risk-network 0.0.12b5__py3-none-any.whl → 0.0.13b0__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.12-beta.5"
+__version__ = "0.0.13-beta.0"

risk/annotation/io.py

@@ -39,7 +39,7 @@ class AnnotationIO:
         params.log_annotation(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_annotation(filetype, filepath=filepath)
 
         # Load the JSON file into a dictionary
         with open(filepath, "r", encoding="utf-8") as file:
@@ -78,7 +78,7 @@ class AnnotationIO:
         params.log_annotation(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_annotation(filetype, filepath=filepath)
 
         # Load the specified sheet from the Excel file
         annotation = pd.read_excel(filepath, sheet_name=sheet_name)
@@ -120,7 +120,7 @@ class AnnotationIO:
         params.log_annotation(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_annotation(filetype, filepath=filepath)
 
         # Load the CSV file into a dictionary
         annotation_input = self._load_matrix_file(
@@ -158,7 +158,7 @@ class AnnotationIO:
         params.log_annotation(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_annotation(filetype, filepath=filepath)
 
         # Load the TSV file into a dictionary
         annotation_input = self._load_matrix_file(
@@ -193,7 +193,7 @@ class AnnotationIO:
         filetype = "Dictionary"
         # Log the loading of the annotation from the dictionary
         params.log_annotation(filepath="In-memory dictionary", filetype=filetype)
-        self._log_loading(filetype, "In-memory dictionary")
+        self._log_loading_annotation(filetype, "In-memory dictionary")
 
         # Load the annotation as a dictionary from the provided dictionary
         return load_annotation(network, content, min_nodes_per_term)
@@ -228,8 +228,8 @@ class AnnotationIO:
         label_node_dict = annotation.set_index(label_colname)[nodes_colname].to_dict()
         return label_node_dict
 
-    def _log_loading(self, filetype: str, filepath: str = "") -> None:
-        """Log information about the network file being loaded.
+    def _log_loading_annotation(self, filetype: str, filepath: str = "") -> None:
+        """Log the loading of annotation files.
 
         Args:
             filetype (str): The type of the file being loaded (e.g., 'Cytoscape').

risk/neighborhoods/neighborhoods.py

@@ -449,7 +449,7 @@ def _prune_neighbors(
     )
 
 
-def _get_euclidean_distance(node1: Any, node2: Any, network: nx.Graph) -> np.floating[Any]:
+def _get_euclidean_distance(node1: Any, node2: Any, network: nx.Graph) -> float:
     """Calculate the Euclidean distance between two nodes in the network.
 
     Args:
@@ -458,7 +458,7 @@ def _get_euclidean_distance(node1: Any, node2: Any, network: nx.Graph) -> np.flo
         network (nx.Graph): The network graph containing the nodes.
 
     Returns:
-        np.floating[Any]: The Euclidean distance between the two nodes.
+        float: The Euclidean distance between the two nodes.
     """
     pos1 = _get_node_position(network, node1)
     pos2 = _get_node_position(network, node2)

risk/network/io.py

@@ -85,7 +85,7 @@ class NetworkIO:
         filetype = "GPickle"
         # Log the loading of the GPickle file
         params.log_network(filetype=filetype, filepath=filepath)
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_network(filetype, filepath=filepath)
 
         with open(filepath, "rb") as f:
             G = pickle.load(f)
@@ -130,7 +130,7 @@ class NetworkIO:
         filetype = "NetworkX"
         # Log the loading of the NetworkX graph
         params.log_network(filetype=filetype)
-        self._log_loading(filetype)
+        self._log_loading_network(filetype)
 
         # Important: Make a copy of the network to avoid modifying the original
         network_copy = copy.deepcopy(network)
@@ -198,7 +198,7 @@ class NetworkIO:
         filetype = "Cytoscape"
         # Log the loading of the Cytoscape file
         params.log_network(filetype=filetype, filepath=str(filepath))
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_network(filetype, filepath=filepath)
 
         cys_files = []
         tmp_dir = ".tmp_cytoscape"
@@ -354,7 +354,7 @@ class NetworkIO:
         filetype = "Cytoscape JSON"
         # Log the loading of the Cytoscape JSON file
         params.log_network(filetype=filetype, filepath=str(filepath))
-        self._log_loading(filetype, filepath=filepath)
+        self._log_loading_network(filetype, filepath=filepath)
 
         # Load the Cytoscape JSON file
         with open(filepath, "r") as f:
@@ -672,12 +672,12 @@ class NetworkIO:
 
         return G
 
-    def _log_loading(
+    def _log_loading_network(
         self,
         filetype: str,
         filepath: str = "",
     ) -> None:
-        """Log the initialization details of the RISK class.
+        """Log the loading of the network with relevant parameters.
 
         Args:
             filetype (str): The type of the file being loaded (e.g., 'CSV', 'JSON').

{risk_network-0.0.12b5.dist-info → risk_network-0.0.13b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.12b5
+Version: 0.0.13b0
 Summary: A Python package for biological network analysis
 Author-email: Ira Horecka <ira89@icloud.com>
 License: GPL-3.0-or-later
@@ -88,9 +88,10 @@ This figure highlights RISK’s capability to detect both established and novel
 
 ## Citation
 
-If you use RISK in your research, please cite:
+If you use RISK in your research, please reference the following:
 
-**Horecka et al.**, "RISK: a next-generation tool for biological network annotation and visualization", **Bioinformatics**, 2025. DOI: [10.1234/zenodo.xxxxxxx](https://doi.org/10.1234/zenodo.xxxxxxx)
+**Horecka et al.**, *"RISK: a next-generation tool for biological network annotation and visualization"*, 2025.  
+DOI: [10.1234/zenodo.xxxxxxx](https://doi.org/10.1234/zenodo.xxxxxxx)
 
 ## Software Architecture and Implementation
 

{risk_network-0.0.12b5.dist-info → risk_network-0.0.13b0.dist-info}/RECORD

@@ -1,8 +1,8 @@
-risk/__init__.py,sha256=QfU0Xz8hpfewV61_Rd9RSxU0ezt6Gwd6i2eNpMLqipg,127
+risk/__init__.py,sha256=7SRIa1BqrKwhmaDeyiuVouldzK3W4LLNYLgF4sVfYUw,127
 risk/risk.py,sha256=Wjuxob5bI70Tpz9t71i05g94AQ3qXEMjfEcm5IV9HSY,1118
 risk/annotation/__init__.py,sha256=1EbGo41ClQb5ESTtitjOhrZhaLzzwr5aT-RYDX8w-h4,185
 risk/annotation/annotation.py,sha256=OE859FpVnp69hDi1cN_CQqeiG0SrJ2ZCuIdQKzY-gt0,14675
-risk/annotation/io.py,sha256=iffCXePQuMluytYQDg5tbu34g9ZsCUq1H4j-z-W25lE,10695
+risk/annotation/io.py,sha256=BF-hBSslHh6AlgL2FqVFBeH4swvVmdMYXJI0wu1W-gI,10745
 risk/annotation/nltk_setup.py,sha256=14B6L56_dwIgAOC9Rl4dNd4-b-aEngUCoJP9L9kEilU,3572
 risk/log/__init__.py,sha256=en-hKzuFtQWos4oZd8PxJ9u9Pe5bdihiqH9-qk_5ppw,217
 risk/log/console.py,sha256=PgjyEvyhYLUSHXPUKEqOmxsDsfrjPICIgqo_cAHq0N8,4575
@@ -11,14 +11,14 @@ risk/neighborhoods/__init__.py,sha256=CNS0VNbh_IdxldXjDkPqeTrxgY4hqi_Tc_MTADW_tz
 risk/neighborhoods/api.py,sha256=TXbjbHfQDi2eZeD9086BBsUjhDiJq2BNEYALiGs_rPc,23299
 risk/neighborhoods/community.py,sha256=0YdTh6wgMLiGMdtlaD7Vu_uxOVoZ9vDBjxbkglkrTV8,17808
 risk/neighborhoods/domains.py,sha256=9cWcGYGALcYruvAjWKztnEZlnYyT6DSoAPP6VsgA2wQ,14601
-risk/neighborhoods/neighborhoods.py,sha256=g08IFsMjsadkkfl9FI9oIrzlQ5KgWK_BMRN0VmCzDbs,21694
+risk/neighborhoods/neighborhoods.py,sha256=ykJu2d0Z6gRCOAMyBtpWpxXQ2Dei4nOv7w3XN0LpiX8,21672
 risk/neighborhoods/stats/__init__.py,sha256=1evLEAa7trCWj2DapCV4vW_f0zsyKHqTsn4--E_fDPg,306
 risk/neighborhoods/stats/tests.py,sha256=Z14H8G2qHzM5AOhKqp4YfCOL_wp3QwzUzfeGQJOqTTU,12060
 risk/neighborhoods/stats/permutation/__init__.py,sha256=V-uLSoi4SIPKjSRl7rhcDR4HJ4tquAn3QxNTXH9KzK8,169
 risk/neighborhoods/stats/permutation/permutation.py,sha256=k9-Yw-1wWBqeD9cGcTh_d2ypqN-HzoJrcCEAR5-BK0o,10673
 risk/neighborhoods/stats/permutation/test_functions.py,sha256=Wuop4WDY3foGeKp-hMGc2Gdqf85s-x9BDXGB8ifp0oE,3147
 risk/network/__init__.py,sha256=C9GisdyJM7fizwUIipy1vC4lbry9ceqLn1iBcW0-mZg,34
-risk/network/io.py,sha256=1JViOU1YY0DgRP-dK-n-Tkj2ZrpVJJm4vq-5mzvK7kM,27856
+risk/network/io.py,sha256=oD7jZ0qrZr78OHJHDS2hj9J5FsYpqV7vJ3TNmJfC9Cg,27903
 risk/network/graph/__init__.py,sha256=iG6IlE8xtAyF6_NuCBUpsJrjrjd1vsXO1Ajsr0K8EA0,46
 risk/network/graph/api.py,sha256=gXheVl1xw7vFDHOOQdRxCFwVy4ajEJ1dk4GQxm13sCI,8528
 risk/network/graph/graph.py,sha256=jPNJea9JiLKedGFvSKmZ5Kf2R9go0HJkZ4wYNJwZRJI,12410
@@ -33,8 +33,8 @@ risk/network/plotter/network.py,sha256=c9rPQ5mjil0sxVQnprRaKMAUqT6PZmKiATWz0m-Tv
 risk/network/plotter/plotter.py,sha256=WZcOrBW3vBQ_aLwv8c8pXJO8ZlyswHHHfEsiLxzEYaI,6121
 risk/network/plotter/utils/colors.py,sha256=xZt4877ORTQqySiMh-tUGe0sXvhLbXO04iGNeBDkbbw,19144
 risk/network/plotter/utils/layout.py,sha256=Lty16T-Q-oWwo9fXqm-nnS_dMS3BMhuFt4SFqxFC3Ng,3610
-risk_network-0.0.12b5.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.12b5.dist-info/METADATA,sha256=ppOpn9JoTt205DXG6Mhr0xB82udY8T1vOsEvRxXTLH8,6667
-risk_network-0.0.12b5.dist-info/WHEEL,sha256=ooBFpIzZCPdw3uqIQsOo4qqbA4ZRPxHnOH7peeONza0,91
-risk_network-0.0.12b5.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.12b5.dist-info/RECORD,,
+risk_network-0.0.13b0.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.13b0.dist-info/METADATA,sha256=VySq4M1F3ngSP-yVOii8nMjSNNktg_E1owpA5ioXmQo,6670
+risk_network-0.0.13b0.dist-info/WHEEL,sha256=ooBFpIzZCPdw3uqIQsOo4qqbA4ZRPxHnOH7peeONza0,91
+risk_network-0.0.13b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.13b0.dist-info/RECORD,,