risk-network 0.0.7b12__tar.gz → 0.0.8__tar.gz

{risk_network-0.0.7b12 → risk_network-0.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b12
+Version: 0.0.8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -709,42 +709,105 @@ Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
-<p align="center">
-  <img src="https://i.imgur.com/Fo9EmnK.png" width="400" />
-</p>
+# RISK Network
 
 <p align="center">
-  <a href="https://pypi.python.org/pypi/risk-network"><img src="https://img.shields.io/pypi/v/risk-network.svg" alt="pypiv"></a>
-  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.8+-blue.svg" alt="Python 3.8+"></a>
-  <a href="https://raw.githubusercontent.com/irahorecka/chrono24/main/LICENSE"><img src="https://img.shields.io/badge/License-GPLv3-blue.svg" alt="License: GPL v3"></a>
+  <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
 </p>
 
-## RISK
+<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)
+![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 Infers Spatial Kinships
+## Documentation and Tutorial
+
+- **Documentation**: Comprehensive documentation is available [here](Documentation link).
+- **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 leverage RISK's capabilities.
+
+## Installation
 
-RISK is a software tool for visualizing spatial relationships in networks. It aims to enhance network analysis by integrating advanced network annotation algorithms, such as Louvain and Markov Clustering, to identify key functional modules and pathways.
+RISK is compatible with Python 3.8 and later versions and operates on all major operating systems. Install RISK via pip:
+
+```bash
+pip install risk-network
+```
 
 ## Features
 
-- Spatial analysis of biological networks
-- Functional enrichment detection
-- Optimized performance
+- **Comprehensive Network Analysis**: Analyze biological networks such as protein–protein interaction (PPI) and gene regulatory networks, as well as non-biological networks.
+- **Advanced Clustering Algorithms**: Utilize algorithms like Louvain, Markov Clustering, Spinglass, and more to identify key functional modules.
+- **Flexible Visualization**: Generate clear, publication-quality figures with customizable node and edge attributes, including colors, shapes, sizes, and labels.
+- **Efficient Data Handling**: Optimized for large datasets, supporting multiple file formats such as JSON, CSV, TSV, Excel, Cytoscape, and GPickle.
+- **Statistical Analysis**: Integrated statistical tests, including hypergeometric, permutation, and Poisson tests, to assess the significance of enriched regions.
+- **Cross-Domain Applicability**: Suitable for network analysis across biological and non-biological domains, including social and communication networks.
 
-## Example
+## Example Usage
 
-*Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
+We applied RISK to a *Saccharomyces cerevisiae* protein–protein interaction network, revealing both established and novel functional relationships. The visualization below highlights key biological processes such as ribosomal assembly and mitochondrial organization.
 
-![PPI Network Demo](https://i.imgur.com/NnyK6nO.png)
+![RISK Main Figure](https://i.imgur.com/5OP3Hqe.jpeg)
 
-## Installation
+RISK successfully detected both known and novel functional clusters within the yeast interactome. Clusters related to Golgi transport and actin nucleation were clearly defined and closely located, showcasing RISK's ability to map well-characterized interactions. Additionally, RISK identified links between mRNA processing pathways and vesicle trafficking proteins, consistent with recent studies demonstrating the role of vesicles in mRNA localization and stability.
+
+## Citation
+
+If you use RISK in your research, please cite the following:
+
+**Horecka**, *et al.*, "RISK: a next-generation tool for biological network annotation and visualization", **[Journal Name]**, 2024. DOI: [10.1234/zenodo.xxxxxxx](https://doi.org/10.1234/zenodo.xxxxxxx)
+
+## Software Architecture and Implementation
 
-Coming soon...
+RISK features a streamlined, modular architecture designed to meet diverse research needs. Each module focuses on a specific task—such as network input/output, statistical analysis, or visualization—ensuring ease of adaptation and extension. This design enhances flexibility and reduces development overhead for users integrating RISK into their workflows.
 
-## Usage
+### Supported Data Formats
 
-Coming soon...
+- **Input/Output**: JSON, CSV, TSV, Excel, Cytoscape, GPickle.
+- **Visualization Outputs**: SVG, PNG, PDF.
+
+### Clustering Algorithms
+
+- **Available Algorithms**:
+  - Greedy Modularity
+  - Label Propagation
+  - Louvain
+  - Markov Clustering
+  - Spinglass
+  - Walktrap
+- **Distance Metrics**: Supports both spherical and Euclidean distance metrics.
+
+### Statistical Tests
+
+- **Hypergeometric Test**
+- **Permutation Test** (single- or multi-process modes)
+- **Poisson Test**
+
+## Performance and Efficiency
+
+In benchmarking tests using the yeast interactome network, RISK demonstrated substantial improvements over previous tools in both computational performance and memory efficiency. RISK processed the dataset approximately **3.25 times faster**, reducing CPU time by **69%**, and required **25% less peak memory usage**, underscoring its efficient utilization of computational resources.
+
+## Contributing
+
+We welcome contributions from the community. Please use the following resources:
+
+- [Issues Tracker](https://github.com/irahorecka/risk/issues)
+- [Source Code](https://github.com/irahorecka/risk/tree/main/risk)
+
+## Support
+
+If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/irahorecka/risk/issues) on GitHub.
 
 ## License
 
-This project is licensed under the GPL-3.0 license.
+RISK is freely available as open-source software 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 provided in the [Documentation and Tutorial](#documentation-and-tutorial) section.

risk_network-0.0.8/README.md

@@ -0,0 +1,102 @@
+# 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)
+![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.
+
+## Documentation and Tutorial
+
+- **Documentation**: Comprehensive documentation is available [here](Documentation link).
+- **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 leverage RISK's capabilities.
+
+## Installation
+
+RISK is compatible with Python 3.8 and later versions and operates on all major operating systems. Install RISK via pip:
+
+```bash
+pip install risk-network
+```
+
+## Features
+
+- **Comprehensive Network Analysis**: Analyze biological networks such as protein–protein interaction (PPI) and gene regulatory networks, as well as non-biological networks.
+- **Advanced Clustering Algorithms**: Utilize algorithms like Louvain, Markov Clustering, Spinglass, and more to identify key functional modules.
+- **Flexible Visualization**: Generate clear, publication-quality figures with customizable node and edge attributes, including colors, shapes, sizes, and labels.
+- **Efficient Data Handling**: Optimized for large datasets, supporting multiple file formats such as JSON, CSV, TSV, Excel, Cytoscape, and GPickle.
+- **Statistical Analysis**: Integrated statistical tests, including hypergeometric, permutation, and Poisson tests, to assess the significance of enriched regions.
+- **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, revealing both established and novel functional relationships. The visualization below highlights key biological processes such as ribosomal assembly and mitochondrial organization.
+
+![RISK Main Figure](https://i.imgur.com/5OP3Hqe.jpeg)
+
+RISK successfully detected both known and novel functional clusters within the yeast interactome. Clusters related to Golgi transport and actin nucleation were clearly defined and closely located, showcasing RISK's ability to map well-characterized interactions. Additionally, RISK identified links between mRNA processing pathways and vesicle trafficking proteins, consistent with recent studies demonstrating the role of vesicles in mRNA localization and stability.
+
+## Citation
+
+If you use RISK in your research, please cite the following:
+
+**Horecka**, *et al.*, "RISK: a next-generation tool for biological network annotation and visualization", **[Journal Name]**, 2024. 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. Each module focuses on a specific task—such as network input/output, statistical analysis, or visualization—ensuring ease of adaptation and extension. This design enhances flexibility and reduces development overhead for users integrating RISK into their workflows.
+
+### Supported Data Formats
+
+- **Input/Output**: JSON, CSV, TSV, Excel, Cytoscape, GPickle.
+- **Visualization Outputs**: SVG, PNG, PDF.
+
+### Clustering Algorithms
+
+- **Available Algorithms**:
+  - Greedy Modularity
+  - Label Propagation
+  - Louvain
+  - Markov Clustering
+  - Spinglass
+  - Walktrap
+- **Distance Metrics**: Supports both spherical and Euclidean distance metrics.
+
+### Statistical Tests
+
+- **Hypergeometric Test**
+- **Permutation Test** (single- or multi-process modes)
+- **Poisson Test**
+
+## Performance and Efficiency
+
+In benchmarking tests using the yeast interactome network, RISK demonstrated substantial improvements over previous tools in both computational performance and memory efficiency. RISK processed the dataset approximately **3.25 times faster**, reducing CPU time by **69%**, and required **25% less peak memory usage**, underscoring its efficient utilization of computational resources.
+
+## Contributing
+
+We welcome contributions from the community. Please use the following resources:
+
+- [Issues Tracker](https://github.com/irahorecka/risk/issues)
+- [Source Code](https://github.com/irahorecka/risk/tree/main/risk)
+
+## Support
+
+If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/irahorecka/risk/issues) on GitHub.
+
+## License
+
+RISK is freely available as open-source software 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 provided in the [Documentation and Tutorial](#documentation-and-tutorial) section.

{risk_network-0.0.7b12 → risk_network-0.0.8}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.7-beta.12"
+__version__ = "0.0.8"

risk_network-0.0.8/risk/annotations/__init__.py

@@ -0,0 +1,7 @@
+"""
+risk/annotations
+~~~~~~~~~~~~~~~~
+"""
+
+from .annotations import define_top_annotations, get_weighted_description
+from .io import AnnotationsIO

{risk_network-0.0.7b12 → risk_network-0.0.8}/risk/annotations/annotations.py

@@ -3,6 +3,7 @@ risk/annotations/annotations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
+import re
 from collections import Counter
 from itertools import compress
 from typing import Any, Dict, List, Set
@@ -30,27 +31,30 @@ def _setup_nltk():
 
 # Ensure you have the necessary NLTK data
 _setup_nltk()
+# Initialize English stopwords
+stop_words = set(stopwords.words("english"))
 
 
 def load_annotations(network: nx.Graph, annotations_input: Dict[str, Any]) -> Dict[str, Any]:
     """Convert annotations input to a DataFrame and reindex based on the network's node labels.
 
     Args:
-        annotations_input (dict): A dictionary with annotations.
+        network (nx.Graph): The network graph.
+        annotations_input (Dict[str, Any]): A dictionary with annotations.
 
     Returns:
-        dict: A dictionary containing ordered nodes, ordered annotations, and the binary annotations matrix.
+        Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the binary annotations matrix.
     """
     # Flatten the dictionary to a list of tuples for easier DataFrame creation
     flattened_annotations = [
         (node, annotation) for annotation, nodes in annotations_input.items() for node in nodes
     ]
     # Create a DataFrame from the flattened list
-    annotations = pd.DataFrame(flattened_annotations, columns=["Node", "Annotations"])
-    annotations["Is Member"] = 1
+    annotations = pd.DataFrame(flattened_annotations, columns=["node", "annotations"])
+    annotations["is_member"] = 1
     # Pivot to create a binary matrix with nodes as rows and annotations as columns
     annotations_pivot = annotations.pivot_table(
-        index="Node", columns="Annotations", values="Is Member", fill_value=0, dropna=False
+        index="node", columns="annotations", values="is_member", fill_value=0, dropna=False
     )
     # Reindex the annotations matrix based on the node labels from the network
     node_label_order = list(nx.get_node_attributes(network, "label").values())
@@ -80,7 +84,8 @@ def define_top_annotations(
     network: nx.Graph,
     ordered_annotation_labels: List[str],
     neighborhood_enrichment_sums: List[int],
-    binary_enrichment_matrix: np.ndarray,
+    significant_enrichment_matrix: np.ndarray,
+    significant_binary_enrichment_matrix: np.ndarray,
     min_cluster_size: int = 5,
     max_cluster_size: int = 1000,
 ) -> pd.DataFrame:
@@ -90,42 +95,52 @@ def define_top_annotations(
         network (NetworkX graph): The network graph.
         ordered_annotation_labels (list of str): List of ordered annotation labels.
         neighborhood_enrichment_sums (list of int): List of neighborhood enrichment sums.
-        binary_enrichment_matrix (np.ndarray): Binary enrichment matrix below alpha threshold.
+        significant_enrichment_matrix (np.ndarray): Enrichment matrix below alpha threshold.
+        significant_binary_enrichment_matrix (np.ndarray): Binary enrichment matrix below alpha threshold.
         min_cluster_size (int, optional): Minimum cluster size. Defaults to 5.
         max_cluster_size (int, optional): Maximum cluster size. Defaults to 1000.
 
     Returns:
         pd.DataFrame: DataFrame with top annotations and their properties.
     """
-    # Create DataFrame to store annotations and their neighborhood enrichment sums
+    # Sum the columns of the significant enrichment matrix (positive floating point values)
+    significant_enrichment_scores = significant_enrichment_matrix.sum(axis=0)
+    # Create DataFrame to store annotations, their neighborhood enrichment sums, and enrichment scores
     annotations_enrichment_matrix = pd.DataFrame(
         {
             "id": range(len(ordered_annotation_labels)),
-            "words": ordered_annotation_labels,
-            "neighborhood enrichment sums": neighborhood_enrichment_sums,
+            "full_terms": ordered_annotation_labels,
+            "significant_neighborhood_enrichment_sums": neighborhood_enrichment_sums,
+            "significant_enrichment_score": significant_enrichment_scores,
         }
     )
-    annotations_enrichment_matrix["top attributes"] = False
-    # Apply size constraints to identify potential top attributes
+    annotations_enrichment_matrix["significant_annotations"] = False
+    # Apply size constraints to identify potential significant annotations
     annotations_enrichment_matrix.loc[
-        (annotations_enrichment_matrix["neighborhood enrichment sums"] >= min_cluster_size)
-        & (annotations_enrichment_matrix["neighborhood enrichment sums"] <= max_cluster_size),
-        "top attributes",
+        (
+            annotations_enrichment_matrix["significant_neighborhood_enrichment_sums"]
+            >= min_cluster_size
+        )
+        & (
+            annotations_enrichment_matrix["significant_neighborhood_enrichment_sums"]
+            <= max_cluster_size
+        ),
+        "significant_annotations",
     ] = True
     # Initialize columns for connected components analysis
-    annotations_enrichment_matrix["num connected components"] = 0
-    annotations_enrichment_matrix["size connected components"] = None
-    annotations_enrichment_matrix["size connected components"] = annotations_enrichment_matrix[
-        "size connected components"
+    annotations_enrichment_matrix["num_connected_components"] = 0
+    annotations_enrichment_matrix["size_connected_components"] = None
+    annotations_enrichment_matrix["size_connected_components"] = annotations_enrichment_matrix[
+        "size_connected_components"
     ].astype(object)
-    annotations_enrichment_matrix["num large connected components"] = 0
+    annotations_enrichment_matrix["num_large_connected_components"] = 0
 
     for attribute in annotations_enrichment_matrix.index.values[
-        annotations_enrichment_matrix["top attributes"]
+        annotations_enrichment_matrix["significant_annotations"]
     ]:
         # Identify enriched neighborhoods based on the binary enrichment matrix
         enriched_neighborhoods = list(
-            compress(list(network), binary_enrichment_matrix[:, attribute])
+            compress(list(network), significant_binary_enrichment_matrix[:, attribute])
         )
         enriched_network = nx.subgraph(network, enriched_neighborhoods)
         # Analyze connected components within the enriched subnetwork
@@ -144,57 +159,74 @@ def define_top_annotations(
         num_large_connected_components = len(filtered_size_connected_components)
 
         # Assign the number of connected components
-        annotations_enrichment_matrix.loc[attribute, "num connected components"] = (
+        annotations_enrichment_matrix.loc[attribute, "num_connected_components"] = (
             num_connected_components
         )
         # Filter out attributes with more than one connected component
         annotations_enrichment_matrix.loc[
-            annotations_enrichment_matrix["num connected components"] > 1, "top attributes"
+            annotations_enrichment_matrix["num_connected_components"] > 1, "significant_annotations"
         ] = False
         # Assign the number of large connected components
-        annotations_enrichment_matrix.loc[attribute, "num large connected components"] = (
+        annotations_enrichment_matrix.loc[attribute, "num_large_connected_components"] = (
             num_large_connected_components
         )
         # Assign the size of connected components, ensuring it is always a list
-        annotations_enrichment_matrix.at[attribute, "size connected components"] = (
+        annotations_enrichment_matrix.at[attribute, "size_connected_components"] = (
             filtered_size_connected_components.tolist()
         )
 
     return annotations_enrichment_matrix
 
 
-def get_description(words_column: pd.Series) -> str:
-    """Process input Series to identify and return the top frequent, significant words,
-    filtering based on stopwords and gracefully handling numerical strings.
+def get_weighted_description(words_column: pd.Series, scores_column: pd.Series) -> str:
+    """Generate a weighted description from words and their corresponding scores,
+    with support for stopwords filtering and improved weighting logic.
 
     Args:
         words_column (pd.Series): A pandas Series containing strings to process.
+        scores_column (pd.Series): A pandas Series containing enrichment scores to weigh the terms.
 
     Returns:
-        str: A coherent description formed from the most frequent and significant words.
+        str: A coherent description formed from the most frequent and significant words, weighed by enrichment scores.
     """
-    # Concatenate all rows into a single string and tokenize into words
-    all_words = words_column.str.cat(sep=" ")
-    tokens = word_tokenize(all_words)
-
-    # Separate numeric tokens
-    numeric_tokens = [token for token in tokens if token.replace(".", "", 1).isdigit()]
-    # If there's only one unique numeric value, return it directly as a string
-    unique_numeric_values = set(numeric_tokens)
-    if len(unique_numeric_values) == 1:
-        return f"{list(unique_numeric_values)[0]}"
-
-    # Ensure that all values in 'words' are strings and include both alphabetic and numeric tokens
-    words = [
-        str(
-            word.lower() if word.istitle() else word
-        )  # Convert to string and lowercase all words except proper nouns (e.g., RNA, mRNA)
-        for word in tokens
-        if word.isalpha()
-        or word.replace(".", "", 1).isdigit()  # Keep alphabetic words and numeric strings
-    ]
-    # Generate a coherent description from the processed words
-    description = _generate_coherent_description(words)
+    # Handle case where all scores are the same
+    if scores_column.max() == scores_column.min():
+        normalized_scores = pd.Series([1] * len(scores_column))
+    else:
+        # Normalize the enrichment scores to be between 0 and 1
+        normalized_scores = (scores_column - scores_column.min()) / (
+            scores_column.max() - scores_column.min()
+        )
+
+    # Combine words and normalized scores to create weighted words
+    weighted_words = []
+    for word, score in zip(words_column, normalized_scores):
+        word = str(word)
+        if word not in stop_words:  # Skip stopwords
+            weight = max(1, int((0 if pd.isna(score) else score) * 10))
+            weighted_words.extend([word] * weight)
+
+    # Tokenize the weighted words, but preserve number-word patterns like '4-alpha'
+    tokens = word_tokenize(" ".join(weighted_words))
+    # Ensure we treat "4-alpha" or other "number-word" patterns as single tokens
+    combined_tokens = []
+    for token in tokens:
+        # Match patterns like '4-alpha' or '5-hydroxy' and keep them together
+        if re.match(r"^\d+-\w+", token):
+            combined_tokens.append(token)
+        elif token.replace(".", "", 1).isdigit():  # Handle pure numeric tokens
+            # Ignore pure numbers as descriptions unless necessary
+            continue
+        else:
+            combined_tokens.append(token)
+
+    # Prevent descriptions like just '4' from being selected
+    if len(combined_tokens) == 1 and combined_tokens[0].isdigit():
+        return "N/A"  # Return "N/A" for cases where it's just a number
+
+    # Simplify the word list and generate the description
+    simplified_words = _simplify_word_list(combined_tokens)
+    description = _generate_coherent_description(simplified_words)
 
     return description
 
@@ -257,7 +289,7 @@ def _generate_coherent_description(words: List[str]) -> str:
     If there is only one unique entry, return it directly.
 
     Args:
-        words (list): A list of words or numerical string values.
+        words (List): A list of words or numerical string values.
 
     Returns:
         str: A coherent description formed by arranging the words in a logical sequence.

{risk_network-0.0.7b12 → risk_network-0.0.8}/risk/annotations/io.py

@@ -33,7 +33,7 @@ class AnnotationsIO:
             filepath (str): Path to the JSON annotations file.
 
         Returns:
-            dict: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
+            Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
         """
         filetype = "JSON"
         # Log the loading of the JSON file
@@ -158,10 +158,10 @@ class AnnotationsIO:
 
         Args:
             network (NetworkX graph): The network to which the annotations are related.
-            content (dict): The annotations dictionary to load.
+            content (Dict[str, Any]): The annotations dictionary to load.
 
         Returns:
-            dict: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
+            Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
         """
         # Ensure the input content is a dictionary
         if not isinstance(content, dict):

{risk_network-0.0.7b12 → risk_network-0.0.8}/risk/log/__init__.py

@@ -3,7 +3,7 @@ risk/log
 ~~~~~~~~
 """
 
-from .config import logger, log_header, set_global_verbosity
+from .console import logger, log_header, set_global_verbosity
 from .params import Params
 
 params = Params()

risk_network-0.0.7b12/risk/log/config.py → risk_network-0.0.8/risk/log/console.py

@@ -1,6 +1,6 @@
 """
-risk/log/config
-~~~~~~~~~~~~~~~
+risk/log/console
+~~~~~~~~~~~~~~~~
 """
 
 import logging

{risk_network-0.0.7b12 → risk_network-0.0.8}/risk/log/params.py

@@ -12,7 +12,7 @@ from typing import Any, Dict
 
 import numpy as np
 
-from .config import logger, log_header
+from .console import logger, log_header
 
 # Suppress all warnings - this is to resolve warnings from multiprocessing
 warnings.filterwarnings("ignore")
@@ -159,7 +159,7 @@ class Params:
         """Load and process various parameters, converting any np.ndarray values to lists.
 
         Returns:
-            dict: A dictionary containing the processed parameters.
+            Dict[str, Any]: A dictionary containing the processed parameters.
         """
         log_header("Loading parameters")
         return _convert_ndarray_to_list(
@@ -174,14 +174,14 @@ class Params:
         )
 
 
-def _convert_ndarray_to_list(d: Any) -> Any:
+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): The dictionary to process.
+        d (Dict[str, Any]): The dictionary to process.
 
     Returns:
-        dict: The processed dictionary with np.ndarray values converted to lists.
+        Dict[str, Any]: The processed dictionary with np.ndarray values converted to lists.
     """
     if isinstance(d, dict):
         # Recursively process each value in the dictionary
@@ -193,5 +193,5 @@ def _convert_ndarray_to_list(d: Any) -> Any:
         # Convert numpy arrays to lists
         return d.tolist()
     else:
-        # Return the value unchanged if it's not a dict, list, or ndarray
+        # Return the value unchanged if it's not a dict, List, or ndarray
         return d