risk-network 0.0.7b7__tar.gz → 0.0.7b8__tar.gz

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b7
+Version: 0.0.7b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.7-beta.7"
+__version__ = "0.0.7-beta.8"

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/risk/neighborhoods/domains.py

@@ -4,6 +4,7 @@ risk/neighborhoods/domains
 """
 
 from contextlib import suppress
+from itertools import product
 from tqdm import tqdm
 from typing import Tuple
 
@@ -165,21 +166,20 @@ def _optimize_silhouette_across_linkage_and_metrics(
     total_combinations = len(linkage_methods) * len(linkage_metrics)
 
     # Evaluating optimal linkage method and metric
-    for method in tqdm(
-        linkage_methods,
+    for method, metric in tqdm(
+        product(linkage_methods, linkage_metrics),
         desc="Evaluating optimal linkage method and metric",
         total=total_combinations,
         bar_format="{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}]",
     ):
-        for metric in linkage_metrics:
-            with suppress(Exception):
-                Z = linkage(m, method=method, metric=metric)
-                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
+        with suppress(Exception):
+            Z = linkage(m, method=method, metric=metric)
+            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
 
     return best_overall_method, best_overall_metric, best_overall_threshold
 

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/risk/stats/hypergeom.py

@@ -22,9 +22,7 @@ def compute_hypergeom_test(
     Returns:
         dict: Dictionary containing depletion and enrichment p-values.
     """
-    # Ensure both matrices are binary (presence/absence)
-    neighborhoods = (neighborhoods > 0).astype(int)
-    annotations = (annotations > 0).astype(int)
+    # Get the total number of nodes in the network
     total_node_count = neighborhoods.shape[0]
 
     if null_distribution == "network":

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/risk/stats/poisson.py

@@ -22,9 +22,6 @@ def compute_poisson_test(
     Returns:
         dict: Dictionary containing depletion and enrichment p-values.
     """
-    # Ensure both matrices are binary (presence/absence)
-    neighborhoods = (neighborhoods > 0).astype(int)
-    annotations = (annotations > 0).astype(int)
     # Matrix multiplication to get the number of annotated nodes in each neighborhood
     annotated_in_neighborhood = neighborhoods @ annotations
 

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b7
+Version: 0.0.7b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b7 → risk_network-0.0.7b8}/risk/neighborhoods/neighborhoods.py

@@ -54,10 +54,10 @@ def get_network_neighborhoods(
         network, edge_length_percentile=edge_length_threshold
     )
 
-    if distance_metric == "greedy_modularity":
-        return calculate_greedy_modularity_neighborhoods(network)
     if distance_metric == "louvain":
         return calculate_louvain_neighborhoods(network, louvain_resolution, random_seed=random_seed)
+    if distance_metric == "greedy_modularity":
+        return calculate_greedy_modularity_neighborhoods(network)
     if distance_metric == "label_propagation":
         return calculate_label_propagation_neighborhoods(network)
     if distance_metric == "markov_clustering":