significant_size (int): Size for significant nodes. Defaults to 50.

risk/{network/plotter/plotter.py → _network/_plotter/_plotter.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/plotter
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_plotter
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import List, Tuple, Union
@@ -8,18 +8,18 @@ from typing import List, Tuple, Union
 import matplotlib.pyplot as plt
 import numpy as np
 
-from risk.log import params
-from risk.network.graph.graph import Graph
-from risk.network.plotter.canvas import Canvas
-from risk.network.plotter.contour import Contour
-from risk.network.plotter.labels import Labels
-from risk.network.plotter.network import Network
-from risk.network.plotter.utils.colors import to_rgba
-from risk.network.plotter.utils.layout import calculate_bounding_box
+from ..._log import params
+from .._graph._graph import Graph
+from ._canvas import Canvas
+from ._contour import Contour
+from ._labels import Labels
+from ._network import Network
+from ._utils import calculate_bounding_box, to_rgba
 
 
 class Plotter(Canvas, Network, Contour, Labels):
-    """A class for visualizing network graphs with customizable options.
+    """
+    A class for visualizing network graphs with customizable options.
 
     The Plotter class uses a Graph object and provides methods to plot the network with
     flexible node and edge properties. It also supports plotting labels, contours, drawing the network's
@@ -34,7 +34,8 @@ class Plotter(Canvas, Network, Contour, Labels):
         background_alpha: Union[float, None] = 1.0,
         pad: float = 0.3,
     ) -> None:
-        """Initialize the Plotter with a Graph object and plotting parameters.
+        """
+        Initialize the Plotter with a Graph object and plotting parameters.
 
         Args:
             graph (Graph): The network data and attributes to be visualized.
@@ -63,7 +64,8 @@ class Plotter(Canvas, Network, Contour, Labels):
         background_alpha: Union[float, None],
         pad: float,
     ) -> plt.Axes:
-        """Set up the plot with figure size and background color.
+        """
+        Set up the plot with figure size and background color.
 
         Args:
             graph (Graph): The network data and attributes to be visualized.
@@ -115,7 +117,8 @@ class Plotter(Canvas, Network, Contour, Labels):
         return ax
 
     def savefig(self, *args, pad_inches: float = 0.5, dpi: int = 100, **kwargs) -> None:
-        """Save the current plot to a file with additional export options.
+        """
+        Save the current plot to a file with additional export options.
 
         Args:
             *args: Positional arguments passed to `plt.savefig`.
@@ -132,7 +135,8 @@ class Plotter(Canvas, Network, Contour, Labels):
         plt.savefig(*args, **kwargs)
 
     def show(self, *args, **kwargs) -> None:
-        """Display the current plot.
+        """
+        Display the current plot.
 
         Args:
             *args: Positional arguments passed to `plt.show`.

risk/_network/_plotter/_utils/__init__.py

@@ -0,0 +1,7 @@
+"""
+risk/_network/_plotter/_utils
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from ._colors import get_annotated_domain_colors, get_domain_colors, to_rgba
+from ._layout import calculate_bounding_box, calculate_centroids

risk/{network/plotter/utils/colors.py → _network/_plotter/_utils/_colors.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/utils/colors
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_utils/_colors
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple, Union
@@ -9,7 +9,7 @@ import matplotlib
 import matplotlib.colors as mcolors
 import numpy as np
 
-from risk.network.graph.graph import Graph
+from ..._graph import Graph
 
 
 def get_annotated_domain_colors(
@@ -24,7 +24,8 @@ def get_annotated_domain_colors(
     ids_to_colors: Union[Dict[int, Any], None] = None,
     random_seed: int = 888,
 ) -> List[Tuple]:
-    """Get colors for the domains based on node annotation, or use a specified color.
+    """
+    Get colors for the domains based on node annotation, or use a specified color.
 
     Args:
         graph (Graph): The network data and attributes to be visualized.
@@ -85,7 +86,8 @@ def get_domain_colors(
     ids_to_colors: Union[Dict[int, Any], None] = None,
     random_seed: int = 888,
 ) -> np.ndarray:
-    """Generate composite colors for domains based on significance or specified colors.
+    """
+    Generate composite colors for domains based on significance or specified colors.
 
     Args:
         graph (Graph): The network data and attributes to be visualized.
@@ -135,7 +137,8 @@ def _get_domain_ids_to_colors(
     ids_to_colors: Union[Dict[int, Any], None] = None,
     random_seed: int = 888,
 ) -> Dict[int, Any]:
-    """Get colors for each domain.
+    """
+    Get colors for each domain.
 
     Args:
         graph (Graph): The network data and attributes to be visualized.
@@ -174,7 +177,8 @@ def _get_composite_node_colors(
     blend_colors: bool = False,
     blend_gamma: float = 2.2,
 ) -> np.ndarray:
-    """Generate composite colors for nodes based on domain colors and significance values, with optional color blending.
+    """
+    Generate composite colors for nodes based on domain colors and significance values, with optional color blending.
 
     Args:
         graph (Graph): The network data and attributes to be visualized.
@@ -233,7 +237,8 @@ def _get_colors(
     color: Union[str, List, Tuple, np.ndarray, None] = None,
     random_seed: int = 888,
 ) -> List[Tuple]:
-    """Generate a list of RGBA colors for domains, ensuring maximally separated colors for nearby domains.
+    """
+    Generate a list of RGBA colors for domains, ensuring maximally separated colors for nearby domains.
 
     Args:
         domain_id_to_node_ids_map (Dict[int, Any]): Mapping from domain IDs to lists of node IDs.
@@ -266,7 +271,8 @@ def _get_colors(
 def _blend_colors_perceptually(
     colors: Union[List, Tuple, np.ndarray], significances: List[float], gamma: float = 2.2
 ) -> Tuple[float, float, float, float]:
-    """Blends a list of RGBA colors using gamma correction for perceptually uniform color mixing.
+    """
+    Blends a list of RGBA colors using gamma correction for perceptually uniform color mixing.
 
     Args:
         colors (List, Tuple, np.ndarray): List of RGBA colors. Can be a list, tuple, or NumPy array of RGBA values.
@@ -297,7 +303,8 @@ def _transform_colors(
     max_scale: float = 1.0,
     scale_factor: float = 1.0,
 ) -> np.ndarray:
-    """Transform colors using power scaling to emphasize high significance sums more. Black colors are replaced with
+    """
+    Transform colors using power scaling to emphasize high significance sums more. Black colors are replaced with
     very dark grey to avoid issues with color scaling (rgb(0.1, 0.1, 0.1)).
 
     Args:
@@ -349,7 +356,8 @@ def to_rgba(
     alpha: Union[float, None] = None,
     num_repeats: Union[int, None] = None,
 ) -> np.ndarray:
-    """Convert color(s) to RGBA format, applying alpha and repeating as needed.
+    """
+    Convert color(s) to RGBA format, applying alpha and repeating as needed.
 
     Args:
         color (str, List, Tuple, np.ndarray, None): The color(s) to convert. Can be a string (e.g., 'red'), a list or tuple of RGB/RGBA values,

risk/{network/plotter/utils/layout.py → _network/_plotter/_utils/_layout.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/utils/layout
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_utils/_layout
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple
@@ -12,7 +12,8 @@ import numpy as np
 def calculate_bounding_box(
     node_coordinates: np.ndarray, radius_margin: float = 1.05
 ) -> Tuple[Tuple, float]:
-    """Calculate the bounding box of the network based on node coordinates.
+    """
+    Calculate the bounding box of the network based on node coordinates.
 
     Args:
         node_coordinates (np.ndarray): Array of node coordinates (x, y).
@@ -37,7 +38,8 @@ def refine_center_iteratively(
     max_iterations: int = 10,
     tolerance: float = 1e-2,
 ) -> Tuple[np.ndarray, float]:
-    """Refine the center of the graph iteratively to minimize skew in node distribution.
+    """
+    Refine the center of the graph iteratively to minimize skew in node distribution.
 
     Args:
         node_coordinates (np.ndarray): Array of node coordinates (x, y).
@@ -72,7 +74,8 @@ def refine_center_iteratively(
 def calculate_centroids(
     network: nx.Graph, domain_id_to_node_ids_map: Dict[int, Any]
 ) -> List[Tuple[float, float]]:
-    """Calculate the centroid for each domain based on node x and y coordinates in the network.
+    """
+    Calculate the centroid for each domain based on node x and y coordinates in the network.
 
     Args:
         network (nx.Graph): The graph representing the network.

risk/risk.py

@@ -3,16 +3,15 @@ risk/risk
 ~~~~~~~~~
 """
 
-from risk.annotation.io import AnnotationIO
-from risk.log import params, set_global_verbosity
-from risk.neighborhoods.api import NeighborhoodsAPI
-from risk.network.graph.api import GraphAPI
-from risk.network.io import NetworkIO
-from risk.network.plotter.api import PlotterAPI
+from ._annotation import AnnotationIO
+from ._log import params, set_global_verbosity
+from ._neighborhoods import NeighborhoodsAPI
+from ._network import GraphAPI, NetworkIO, PlotterAPI
 
 
 class RISK(NetworkIO, AnnotationIO, NeighborhoodsAPI, GraphAPI, PlotterAPI):
-    """RISK: A class for network analysis and visualization.
+    """
+    RISK: A class for network analysis and visualization.
 
     The RISK class integrates functionalities for loading networks, processing annotations,
     performing network-based statistical analysis to quantify neighborhood relationships,
@@ -20,7 +19,8 @@ class RISK(NetworkIO, AnnotationIO, NeighborhoodsAPI, GraphAPI, PlotterAPI):
     """
 
     def __init__(self, verbose: bool = True):
-        """Initialize the RISK class with configuration settings.
+        """
+        Initialize the RISK class with configuration settings.
 
         Args:
             verbose (bool): If False, suppresses all log messages to the console. Defaults to True.

{risk_network-0.0.13b4.dist-info → risk_network-0.0.13b5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.13b4
+Version: 0.0.13b5
 Summary: A Python package for scalable network analysis and high-quality visualization.
 Author-email: Ira Horecka <ira89@icloud.com>
 License: GPL-3.0-or-later

risk_network-0.0.13b5.dist-info/RECORD

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+risk/_network/_plotter/_api.py,sha256=MHZIMTlul2u-Ve5m9r-eUljI2oC3IRklNn7AVlfmzGs,1773
+risk/_network/_plotter/_canvas.py,sha256=H7rPz4Gv7ED3bDHMif4cf2usdU4ifmxzXeug5A_no68,13599
+risk/_network/_plotter/_contour.py,sha256=E3ILjlv-VBSbK3ClwObB84TvP1D48_B47ODXwtApjIE,15557
+risk/_network/_plotter/_labels.py,sha256=8JXzEOIBQefwr1ngF-2ZYCnYLZXs2Erz-R1c28NnsL0,46915
+risk/_network/_plotter/_network.py,sha256=W9eUUER9_qi1ubGaUfMp12gxAANZP-JNFKcG27I1nAk,14198
+risk/_network/_plotter/_plotter.py,sha256=F2hw-spUdsXjvuG36o0YFR3Pnd-CZOHYUq4vW0Qxzlk,6011
+risk/_network/_plotter/_utils/__init__.py,sha256=JXgjKiBWvXx0X2IeFnrOh5YZQGQoELbhJZ0Zh2mFEOo,211
+risk/_network/_plotter/_utils/_colors.py,sha256=JCliSvz8_-TsjilaRHSEsqdXFBUYlzhXKOSRGdCm9Kw,19177
+risk/_network/_plotter/_utils/_layout.py,sha256=GyGLc2U1WWUVL1Te9uPi_CLqlW_E4TImXRAL5TeA5D8,3633
+risk_network-0.0.13b5.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.13b5.dist-info/METADATA,sha256=dkYs8JCdMr945DZ-7bJ95MX0zuxfbkw1VpOhuLtCE_U,6853
+risk_network-0.0.13b5.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+risk_network-0.0.13b5.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.13b5.dist-info/RECORD,,

{risk_network-0.0.13b4.dist-info → risk_network-0.0.13b5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.3.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

risk/annotation/__init__.py

@@ -1,10 +0,0 @@
-"""
-risk/annotation
-~~~~~~~~~~~~~~~
-"""
-
-from risk.annotation.annotation import (
-    define_top_annotation,
-    get_weighted_description,
-)
-from risk.annotation.io import AnnotationIO

risk/log/__init__.py

@@ -1,11 +0,0 @@
-"""
-risk/log
-~~~~~~~~
-"""
-
-from risk.log.console import log_header, logger, set_global_verbosity
-from risk.log.parameters import Params
-
-# Initialize the global parameters logger
-params = Params()
-params.initialize()

risk/neighborhoods/__init__.py

@@ -1,7 +0,0 @@
-"""
-risk/neighborhoods
-~~~~~~~~~~~~~~~~~~
-"""
-
-from risk.neighborhoods.domains import define_domains, trim_domains
-from risk.neighborhoods.neighborhoods import process_neighborhoods

risk/neighborhoods/stats/__init__.py

@@ -1,13 +0,0 @@
-"""
-risk/neighborhoods/stats
-~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from risk.neighborhoods.stats.permutation import compute_permutation_test
-from risk.neighborhoods.stats.tests import (
-    compute_binom_test,
-    compute_chi2_test,
-    compute_hypergeom_test,
-    compute_poisson_test,
-    compute_zscore_test,
-)

risk/neighborhoods/stats/permutation/__init__.py

@@ -1,6 +0,0 @@
-"""
-risk/neighborhoods/stats/permutation
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from risk.neighborhoods.stats.permutation.permutation import compute_permutation_test

risk/network/__init__.py

@@ -1,4 +0,0 @@
-"""
-risk/network
-~~~~~~~~~~~~
-"""

risk/network/graph/__init__.py

@@ -1,4 +0,0 @@
-"""
-risk/network/graph
-~~~~~~~~~~~~~~~~~~
-"""

risk/network/plotter/__init__.py

@@ -1,4 +0,0 @@
-"""
-risk/network/plotter
-~~~~~~~~~~~~~~~~~~~~
-"""