risk-network 0.0.11__tar.gz → 0.0.12b1__tar.gz

risk_network-0.0.12b1/PKG-INFO

@@ -0,0 +1,122 @@
+Metadata-Version: 2.4
+Name: risk-network
+Version: 0.0.12b1
+Summary: A Python package for biological network analysis
+Author-email: Ira Horecka <ira89@icloud.com>
+License: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/riskportal/network
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Development Status :: 4 - Beta
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ipywidgets
+Requires-Dist: leidenalg
+Requires-Dist: markov_clustering
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Requires-Dist: nltk
+Requires-Dist: numpy
+Requires-Dist: openpyxl
+Requires-Dist: pandas
+Requires-Dist: python-igraph
+Requires-Dist: python-louvain
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: statsmodels
+Requires-Dist: threadpoolctl
+Requires-Dist: tqdm
+Dynamic: license-file
+
+# RISK Network
+
+<p align="center">
+  <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
+</p>
+
+<br>
+
+![Python](https://img.shields.io/badge/python-3.8%2B-yellow)
+[![pypiv](https://img.shields.io/pypi/v/risk-network.svg)](https://pypi.python.org/pypi/risk-network)
+![License](https://img.shields.io/badge/license-GPLv3-purple)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.xxxxxxx.svg)](https://doi.org/10.5281/zenodo.xxxxxxx)
+![Downloads](https://img.shields.io/pypi/dm/risk-network)
+![Tests](https://github.com/riskportal/network/actions/workflows/ci.yml/badge.svg)
+
+**RISK** (Regional Inference of Significant Kinships) is a next-generation tool for biological network annotation and visualization. RISK integrates community detection-based clustering, rigorous statistical enrichment analysis, and a modular framework to uncover biologically meaningful relationships and generate high-resolution visualizations. RISK supports diverse data formats and is optimized for large-scale network analysis, making it a valuable resource for researchers in systems biology and beyond.
+
+## Documentation and Tutorial
+
+Full documentation is available at:
+
+- **Docs:** [https://riskportal.github.io/network-tutorial](https://riskportal.github.io/network-tutorial)  
+- **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/network-tutorial](https://github.com/riskportal/network-tutorial)
+
+## Installation
+
+RISK is compatible with Python 3.8 or later and runs on all major operating systems. To install the latest version of RISK, run:
+
+```bash
+pip install risk-network --upgrade
+```
+
+## Features
+
+- **Comprehensive Network Analysis**: Analyze biological networks (e.g., protein–protein interaction and genetic interaction networks) as well as non-biological networks.
+- **Advanced Clustering Algorithms**: Supports Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap for identifying structured network regions.
+- **Flexible Visualization**: Produce customizable, high-resolution network visualizations with kernel density estimate overlays, adjustable node and edge attributes, and export options in SVG, PNG, and PDF formats.
+- **Efficient Data Handling**: Supports multiple input/output formats, including JSON, CSV, TSV, Excel, Cytoscape, and GPickle.
+- **Statistical Analysis**: Assess functional enrichment using hypergeometric, permutation (network-aware), binomial, chi-squared, Poisson, and z-score tests, ensuring statistical adaptability across datasets.
+- **Cross-Domain Applicability**: Suitable for network analysis across biological and non-biological domains, including social and communication networks.
+
+## Example Usage
+
+We applied RISK to a *Saccharomyces cerevisiae* protein–protein interaction network from Michaelis et al. (2023), filtering for proteins with six or more interactions to emphasize core functional relationships. RISK identified compact, statistically enriched clusters corresponding to biological processes such as ribosomal assembly and mitochondrial organization.
+
+[![Figure 1](https://i.imgur.com/lJHJrJr.jpeg)](https://i.imgur.com/lJHJrJr.jpeg)
+
+This figure highlights RISK’s capability to detect both established and novel functional modules within the yeast interactome.
+
+## Citation
+
+If you use RISK in your research, please cite:
+
+**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)
+
+## Software Architecture and Implementation
+
+RISK features a streamlined, modular architecture designed to meet diverse research needs. RISK’s modular design enables users to run individual components—such as clustering, statistical testing, or visualization—independently or in combination, depending on the analysis workflow. It includes dedicated modules for:
+
+- **Data I/O**: Supports JSON, CSV, TSV, Excel, Cytoscape, and GPickle formats.
+- **Clustering**: Supports multiple clustering methods, including Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap. Provides flexible distance metrics tailored to network structure.
+- **Statistical Analysis**: Provides a suite of tests for overrepresentation analysis of annotations.
+- **Visualization**: Offers customizable, high-resolution output in multiple formats, including SVG, PNG, and PDF.
+- **Configuration Management**: Centralized parameters in risk.params ensure reproducibility and easy tuning for large-scale analyses.
+
+## Performance and Efficiency
+
+Benchmarking results demonstrate that RISK efficiently scales to networks exceeding hundreds of thousands of edges, maintaining low execution times and optimal memory usage across statistical tests.
+
+## Contributing
+
+We welcome contributions from the community:
+
+- [Issues Tracker](https://github.com/riskportal/network/issues)
+- [Source Code](https://github.com/riskportal/network/tree/main/risk)
+
+## Support
+
+If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/network/issues) on GitHub.
+
+## License
+
+RISK is open source under the [GNU General Public License v3.0](https://www.gnu.org/licenses/gpl-3.0.en.html).

{risk_network-0.0.11 → risk_network-0.0.12b1}/README.md

@@ -17,7 +17,10 @@
 
 ## Documentation and Tutorial
 
-An interactive Jupyter notebook tutorial can be found [here](https://github.com/riskportal/network-tutorial). We highly recommend new users to consult the documentation and tutorial early on to fully utilize RISK's capabilities.
+Full documentation is available at:
+
+- **Docs:** [https://riskportal.github.io/network-tutorial](https://riskportal.github.io/network-tutorial)  
+- **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/network-tutorial](https://github.com/riskportal/network-tutorial)
 
 ## Installation
 
@@ -33,7 +36,7 @@ pip install risk-network --upgrade
 - **Advanced Clustering Algorithms**: Supports Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap for identifying structured network regions.
 - **Flexible Visualization**: Produce customizable, high-resolution network visualizations with kernel density estimate overlays, adjustable node and edge attributes, and export options in SVG, PNG, and PDF formats.
 - **Efficient Data Handling**: Supports multiple input/output formats, including JSON, CSV, TSV, Excel, Cytoscape, and GPickle.
-- **Statistical Analysis**: Assess functional enrichment using hypergeometric, permutation, binomial, chi-squared, Poisson, and z-score tests, ensuring statistical adaptability across datasets.
+- **Statistical Analysis**: Assess functional enrichment using hypergeometric, permutation (network-aware), binomial, chi-squared, Poisson, and z-score tests, ensuring statistical adaptability across datasets.
 - **Cross-Domain Applicability**: Suitable for network analysis across biological and non-biological domains, including social and communication networks.
 
 ## Example Usage
@@ -52,12 +55,13 @@ If you use RISK in your research, please cite:
 
 ## Software Architecture and Implementation
 
-RISK features a streamlined, modular architecture designed to meet diverse research needs. It includes dedicated modules for:
+RISK features a streamlined, modular architecture designed to meet diverse research needs. RISK’s modular design enables users to run individual components—such as clustering, statistical testing, or visualization—independently or in combination, depending on the analysis workflow. It includes dedicated modules for:
 
 - **Data I/O**: Supports JSON, CSV, TSV, Excel, Cytoscape, and GPickle formats.
 - **Clustering**: Supports multiple clustering methods, including Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap. Provides flexible distance metrics tailored to network structure.
 - **Statistical Analysis**: Provides a suite of tests for overrepresentation analysis of annotations.
 - **Visualization**: Offers customizable, high-resolution output in multiple formats, including SVG, PNG, and PDF.
+- **Configuration Management**: Centralized parameters in risk.params ensure reproducibility and easy tuning for large-scale analyses.
 
 ## Performance and Efficiency
 
@@ -77,7 +81,3 @@ If you encounter issues or have suggestions for new features, please use the [Is
 ## License
 
 RISK is open source under the [GNU General Public License v3.0](https://www.gnu.org/licenses/gpl-3.0.en.html).
-
----
-
-**Note**: For detailed documentation and to access the interactive tutorial, please visit the links above.

{risk_network-0.0.11 → risk_network-0.0.12b1}/pyproject.toml

@@ -1,20 +1,19 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy"]
+requires = ["setuptools", "numpy"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "risk-network"
-dynamic = ["version"]  # Indicates that version is determined dynamically
+dynamic = ["version"]
 description = "A Python package for biological network analysis"
 authors = [
     { name = "Ira Horecka", email = "ira89@icloud.com" },
 ]
 readme = "README.md"
-license = { file = "LICENSE" }
+requires-python = ">=3.8"
 classifiers = [
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
@@ -43,4 +42,21 @@ dependencies = [
     "threadpoolctl",
     "tqdm",
 ]
-requires-python = ">=3.8"
+
+[project.license]
+text = "GPL-3.0-or-later"
+
+[project.urls]
+"Homepage" = "https://github.com/riskportal/network"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = { attr = "risk.__version__" }
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.11"
+__version__ = "0.0.12-beta.1"

risk_network-0.0.12b1/src/risk/annotations/__init__.py

@@ -0,0 +1,10 @@
+"""
+risk/annotations
+~~~~~~~~~~~~~~~~
+"""
+
+from risk.annotations.annotations import (
+    define_top_annotations,
+    get_weighted_description,
+)
+from risk.annotations.io import AnnotationsIO

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/annotations/io.py

@@ -10,7 +10,7 @@ import networkx as nx
 import pandas as pd
 
 from risk.annotations.annotations import load_annotations
-from risk.log import params, logger, log_header
+from risk.log import log_header, logger, params
 
 
 class AnnotationsIO:
@@ -20,9 +20,6 @@ class AnnotationsIO:
     and to export parameter data to various formats like JSON, CSV, and text files.
     """
 
-    def __init__(self):
-        pass
-
     def load_json_annotation(
         self, network: nx.Graph, filepath: str, min_nodes_per_term: int = 2
     ) -> Dict[str, Any]:
@@ -42,7 +39,7 @@ class AnnotationsIO:
         params.log_annotations(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        _log_loading(filetype, filepath=filepath)
+        self._log_loading(filetype, filepath=filepath)
 
         # Load the JSON file into a dictionary
         with open(filepath, "r", encoding="utf-8") as file:
@@ -81,7 +78,7 @@ class AnnotationsIO:
         params.log_annotations(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        _log_loading(filetype, filepath=filepath)
+        self._log_loading(filetype, filepath=filepath)
 
         # Load the specified sheet from the Excel file
         annotation = pd.read_excel(filepath, sheet_name=sheet_name)
@@ -123,10 +120,10 @@ class AnnotationsIO:
         params.log_annotations(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        _log_loading(filetype, filepath=filepath)
+        self._log_loading(filetype, filepath=filepath)
 
         # Load the CSV file into a dictionary
-        annotations_input = _load_matrix_file(
+        annotations_input = self._load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter=",", nodes_delimiter=nodes_delimiter
         )
 
@@ -161,10 +158,10 @@ class AnnotationsIO:
         params.log_annotations(
             filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
         )
-        _log_loading(filetype, filepath=filepath)
+        self._log_loading(filetype, filepath=filepath)
 
         # Load the TSV file into a dictionary
-        annotations_input = _load_matrix_file(
+        annotations_input = self._load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter="\t", nodes_delimiter=nodes_delimiter
         )
 
@@ -183,6 +180,9 @@ class AnnotationsIO:
 
         Returns:
             Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
+
+        Raises:
+            TypeError: If the content is not a dictionary.
         """
         # Ensure the input content is a dictionary
         if not isinstance(content, dict):
@@ -193,48 +193,49 @@ class AnnotationsIO:
         filetype = "Dictionary"
         # Log the loading of the annotations from the dictionary
         params.log_annotations(filepath="In-memory dictionary", filetype=filetype)
-        _log_loading(filetype, "In-memory dictionary")
+        self._log_loading(filetype, "In-memory dictionary")
 
         # Load the annotations as a dictionary from the provided dictionary
         return load_annotations(network, content, min_nodes_per_term)
 
+    def _load_matrix_file(
+        self,
+        filepath: str,
+        label_colname: str,
+        nodes_colname: str,
+        delimiter: str = ",",
+        nodes_delimiter: str = ";",
+    ) -> Dict[str, Any]:
+        """Load annotations from a CSV or TSV file and convert them to a dictionary.
 
-def _load_matrix_file(
-    filepath: str,
-    label_colname: str,
-    nodes_colname: str,
-    delimiter: str = ",",
-    nodes_delimiter: str = ";",
-) -> Dict[str, Any]:
-    """Load annotations from a CSV or TSV file and convert them to a dictionary.
-
-    Args:
-        filepath (str): Path to the annotation file.
-        label_colname (str): Name of the column containing the labels (e.g., GO terms).
-        nodes_colname (str): Name of the column containing the nodes associated with each label.
-        delimiter (str, optional): Delimiter used to separate columns in the file (default is ',').
-        nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
-
-    Returns:
-        Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes.
-    """
-    # Load the CSV or TSV file into a DataFrame
-    annotation = pd.read_csv(filepath, delimiter=delimiter)
-    # Split the nodes column by the nodes_delimiter to handle multiple nodes per label
-    annotation[nodes_colname] = annotation[nodes_colname].apply(lambda x: x.split(nodes_delimiter))
-    # Create a dictionary pairing labels with their corresponding list of nodes
-    label_node_dict = annotation.set_index(label_colname)[nodes_colname].to_dict()
-    return label_node_dict
+        Args:
+            filepath (str): Path to the annotation file.
+            label_colname (str): Name of the column containing the labels (e.g., GO terms).
+            nodes_colname (str): Name of the column containing the nodes associated with each label.
+            delimiter (str, optional): Delimiter used to separate columns in the file (default is ',').
+            nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
 
+        Returns:
+            Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes.
+        """
+        # Load the CSV or TSV file into a DataFrame
+        annotation = pd.read_csv(filepath, delimiter=delimiter)
+        # Split the nodes column by the nodes_delimiter to handle multiple nodes per label
+        annotation[nodes_colname] = annotation[nodes_colname].apply(
+            lambda x: x.split(nodes_delimiter)
+        )
+        # Create a dictionary pairing labels with their corresponding list of nodes
+        label_node_dict = annotation.set_index(label_colname)[nodes_colname].to_dict()
+        return label_node_dict
 
-def _log_loading(filetype: str, filepath: str = "") -> None:
-    """Log information about the network file being loaded.
+    def _log_loading(self, filetype: str, filepath: str = "") -> None:
+        """Log information about the network file being loaded.
 
-    Args:
-        filetype (str): The type of the file being loaded (e.g., 'Cytoscape').
-        filepath (str, optional): The path to the file being loaded.
-    """
-    log_header("Loading annotations")
-    logger.debug(f"Filetype: {filetype}")
-    if filepath:
-        logger.debug(f"Filepath: {filepath}")
+        Args:
+            filetype (str): The type of the file being loaded (e.g., 'Cytoscape').
+            filepath (str, optional): The path to the file being loaded.
+        """
+        log_header("Loading annotations")
+        logger.debug(f"Filetype: {filetype}")
+        if filepath:
+            logger.debug(f"Filepath: {filepath}")

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/annotations/nltk_setup.py

@@ -8,7 +8,8 @@ import zipfile
 from typing import List, Tuple
 
 import nltk
-from nltk.data import find, path as nltk_data_path
+from nltk.data import find
+from nltk.data import path as nltk_data_path
 
 from risk.log import logger
 

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/log/__init__.py

@@ -3,7 +3,7 @@ risk/log
 ~~~~~~~~
 """
 
-from risk.log.console import logger, log_header, set_global_verbosity
+from risk.log.console import log_header, logger, set_global_verbosity
 from risk.log.parameters import Params
 
 # Initialize the global parameters logger

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/log/parameters.py

@@ -11,7 +11,7 @@ from typing import Any, Dict
 
 import numpy as np
 
-from risk.log.console import logger, log_header
+from risk.log.console import log_header, logger
 
 # Suppress all warnings - this is to resolve warnings from multiprocessing
 warnings.filterwarnings("ignore")
@@ -137,7 +137,7 @@ class Params:
             Dict[str, Any]: A dictionary containing the processed parameters.
         """
         log_header("Loading parameters")
-        return _convert_ndarray_to_list(
+        return self._convert_ndarray_to_list(
             {
                 "annotations": self.annotations,
                 "datetime": self.datetime,
@@ -148,25 +148,24 @@ class Params:
             }
         )
 
+    def _convert_ndarray_to_list(self, d: Dict[str, Any]) -> Dict[str, Any]:
+        """Recursively convert all np.ndarray values in the dictionary to lists.
 
-def _convert_ndarray_to_list(d: Dict[str, Any]) -> Dict[str, Any]:
-    """Recursively convert all np.ndarray values in the dictionary to lists.
-
-    Args:
-        d (Dict[str, Any]): The dictionary to process.
+        Args:
+            d (Dict[str, Any]): The dictionary to process.
 
-    Returns:
-        Dict[str, Any]: The processed dictionary with np.ndarray values converted to lists.
-    """
-    if isinstance(d, dict):
-        # Recursively process each value in the dictionary
-        return {k: _convert_ndarray_to_list(v) for k, v in d.items()}
-    if isinstance(d, list):
-        # Recursively process each item in the list
-        return [_convert_ndarray_to_list(v) for v in d]
-    if isinstance(d, np.ndarray):
-        # Convert numpy arrays to lists
-        return d.tolist()
-
-    # Return the value unchanged if it's not a dict, List, or ndarray
-    return d
+        Returns:
+            Dict[str, Any]: The processed dictionary with np.ndarray values converted to lists.
+        """
+        if isinstance(d, dict):
+            # Recursively process each value in the dictionary
+            return {k: self._convert_ndarray_to_list(v) for k, v in d.items()}
+        if isinstance(d, list):
+            # Recursively process each item in the list
+            return [self._convert_ndarray_to_list(v) for v in d]
+        if isinstance(d, np.ndarray):
+            # Convert numpy arrays to lists
+            return d.tolist()
+
+        # Return the value unchanged if it's not a dict, List, or ndarray
+        return d

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/neighborhoods/__init__.py

@@ -4,5 +4,4 @@ risk/neighborhoods
 """
 
 from risk.neighborhoods.domains import define_domains, trim_domains
-from risk.neighborhoods.api import NeighborhoodsAPI
 from risk.neighborhoods.neighborhoods import process_neighborhoods

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/neighborhoods/api.py

@@ -10,9 +10,9 @@ import networkx as nx
 import numpy as np
 from scipy.sparse import csr_matrix
 
-from risk.log import logger, log_header, params
+from risk.log import log_header, logger, params
 from risk.neighborhoods.neighborhoods import get_network_neighborhoods
-from risk.stats import (
+from risk.neighborhoods.stats import (
     compute_binom_test,
     compute_chi2_test,
     compute_hypergeom_test,

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/neighborhoods/community.py

@@ -8,7 +8,7 @@ import igraph as ig
 import markov_clustering as mc
 import networkx as nx
 import numpy as np
-from leidenalg import find_partition, RBConfigurationVertexPartition
+from leidenalg import RBConfigurationVertexPartition, find_partition
 from networkx.algorithms.community import greedy_modularity_communities
 from scipy.sparse import csr_matrix
 
@@ -27,6 +27,10 @@ def calculate_greedy_modularity_neighborhoods(
 
     Returns:
         csr_matrix: A binary neighborhood matrix (CSR) where nodes in the same community have 1, and others have 0.
+
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -67,6 +71,10 @@ def calculate_label_propagation_neighborhoods(
 
     Returns:
         csr_matrix: A binary neighborhood matrix (CSR) on Label Propagation.
+
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -115,6 +123,10 @@ def calculate_leiden_neighborhoods(
 
     Returns:
         csr_matrix: A binary neighborhood matrix (CSR) where nodes in the same community have 1, and others have 0.
+
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -167,6 +179,10 @@ def calculate_louvain_neighborhoods(
 
     Returns:
         csr_matrix: A binary neighborhood matrix in CSR format.
+
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -215,9 +231,10 @@ def calculate_markov_clustering_neighborhoods(
     Returns:
         csr_matrix: A binary neighborhood matrix (CSR) on Markov Clustering.
 
-    Warning:
-        This function temporarily converts the adjacency matrix to a dense format, which may lead to
-        high memory consumption for large graphs.
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        RuntimeError: If MCL fails to run.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -283,6 +300,10 @@ def calculate_spinglass_neighborhoods(
 
     Returns:
         csr_matrix: A binary neighborhood matrix (CSR) based on Spinglass communities.
+
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -343,6 +364,10 @@ def calculate_walktrap_neighborhoods(
 
     Returns:
         csr_matrix: A binary neighborhood matrix (CSR) on Walktrap communities.
+
+    Raises:
+        ValueError: If the subgraph has no edges after filtering.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
@@ -384,6 +409,10 @@ def _create_percentile_limited_subgraph(G: nx.Graph, fraction_shortest_edges: fl
     Returns:
         nx.Graph: A subgraph with nodes and edges where the edges are within the shortest
         specified rank fraction.
+
+    Raises:
+        ValueError: If no edges with 'length' attributes are found in the graph.
+        Warning: If the resulting subgraph has no edges after filtering.
     """
     # Step 1: Extract edges with their lengths
     edges_with_length = [(u, v, d) for u, v, d in G.edges(data=True) if "length" in d]

{risk_network-0.0.11 → risk_network-0.0.12b1/src}/risk/neighborhoods/domains.py

@@ -9,19 +9,18 @@ from typing import Tuple, Union
 import numpy as np
 import pandas as pd
 from numpy.linalg import LinAlgError
-from scipy.cluster.hierarchy import linkage, fcluster
+from scipy.cluster.hierarchy import fcluster, linkage
 from sklearn.metrics import silhouette_score
 from tqdm import tqdm
 
 from risk.annotations import get_weighted_description
 from risk.log import logger
 
-
 # Define constants for clustering
 # fmt: off
 LINKAGE_METHODS = {"single", "complete", "average", "weighted", "centroid", "median", "ward"}
 LINKAGE_METRICS = {
-    "braycurtis","canberra", "chebyshev", "cityblock", "correlation", "cosine", "dice", "euclidean",
+    "braycurtis", "canberra", "chebyshev", "cityblock", "correlation", "cosine", "dice", "euclidean",
     "hamming", "jaccard", "jensenshannon", "kulczynski1", "mahalanobis", "matching", "minkowski",
     "rogerstanimoto", "russellrao", "seuclidean", "sokalmichener", "sokalsneath", "sqeuclidean", "yule",
 }
@@ -49,6 +48,9 @@ def define_domains(
 
     Returns:
         pd.DataFrame: DataFrame with the primary domain for each node.
+
+    Raises:
+        ValueError: If the clustering criterion is set to "off" or if an error occurs during clustering.
     """
     try:
         if linkage_criterion == "off":
@@ -242,7 +244,7 @@ def _optimize_silhouette_across_linkage_and_metrics(
     # Evaluating optimal linkage method and metric
     for method, metric in tqdm(
         product(linkage_methods, linkage_metrics),
-        desc="Evaluating optimal linkage method and metric",
+        desc="Evaluating linkage methods and metrics",
         total=total_combinations,
         bar_format="{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}]",
     ):