risk-network 0.0.7b7__py3-none-any.whl → 0.0.7b9__py3-none-any.whl

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.9"

risk/annotations/annotations.py

@@ -177,19 +177,18 @@ def get_description(words_column: pd.Series) -> str:
     all_words = words_column.str.cat(sep=" ")
     tokens = word_tokenize(all_words)
 
-    # Check if all tokens are numeric strings or contain a mixture of strings and numbers
+    # Separate numeric tokens
     numeric_tokens = [token for token in tokens if token.replace(".", "", 1).isdigit()]
-    non_numeric_tokens = [token for token in tokens if not token.replace(".", "", 1).isdigit()]
     # If there's only one unique numeric value, return it directly as a string
     unique_numeric_values = set(numeric_tokens)
     if len(unique_numeric_values) == 1:
         return f"{list(unique_numeric_values)[0]}"
 
-    # Allow the inclusion of both alphabetic and numeric tokens if mixture is detected
+    # Ensure that all values in 'words' are strings and include both alphabetic and numeric tokens
     words = [
-        (
+        str(
             word.lower() if word.istitle() else word
-        )  # Lowercase all words except proper nouns (e.g., RNA, mRNA)
+        )  # Convert to string and lowercase all words except proper nouns (e.g., RNA, mRNA)
         for word in tokens
         if word.isalpha()
         or word.replace(".", "", 1).isdigit()  # Keep alphabetic words and numeric strings
@@ -263,11 +262,11 @@ def _generate_coherent_description(words: List[str]) -> str:
     Returns:
         str: A coherent description formed by arranging the words in a logical sequence.
     """
-    # If there are no words or the input is invalid, raise an error
-    if not words or not isinstance(words, list) or not all(isinstance(word, str) for word in words):
-        raise ValueError("Input must be a list of strings.")
+    # If there are no words, return a keyword indicating no data is available
+    if not words:
+        return "N/A"
 
-    # If there's only one unique word, return it directly (even if it's a number-like string)
+    # If there's only one unique word, return it directly
     unique_words = set(words)
     if len(unique_words) == 1:
         return list(unique_words)[0]

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/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":

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/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.dist-info → risk_network-0.0.7b9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b7
+Version: 0.0.7b9
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b7.dist-info → risk_network-0.0.7b9.dist-info}/RECORD

@@ -1,30 +1,30 @@
-risk/__init__.py,sha256=0dNrjhRgqzBRG5Rqy_GKy_8ETWm10xSCYvaOm6fdI0Q,112
+risk/__init__.py,sha256=Pj1ulqySghRcgi9kiMTvpjr7Mw5dg4vtjEdAkyImDFU,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=6666BzdMTgOaQl98ZKiJ19c6XBot26eTJ0iIlk-ZCZQ,20515
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
-risk/annotations/annotations.py,sha256=k9LGTL2uqdYvI5F3jU3UKz-O855B-DoazGPMzSn-XUc,11673
+risk/annotations/annotations.py,sha256=3FFyJE9Gp5oRN72_8iVAUnecsmTtx2G2fp5AlCY1oUk,11405
 risk/annotations/io.py,sha256=lo7NKqOVkeeBp58JBxWJHtA0xjL5Yoxqe9Ox0daKlZk,9457
 risk/log/__init__.py,sha256=xuLImfxFlKpnVhzi_gDYlr2_c9cLkrw2c_3iEsXb1as,107
 risk/log/console.py,sha256=im9DRExwf6wHlcn9fewoDcKIpo3vPcorZIaNAl-0csY,355
 risk/log/params.py,sha256=Rfdg5UcGCrG80m6V79FyORERWUqIzHFO7tGiY4zAImM,6347
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
 risk/neighborhoods/community.py,sha256=stYYBXeZlGLMV-k8ckQeIqThT6v9y-S3hETobAo9590,6817
-risk/neighborhoods/domains.py,sha256=bxJUxqFTynzX0mf3E8-AA4_Rfccje1reeVVhfzb1-pE,10672
-risk/neighborhoods/neighborhoods.py,sha256=r-JeUb6dTjzMtnaMDvJy6MI3mTl-yUzILcdcjtOhFdM,18218
+risk/neighborhoods/domains.py,sha256=vTCKtRE0oFcY862squrF7_cqCjnckiC9Sl0Qh2FM81k,10665
+risk/neighborhoods/neighborhoods.py,sha256=5WVXCZ0f-MzUfDITdNlL0NgDS3DBamdc_ZVPA-p9j7U,18218
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
 risk/network/graph.py,sha256=_LEoom4EEowGALuJKSXcev9RAAHu2FqIeq3u7mkifW0,16479
 risk/network/io.py,sha256=gG50kOknO-D3HkW1HsbHMkTMvjUtn3l4W4Jwd-rXNr8,21202
 risk/network/plot.py,sha256=3OucCoKJwx9M9H4lqAvcQdM9YiCSyIxz21jyqDbpffc,62286
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
-risk/stats/hypergeom.py,sha256=DcGYjmfcgt1qshNZPJt5IHGIHtxw9tWRS1r6QJ6V3dI,2378
-risk/stats/poisson.py,sha256=CnLk65CHViR4YhAaN3ix37iyLm_YQYGo851bSnGyyxY,1950
+risk/stats/hypergeom.py,sha256=o6Qnj31gCAKxr2uQirXrbv7XvdDJGEq69MFW-ubx_hA,2272
+risk/stats/poisson.py,sha256=8x9hB4DCukq4gNIlIKO-c_jYG1-BTwTX53oLauFyfj8,1793
 risk/stats/stats.py,sha256=kvShov-94W6ffgDUTb522vB9hDJQSyTsYif_UIaFfSM,7059
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=kmSZ7bQ-AD0TFiQDgIwfxTeqHa4pjp7fIcOzAqyhUNY,9714
 risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.7b7.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.7b7.dist-info/METADATA,sha256=LDTOo8S-g09TbNgixGR4nCBkyaHW_usy0zE8kNsqTRg,43142
-risk_network-0.0.7b7.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-risk_network-0.0.7b7.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.7b7.dist-info/RECORD,,
+risk_network-0.0.7b9.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.7b9.dist-info/METADATA,sha256=SMrU7EhdEUAHteWWFDPCCQ5PxRjcAOoNfGlOKMpp-w4,43142
+risk_network-0.0.7b9.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+risk_network-0.0.7b9.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.7b9.dist-info/RECORD,,