risk-network 0.0.12b5__tar.gz → 0.0.13b0__tar.gz

{risk_network-0.0.12b5/src/risk_network.egg-info → risk_network-0.0.13b0}/PKG-INFO

@@ -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 → risk_network-0.0.13b0}/README.md

@@ -49,9 +49,10 @@ 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 → risk_network-0.0.13b0}/src/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_network-0.0.12b5 → risk_network-0.0.13b0}/src/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_network-0.0.12b5 → risk_network-0.0.13b0}/src/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-0.0.12b5 → risk_network-0.0.13b0}/src/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 → risk_network-0.0.13b0/src/risk_network.egg-info}/PKG-INFO

@@ -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