risk-network 0.0.7b6__tar.gz → 0.0.7b8__tar.gz

{risk_network-0.0.7b6 → risk_network-0.0.7b8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b6
+Version: 0.0.7b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b6 → 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.6"
+__version__ = "0.0.7-beta.8"

{risk_network-0.0.7b6 → 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-0.0.7b6 → 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-0.0.7b6 → risk_network-0.0.7b8}/risk/stats/permutation/permutation.py

@@ -4,6 +4,7 @@ risk/stats/permutation/permutation
 """
 
 from multiprocessing import get_context, Manager
+from multiprocessing.managers import ValueProxy
 from tqdm import tqdm
 from typing import Any, Callable, Dict
 
@@ -111,7 +112,6 @@ def _run_permutation_test(
     # Initialize count matrices for depletion and enrichment
     counts_depletion = np.zeros(observed_neighborhood_scores.shape)
     counts_enrichment = np.zeros(observed_neighborhood_scores.shape)
-
     # Determine the number of permutations to run in each worker process
     subset_size = num_permutations // max_workers
     remainder = num_permutations % max_workers
@@ -121,7 +121,6 @@ def _run_permutation_test(
     manager = Manager()
     progress_counter = manager.Value("i", 0)
     total_progress = num_permutations
-
     # Execute the permutation test using multiprocessing
     with ctx.Pool(max_workers) as pool:
         with tqdm(total=total_progress, desc="Total progress", position=0) as progress:
@@ -135,7 +134,8 @@ def _run_permutation_test(
                     neighborhood_score_func,
                     subset_size + (1 if i < remainder else 0),
                     progress_counter,
-                    rng,  # Pass the RNG to each process
+                    max_workers,
+                    rng,  # Pass the random number generator to each worker
                 )
                 for i in range(max_workers)
             ]
@@ -152,10 +152,10 @@ def _run_permutation_test(
             # Ensure progress bar reaches 100%
             progress.update(total_progress - progress.n)
 
-            # Accumulate results from each worker
-            for local_counts_depletion, local_counts_enrichment in results.get():
-                counts_depletion = np.add(counts_depletion, local_counts_depletion)
-                counts_enrichment = np.add(counts_enrichment, local_counts_enrichment)
+    # Accumulate results from each worker
+    for local_counts_depletion, local_counts_enrichment in results.get():
+        counts_depletion = np.add(counts_depletion, local_counts_depletion)
+        counts_enrichment = np.add(counts_enrichment, local_counts_enrichment)
 
     return counts_depletion, counts_enrichment
 
@@ -167,7 +167,8 @@ def _permutation_process_subset(
     observed_neighborhood_scores: np.ndarray,
     neighborhood_score_func: Callable,
     subset_size: int,
-    progress_counter,
+    progress_counter: ValueProxy,
+    max_workers: int,
     rng: np.random.Generator,
 ) -> tuple:
     """Process a subset of permutations for the permutation test.
@@ -179,7 +180,8 @@ def _permutation_process_subset(
         observed_neighborhood_scores (np.ndarray): Observed neighborhood scores.
         neighborhood_score_func (Callable): Function to calculate neighborhood scores.
         subset_size (int): Number of permutations to run in this subset.
-        progress_counter: Shared counter for tracking progress.
+        progress_counter (multiprocessing.managers.ValueProxy): Shared counter for tracking progress.
+        max_workers (int): Number of workers for multiprocessing.
         rng (np.random.Generator): Random number generator object.
 
     Returns:
@@ -188,10 +190,11 @@ def _permutation_process_subset(
     # Initialize local count matrices for this worker
     local_counts_depletion = np.zeros(observed_neighborhood_scores.shape)
     local_counts_enrichment = np.zeros(observed_neighborhood_scores.shape)
-    # NOTE: Limit the number of threads used by NumPy's BLAS implementation to 1.
-    # This can help prevent oversubscription of CPU resources during multiprocessing,
-    # ensuring that each process doesn't use more than one CPU core.
-    with threadpool_limits(limits=1, user_api="blas"):
+    # NOTE: Limit the number of threads used by NumPy's BLAS implementation to 1 when more than one worker is used.
+    # This can help prevent oversubscription of CPU resources during multiprocessing, ensuring that each process
+    # doesn't use more than one CPU core.
+    limits = None if max_workers == 1 else 1
+    with threadpool_limits(limits=limits, user_api="blas"):
         for _ in range(subset_size):
             # Permute the annotation matrix using the RNG
             annotation_matrix_permut = annotation_matrix[rng.permutation(idxs)]
@@ -209,7 +212,6 @@ def _permutation_process_subset(
                 local_counts_enrichment,
                 permuted_neighborhood_scores >= observed_neighborhood_scores,
             )
-
             # Update the shared progress counter
             progress_counter.value += 1
 

{risk_network-0.0.7b6 → 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-0.0.7b6 → risk_network-0.0.7b8}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b6
+Version: 0.0.7b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b6 → 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":