risk-network 0.0.9b15__py3-none-any.whl → 0.0.9b17__py3-none-any.whl

risk/__init__.py

@@ -2,9 +2,9 @@
 risk
 ~~~~
 
-RISK: RISK Infers Spatial Kinships
+RISK: Regional Inference of Significant Kinships
 """
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.15"
+__version__ = "0.0.9-beta.17"

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/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/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.dist-info → risk_network-0.0.9b17.dist-info}/METADATA

@@ -1,10 +1,10 @@
-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>
-License: GNU GENERAL PUBLIC LICENSE
+License:                     GNU GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
         
          Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
@@ -696,7 +696,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ipywidgets
 Requires-Dist: leidenalg
-Requires-Dist: markov-clustering
+Requires-Dist: markov_clustering
 Requires-Dist: matplotlib
 Requires-Dist: networkx
 Requires-Dist: nltk==3.8.1
@@ -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.dist-info → risk_network-0.0.9b17.dist-info}/RECORD

@@ -1,6 +1,6 @@
-risk/__init__.py,sha256=ETGu8S9_cXRpS9mAcoD97c7JUkhQcr100I7We_cRAls,113
+risk/__init__.py,sha256=95ug0762a0OMBkPuFt_fuQuF8BgPXRfF_Dl3UCP6jMw,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=7OvKwKVEvTdnQk4bYYz_pEtNCw2xYOfDoOC-ZrxrPjA,23592
+risk/risk.py,sha256=nodTixy31O3VK7ld-g74Fb9YEiyvKs_Vbor2lE2ADJ8,23632
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
 risk/annotations/annotations.py,sha256=WVT9wzTm8lTpMw_3SnbyljWR77yExo0rb1zVgJza8nw,14284
 risk/annotations/io.py,sha256=tk1dAsxIwW5oLxB294ppiuZd4__Y5pj8se8KhitRSNA,10554
@@ -19,7 +19,7 @@ risk/network/graph/network.py,sha256=JzYbrgJLiNWFyPIR6_qNSjMtmXmfzRv2FwWSdyg8HjY
 risk/network/graph/summary.py,sha256=7w5gNYNspv02SscDAfHxdx-D1CWKmelSonyBnB9hbrE,9737
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
 risk/network/plot/canvas.py,sha256=W8dFv4XYTzCWXBchgsc0esOQRn4usM4LkwNGPSDMobE,13357
-risk/network/plot/contour.py,sha256=VONX9l6owrZvWtR0mWQ6z2GSd1YXIv5wV_sf5ROQLT4,15581
+risk/network/plot/contour.py,sha256=zM2oRbiGbKHi9fWL7QNcwnTRkxCuQYEwH2mm6TaN_hw,15499
 risk/network/plot/labels.py,sha256=aU_ClDGVPHyQ3H5E_ygx8hsMhrpJB0i9Cn65PlLmw7s,45679
 risk/network/plot/network.py,sha256=0j7pAZgt9PBfFCnOz4QwXnYWTlnLjTrtMm-50I_1G8o,14028
 risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
@@ -30,10 +30,10 @@ risk/stats/hypergeom.py,sha256=oc39f02ViB1vQ-uaDrxG_tzAT6dxQBRjc88EK2EGn78,2282
 risk/stats/poisson.py,sha256=polLgwS08MTCNzupYdmMUoEUYrJOjAbcYtYwjlfeE5Y,1803
 risk/stats/stats.py,sha256=z8NrhiVj4BzJ250bVLfytpmfC7RzYu7mBuIZD_l0aCA,7222
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
-risk/stats/permutation/permutation.py,sha256=meBNSrbRa9P8WJ54n485l0H7VQJlMSfHqdN4aCKYCtQ,10105
+risk/stats/permutation/permutation.py,sha256=jfo7J7bjXTHH-k6_WuZ_5eB31JVynlI6SYMC_7icYyM,10320
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b15.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b15.dist-info/METADATA,sha256=-vbz9K7rwGcks1hRc26hGWGct4nd2JvJ9su-SuJnAVw,47552
-risk_network-0.0.9b15.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b15.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b15.dist-info/RECORD,,
+risk_network-0.0.9b17.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b17.dist-info/METADATA,sha256=7Jh5RwTtOR7nnQIoLnT6wCamrgaAJxAZs6Zzncs0H9g,47627
+risk_network-0.0.9b17.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b17.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b17.dist-info/RECORD,,

{risk_network-0.0.9b15.dist-info → risk_network-0.0.9b17.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any