risk-network 0.0.15b0__tar.gz → 0.0.16b1__tar.gz

{risk_network-0.0.15b0 → risk_network-0.0.16b1}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.15b0
+Version: 0.0.16b1
 Summary: A Python package for scalable network analysis and high-quality visualization.
 Author-email: Ira Horecka <ira89@icloud.com>
 License: GPL-3.0-or-later
-Project-URL: Homepage, https://github.com/riskportal/network
-Project-URL: Issues, https://github.com/riskportal/network/issues
+Project-URL: Homepage, https://github.com/riskportal/risk
+Project-URL: Issues, https://github.com/riskportal/risk/issues
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -39,20 +39,13 @@ 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>
+# RISK
 
 ![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)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17257418.svg)](https://doi.org/10.5281/zenodo.17257418)
+![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
 
 **RISK** (Regional Inference of Significant Kinships) is a next-generation tool for biological network annotation and visualization. It integrates community detection algorithms, rigorous overrepresentation analysis, and a modular framework for diverse network types. RISK identifies biologically coherent relationships within networks and generates publication-ready visualizations, making it a useful tool for biological and interdisciplinary network analysis.
 
@@ -60,14 +53,14 @@ For a full description of RISK and its applications, see:
 <br>
 **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
 <br>
-DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
+DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
 
 ## 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)
+- **Docs:** [https://riskportal.github.io/risk-docs](https://riskportal.github.io/risk-docs)
+- **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/risk-docs](https://github.com/riskportal/risk-docs)
 
 ## Installation
 
@@ -79,17 +72,17 @@ pip install risk-network --upgrade
 
 ## Key Features of RISK
 
-- **Broad Data Compatibility**: Accepts multiple network formats (NetworkX, Cytoscape, GPickle) and user-provided annotations formatted as term–to–gene membership tables (JSON, CSV, TSV, Excel, or Python dictionaries).
+- **Broad Data Compatibility**: Accepts multiple network formats (Cytoscape, Cytoscape JSON, GPickle, NetworkX) and user-provided annotations formatted as term–to–gene membership tables (JSON, CSV, TSV, Excel, Python dictionaries).
 - **Flexible Clustering**: Offers Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap, with user-defined resolution parameters to detect both coarse and fine-grained modules.
-- **Statistical Testing**: Provides hypergeometric, chi-squared, binomial, and permutation tests, balancing speed with statistical rigor.
-- **High-Resolution Visualization**: Generates publication-ready figures with contour overlays, customizable node/edge properties, and export to SVG, PNG, or PDF.
+- **Statistical Testing**: Provides permutation, hypergeometric, chi-squared, and binomial tests, balancing statistical rigor with speed.
+- **High-Resolution Visualization**: Generates publication-ready figures with customizable node/edge properties, contour overlays, and export to SVG, PNG, or PDF.
 
 ## Example Usage
 
-We applied RISK to a _Saccharomyces cerevisiae_ protein–protein interaction (PPI) network (Michaelis _et al_., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner _et al_., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity (P < 0.0001).
+We applied RISK to a _Saccharomyces cerevisiae_ protein–protein interaction (PPI) network (Michaelis _et al_., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner _et al_., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity.
 
-[![RISK analysis of the yeast PPI network](https://i.imgur.com/fSNf5Ad.jpeg)](https://i.imgur.com/fSNf5Ad.jpeg)
-**RISK workflow overview and analysis of the yeast PPI network**. GO BP terms are color-coded to represent key cellular processes—including ribosomal assembly, mitochondrial organization, and RNA polymerase activity (P < 0.0001).
+[![RISK analysis of the yeast PPI network](https://i.imgur.com/pasrVeR.jpeg)](https://i.imgur.com/pasrVeR.jpeg)
+**RISK workflow overview and analysis of the yeast PPI network**. Clusters are color-coded by enriched GO Biological Process terms (p < 0.01).
 
 ## Citation
 
@@ -97,18 +90,18 @@ If you use RISK in your research, please cite the following:
 
 **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
 <br>
-DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
+DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
 
 ## 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)
+- [Issues Tracker](https://github.com/riskportal/risk/issues)
+- [Source Code](https://github.com/riskportal/risk/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.
+If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/risk/issues) on GitHub.
 
 ## License
 

{risk_network-0.0.15b0 → risk_network-0.0.16b1}/README.md

@@ -1,17 +1,10 @@
-# RISK Network
-
-<p align="center">
-  <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
-</p>
-
-<br>
+# RISK
 
 ![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)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17257418.svg)](https://doi.org/10.5281/zenodo.17257418)
+![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
 
 **RISK** (Regional Inference of Significant Kinships) is a next-generation tool for biological network annotation and visualization. It integrates community detection algorithms, rigorous overrepresentation analysis, and a modular framework for diverse network types. RISK identifies biologically coherent relationships within networks and generates publication-ready visualizations, making it a useful tool for biological and interdisciplinary network analysis.
 
@@ -19,14 +12,14 @@ For a full description of RISK and its applications, see:
 <br>
 **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
 <br>
-DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
+DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
 
 ## 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)
+- **Docs:** [https://riskportal.github.io/risk-docs](https://riskportal.github.io/risk-docs)
+- **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/risk-docs](https://github.com/riskportal/risk-docs)
 
 ## Installation
 
@@ -38,17 +31,17 @@ pip install risk-network --upgrade
 
 ## Key Features of RISK
 
-- **Broad Data Compatibility**: Accepts multiple network formats (NetworkX, Cytoscape, GPickle) and user-provided annotations formatted as term–to–gene membership tables (JSON, CSV, TSV, Excel, or Python dictionaries).
+- **Broad Data Compatibility**: Accepts multiple network formats (Cytoscape, Cytoscape JSON, GPickle, NetworkX) and user-provided annotations formatted as term–to–gene membership tables (JSON, CSV, TSV, Excel, Python dictionaries).
 - **Flexible Clustering**: Offers Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap, with user-defined resolution parameters to detect both coarse and fine-grained modules.
-- **Statistical Testing**: Provides hypergeometric, chi-squared, binomial, and permutation tests, balancing speed with statistical rigor.
-- **High-Resolution Visualization**: Generates publication-ready figures with contour overlays, customizable node/edge properties, and export to SVG, PNG, or PDF.
+- **Statistical Testing**: Provides permutation, hypergeometric, chi-squared, and binomial tests, balancing statistical rigor with speed.
+- **High-Resolution Visualization**: Generates publication-ready figures with customizable node/edge properties, contour overlays, and export to SVG, PNG, or PDF.
 
 ## Example Usage
 
-We applied RISK to a _Saccharomyces cerevisiae_ protein–protein interaction (PPI) network (Michaelis _et al_., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner _et al_., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity (P < 0.0001).
+We applied RISK to a _Saccharomyces cerevisiae_ protein–protein interaction (PPI) network (Michaelis _et al_., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner _et al_., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity.
 
-[![RISK analysis of the yeast PPI network](https://i.imgur.com/fSNf5Ad.jpeg)](https://i.imgur.com/fSNf5Ad.jpeg)
-**RISK workflow overview and analysis of the yeast PPI network**. GO BP terms are color-coded to represent key cellular processes—including ribosomal assembly, mitochondrial organization, and RNA polymerase activity (P < 0.0001).
+[![RISK analysis of the yeast PPI network](https://i.imgur.com/pasrVeR.jpeg)](https://i.imgur.com/pasrVeR.jpeg)
+**RISK workflow overview and analysis of the yeast PPI network**. Clusters are color-coded by enriched GO Biological Process terms (p < 0.01).
 
 ## Citation
 
@@ -56,18 +49,18 @@ If you use RISK in your research, please cite the following:
 
 **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
 <br>
-DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
+DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
 
 ## 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)
+- [Issues Tracker](https://github.com/riskportal/risk/issues)
+- [Source Code](https://github.com/riskportal/risk/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.
+If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/risk/issues) on GitHub.
 
 ## License
 

{risk_network-0.0.15b0 → risk_network-0.0.16b1}/pyproject.toml

@@ -48,8 +48,8 @@ dependencies = [
 text = "GPL-3.0-or-later"
 
 [project.urls]
-Homepage = "https://github.com/riskportal/network"
-Issues = "https://github.com/riskportal/network/issues"
+Homepage = "https://github.com/riskportal/risk"
+Issues = "https://github.com/riskportal/risk/issues"
 
 [tool.setuptools]
 package-dir = {"" = "src"}

{risk_network-0.0.15b0 → risk_network-0.0.16b1}/src/risk/__init__.py

@@ -8,4 +8,4 @@ RISK: Regional Inference of Significant Kinships
 from ._risk import RISK
 
 __all__ = ["RISK"]
-__version__ = "0.0.15-beta.0"
+__version__ = "0.0.16-beta.1"

{risk_network-0.0.15b0 → risk_network-0.0.16b1}/src/risk/_annotation/_annotation.py

@@ -252,34 +252,28 @@ def get_weighted_description(words_column: pd.Series, scores_column: pd.Series)
             token_clean = re.sub(r"[^\w\-]", "", token).strip()
             if not token_clean:
                 continue
-            # Skip tokens that are pure numbers
-            if token_clean.isdigit():
-                continue
             # Skip stopwords
             if token_clean in STOP_WORDS:
                 continue
             # Lemmatize the token to merge similar forms
             token_norm = LEMMATIZER.lemmatize(token_clean)
-            weighted_counts[token_norm] = weighted_counts.get(token_norm, 0) + weight
+            # Apply weighting boost for biologically structured number-word hybrids
+            if re.match(r"^\d+[\-\w]+", token_norm):
+                actual_weight = int(weight * 1.5)
+            else:
+                actual_weight = weight
+            weighted_counts[token_norm] = weighted_counts.get(token_norm, 0) + actual_weight
 
     # Reconstruct a weighted token list by repeating each token by its aggregated count.
     weighted_words = []
     for token, count in weighted_counts.items():
         weighted_words.extend([token] * count)
 
-    # Combine tokens that match number-word patterns (e.g. "4-alpha") and remove pure numeric tokens.
+    # Combine tokens that match number-word patterns (e.g. "4-alpha"), but do not remove numeric tokens.
+    # All tokens are included in the final list.
     combined_tokens = []
     for token in weighted_words:
-        if re.match(r"^\d+-\w+", token):
-            combined_tokens.append(token)
-        elif token.replace(".", "", 1).isdigit():
-            continue
-        else:
-            combined_tokens.append(token)
-
-    # If the only token is numeric, return a default value.
-    if len(combined_tokens) == 1 and combined_tokens[0].isdigit():
-        return "N/A"
+        combined_tokens.append(token)
 
     # Simplify the token list to remove near-duplicates based on the Jaccard index.
     simplified_words = _simplify_word_list(combined_tokens)

{risk_network-0.0.15b0 → risk_network-0.0.16b1}/src/risk_network.egg-info/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.15b0
+Version: 0.0.16b1
 Summary: A Python package for scalable network analysis and high-quality visualization.
 Author-email: Ira Horecka <ira89@icloud.com>
 License: GPL-3.0-or-later
-Project-URL: Homepage, https://github.com/riskportal/network
-Project-URL: Issues, https://github.com/riskportal/network/issues
+Project-URL: Homepage, https://github.com/riskportal/risk
+Project-URL: Issues, https://github.com/riskportal/risk/issues
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -39,20 +39,13 @@ 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>
+# RISK
 
 ![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)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17257418.svg)](https://doi.org/10.5281/zenodo.17257418)
+![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
 
 **RISK** (Regional Inference of Significant Kinships) is a next-generation tool for biological network annotation and visualization. It integrates community detection algorithms, rigorous overrepresentation analysis, and a modular framework for diverse network types. RISK identifies biologically coherent relationships within networks and generates publication-ready visualizations, making it a useful tool for biological and interdisciplinary network analysis.
 
@@ -60,14 +53,14 @@ For a full description of RISK and its applications, see:
 <br>
 **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
 <br>
-DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
+DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
 
 ## 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)
+- **Docs:** [https://riskportal.github.io/risk-docs](https://riskportal.github.io/risk-docs)
+- **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/risk-docs](https://github.com/riskportal/risk-docs)
 
 ## Installation
 
@@ -79,17 +72,17 @@ pip install risk-network --upgrade
 
 ## Key Features of RISK
 
-- **Broad Data Compatibility**: Accepts multiple network formats (NetworkX, Cytoscape, GPickle) and user-provided annotations formatted as term–to–gene membership tables (JSON, CSV, TSV, Excel, or Python dictionaries).
+- **Broad Data Compatibility**: Accepts multiple network formats (Cytoscape, Cytoscape JSON, GPickle, NetworkX) and user-provided annotations formatted as term–to–gene membership tables (JSON, CSV, TSV, Excel, Python dictionaries).
 - **Flexible Clustering**: Offers Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap, with user-defined resolution parameters to detect both coarse and fine-grained modules.
-- **Statistical Testing**: Provides hypergeometric, chi-squared, binomial, and permutation tests, balancing speed with statistical rigor.
-- **High-Resolution Visualization**: Generates publication-ready figures with contour overlays, customizable node/edge properties, and export to SVG, PNG, or PDF.
+- **Statistical Testing**: Provides permutation, hypergeometric, chi-squared, and binomial tests, balancing statistical rigor with speed.
+- **High-Resolution Visualization**: Generates publication-ready figures with customizable node/edge properties, contour overlays, and export to SVG, PNG, or PDF.
 
 ## Example Usage
 
-We applied RISK to a _Saccharomyces cerevisiae_ protein–protein interaction (PPI) network (Michaelis _et al_., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner _et al_., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity (P < 0.0001).
+We applied RISK to a _Saccharomyces cerevisiae_ protein–protein interaction (PPI) network (Michaelis _et al_., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner _et al_., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity.
 
-[![RISK analysis of the yeast PPI network](https://i.imgur.com/fSNf5Ad.jpeg)](https://i.imgur.com/fSNf5Ad.jpeg)
-**RISK workflow overview and analysis of the yeast PPI network**. GO BP terms are color-coded to represent key cellular processes—including ribosomal assembly, mitochondrial organization, and RNA polymerase activity (P < 0.0001).
+[![RISK analysis of the yeast PPI network](https://i.imgur.com/pasrVeR.jpeg)](https://i.imgur.com/pasrVeR.jpeg)
+**RISK workflow overview and analysis of the yeast PPI network**. Clusters are color-coded by enriched GO Biological Process terms (p < 0.01).
 
 ## Citation
 
@@ -97,18 +90,18 @@ If you use RISK in your research, please cite the following:
 
 **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
 <br>
-DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
+DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
 
 ## 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)
+- [Issues Tracker](https://github.com/riskportal/risk/issues)
+- [Source Code](https://github.com/riskportal/risk/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.
+If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/risk/issues) on GitHub.
 
 ## License