risk-network 0.0.9b45__tar.gz → 0.0.9b46__tar.gz

{risk_network-0.0.9b45 → risk_network-0.0.9b46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b45
+Version: 0.0.9b46
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b45 → risk_network-0.0.9b46}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.45"
+__version__ = "0.0.9-beta.46"

{risk_network-0.0.9b45 → risk_network-0.0.9b46}/risk/neighborhoods/domains.py

@@ -3,12 +3,12 @@ risk/neighborhoods/domains
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
-from contextlib import suppress
 from itertools import product
 from typing import Tuple, Union
 
 import numpy as np
 import pandas as pd
+from numpy.linalg import LinAlgError
 from scipy.cluster.hierarchy import linkage, fcluster
 from sklearn.metrics import silhouette_score
 from tqdm import tqdm
@@ -73,7 +73,7 @@ def define_domains(
         domains = fcluster(Z, max_d_optimal, criterion=linkage_criterion)
         top_annotations["domain"] = 0
         top_annotations.loc[top_annotations["significant_annotations"], "domain"] = domains
-    except ValueError:
+    except (ValueError, LinAlgError):
         # If a ValueError is encountered, handle it by assigning unique domains
         n_rows = len(top_annotations)
         if linkage_criterion == "off":
@@ -247,16 +247,17 @@ def _optimize_silhouette_across_linkage_and_metrics(
         bar_format="{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}]",
     ):
         # Some linkage methods and metrics may not work with certain data
-        with suppress(ValueError):
+        try:
             Z = linkage(m, method=method, metric=metric)
+        except (ValueError, LinAlgError):
+            # If linkage fails, set a default threshold (a float) and a very poor score
+            current_threshold = 0.0
+            score = -float("inf")
+        else:
             # Only optimize silhouette score if the threshold is "auto"
             if linkage_threshold == "auto":
                 threshold, score = _find_best_silhouette_score(Z, m, metric, linkage_criterion)
-                if score > best_overall_score:
-                    best_overall_score = score
-                    best_overall_threshold = threshold
-                    best_overall_method = method
-                    best_overall_metric = metric
+                current_threshold = threshold
             else:
                 # Use the provided threshold without optimization
                 score = silhouette_score(
@@ -264,11 +265,20 @@ def _optimize_silhouette_across_linkage_and_metrics(
                     fcluster(Z, linkage_threshold * np.max(Z[:, 2]), criterion=linkage_criterion),
                     metric=metric,
                 )
-                if score > best_overall_score:
-                    best_overall_score = score
-                    best_overall_threshold = linkage_threshold
-                    best_overall_method = method
-                    best_overall_metric = metric
+                current_threshold = linkage_threshold
+
+        if score > best_overall_score:
+            best_overall_score = score
+            best_overall_threshold = float(current_threshold)  # Ensure it's a float
+            best_overall_method = method
+            best_overall_metric = metric
+
+    # Ensure that we always return a valid tuple:
+    if best_overall_score == -np.inf:
+        # No valid linkage was found; return default values.
+        best_overall_threshold = float(linkage_threshold) if linkage_threshold != "auto" else 0.0
+        best_overall_method = linkage_method
+        best_overall_metric = linkage_metric
 
     return best_overall_method, best_overall_metric, best_overall_threshold
 

{risk_network-0.0.9b45 → risk_network-0.0.9b46}/risk/network/geometry.py

@@ -12,7 +12,7 @@ def assign_edge_lengths(
     compute_sphere: bool = True,
     surface_depth: float = 0.0,
 ) -> nx.Graph:
-    """Assign edge lengths in the graph, optionally mapping nodes to a sphere and including edge weights.
+    """Assign edge lengths in the graph, optionally mapping nodes to a sphere.
 
     Args:
         G (nx.Graph): The input graph.
@@ -33,9 +33,8 @@ def assign_edge_lengths(
             return np.arccos(np.clip(dot_products, -1.0, 1.0))
         return np.linalg.norm(u_coords - v_coords, axis=1)
 
-    # Normalize graph coordinates and weights
+    # Normalize graph coordinates
     _normalize_graph_coordinates(G)
-    _normalize_weights(G)
 
     # Map nodes to sphere and adjust depth if required
     if compute_sphere:
@@ -110,22 +109,6 @@ def _normalize_graph_coordinates(G: nx.Graph) -> None:
         G.nodes[node]["x"], G.nodes[node]["y"] = normalized_xy[i]
 
 
-def _normalize_weights(G: nx.Graph) -> None:
-    """Normalize the weights of the edges in the graph.
-
-    Args:
-        G (nx.Graph): The input graph with weighted edges.
-    """
-    # "weight" is present for all edges - weights are 1.0 if weight was not specified by the user
-    weights = [data["weight"] for _, _, data in G.edges(data=True)]
-    if weights:  # Ensure there are weighted edges
-        min_weight = min(weights)
-        max_weight = max(weights)
-        range_weight = max_weight - min_weight if max_weight > min_weight else 1
-        for _, _, data in G.edges(data=True):
-            data["normalized_weight"] = (data["weight"] - min_weight) / range_weight
-
-
 def _create_depth(G: nx.Graph, surface_depth: float = 0.0) -> nx.Graph:
     """Adjust the 'z' attribute of each node based on the subcluster strengths and normalized surface depth.
 

{risk_network-0.0.9b45 → risk_network-0.0.9b46}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b45
+Version: 0.0.9b46
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b45 → risk_network-0.0.9b46}/setup.py

@@ -10,8 +10,8 @@ from setuptools import setup, find_packages
 import numpy
 
 
-# Function to extract version from __init__.py
 def find_version():
+    """Function to find the version string in the __init__.py file."""
     with open("risk/__init__.py", "r", encoding="utf-8") as f:
         version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", f.read(), re.M)
         if version_match: