risk-network 0.0.9b15__tar.gz → 0.0.9b17__tar.gz

{risk_network-0.0.9b15 → risk_network-0.0.9b17}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b15
+Version: 0.0.9b17
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -710,6 +710,8 @@ Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
+Dynamic: author
+Dynamic: requires-python
 
 # RISK Network
 
@@ -726,7 +728,7 @@ Requires-Dist: tqdm
 ![Downloads](https://img.shields.io/pypi/dm/risk-network)
 ![Platforms](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey)
 
-**RISK (RISK Infers Spatial Kinships)** is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
+**RISK** (Regional Inference of Significant Kinships) is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
 
 ## Documentation and Tutorial
 

{risk_network-0.0.9b15 → risk_network-0.0.9b17}/README.md

@@ -13,7 +13,7 @@
 ![Downloads](https://img.shields.io/pypi/dm/risk-network)
 ![Platforms](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey)
 
-**RISK (RISK Infers Spatial Kinships)** is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
+**RISK** (Regional Inference of Significant Kinships) is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
 
 ## Documentation and Tutorial
 

risk_network-0.0.9b17/risk/__init__.py

@@ -0,0 +1,10 @@
+"""
+risk
+~~~~
+
+RISK: Regional Inference of Significant Kinships
+"""
+
+from risk.risk import RISK
+
+__version__ = "0.0.9-beta.17"

{risk_network-0.0.9b15 → risk_network-0.0.9b17}/risk/network/plot/contour.py

@@ -242,7 +242,7 @@ class Contour:
             logger.error("Contour levels must be strictly increasing. Skipping contour plot.")
             return None
 
-        # Set the contour color and linestyle
+        # Set the contour color, fill, and linestyle
         contour_colors = [color for _ in range(levels - 1)]
         # Plot the filled contours using fill_alpha for transparency
         if fill_alpha and fill_alpha > 0:
@@ -258,21 +258,19 @@ class Contour:
                 alpha=fill_alpha,
             )
 
-        # Plot the contour lines with the specified RGBA alpha for transparency
-        c = ax.contour(
+        # Plot the base contour line with the specified RGBA alpha for transparency
+        base_contour_color = [color]
+        base_contour_level = [contour_levels[0]]
+        ax.contour(
             x,
             y,
             z,
-            levels=contour_levels,
-            colors=contour_colors,
+            levels=base_contour_level,
+            colors=base_contour_color,
             linestyles=linestyle,
             linewidths=linewidth,
         )
 
-        # Set linewidth for the contour lines to 0 for levels other than the base level
-        for i in range(1, len(contour_levels)):
-            c.collections[i].set_linewidth(0)
-
     def get_annotated_contour_colors(
         self,
         cmap: str = "gist_rainbow",

{risk_network-0.0.9b15 → risk_network-0.0.9b17}/risk/risk.py

@@ -63,7 +63,7 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
@@ -127,7 +127,7 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
@@ -194,7 +194,7 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
@@ -430,7 +430,7 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (pd.DataFrame): The matrix of annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.

{risk_network-0.0.9b15 → risk_network-0.0.9b17}/risk/stats/permutation/permutation.py

@@ -192,7 +192,9 @@ def _permutation_process_subset(
     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 when more than one worker is used.
+    # Limit the number of threads used by NumPy's BLAS implementation to 1 when more than one worker is used
+    # NOTE: This does not work for Mac M chips due to a bug in the threadpoolctl package
+    # This is currently a known issue and is being addressed by the maintainers [https://github.com/joblib/threadpoolctl/issues/135]
     limits = None if max_workers == 1 else 1
     with threadpool_limits(limits=limits, user_api="blas"):
         # Initialize a local counter for batched progress updates

{risk_network-0.0.9b15 → risk_network-0.0.9b17}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b15
+Version: 0.0.9b17
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -710,6 +710,8 @@ Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
+Dynamic: author
+Dynamic: requires-python
 
 # RISK Network
 
@@ -726,7 +728,7 @@ Requires-Dist: tqdm
 ![Downloads](https://img.shields.io/pypi/dm/risk-network)
 ![Platforms](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey)
 
-**RISK (RISK Infers Spatial Kinships)** is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
+**RISK** (Regional Inference of Significant Kinships) is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
 
 ## Documentation and Tutorial
 

risk_network-0.0.9b15/risk/__init__.py

@@ -1,10 +0,0 @@
-"""
-risk
-~~~~
-
-RISK: RISK Infers Spatial Kinships
-"""
-
-from risk.risk import RISK
-
-__version__ = "0.0.9-beta.15"