risk-network 0.0.15__py3-none-any.whl → 0.0.16b0__py3-none-any.whl

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Files changed (7) hide show
  1. risk/__init__.py +1 -1
  2. risk/_annotation/_annotation.py +0 -3
  3. {risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/METADATA +7 -8
  4. {risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/RECORD +7 -7
  5. {risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/WHEEL +0 -0
  6. {risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/licenses/LICENSE +0 -0
  7. {risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/top_level.txt +0 -0
risk/__init__.py CHANGED
@@ -8,4 +8,4 @@ RISK: Regional Inference of Significant Kinships
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  from ._risk import RISK
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  __all__ = ["RISK"]
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- __version__ = "0.0.15"
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+ __version__ = "0.0.16-beta.0"
risk/_annotation/_annotation.py CHANGED
@@ -252,9 +252,6 @@ def get_weighted_description(words_column: pd.Series, scores_column: pd.Series)
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  token_clean = re.sub(r"[^\w\-]", "", token).strip()
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  if not token_clean:
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  continue
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- # Skip tokens that are pure numbers
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- if token_clean.isdigit():
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- continue
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  # Skip stopwords
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  if token_clean in STOP_WORDS:
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  continue
{risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: risk-network
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- Version: 0.0.15
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+ Version: 0.0.16b0
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  Summary: A Python package for scalable network analysis and high-quality visualization.
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  Author-email: Ira Horecka <ira89@icloud.com>
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  License: GPL-3.0-or-later
@@ -44,8 +44,7 @@ Dynamic: license-file
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  ![Python](https://img.shields.io/badge/python-3.8%2B-yellow)
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  [![pypiv](https://img.shields.io/pypi/v/risk-network.svg)](https://pypi.python.org/pypi/risk-network)
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  ![License](https://img.shields.io/badge/license-GPLv3-purple)
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- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.xxxxxxx.svg)](https://doi.org/10.5281/zenodo.xxxxxxx)
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- ![Downloads](https://img.shields.io/pypi/dm/risk-network)
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+ [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17257418.svg)](https://doi.org/10.5281/zenodo.17257418)
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  ![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
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  **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.
@@ -54,7 +53,7 @@ For a full description of RISK and its applications, see:
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  <br>
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  **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
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  <br>
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- DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
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+ DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
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  ## Documentation and Tutorial
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@@ -80,10 +79,10 @@ pip install risk-network --upgrade
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  ## Example Usage
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- 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).
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+ 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.
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- [![RISK analysis of the yeast PPI network](https://i.imgur.com/fSNf5Ad.jpeg)](https://i.imgur.com/fSNf5Ad.jpeg)
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- **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).
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+ [![RISK analysis of the yeast PPI network](https://i.imgur.com/pasrVeR.jpeg)](https://i.imgur.com/pasrVeR.jpeg)
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+ **RISK workflow overview and analysis of the yeast PPI network**. Clusters are color-coded by enriched GO Biological Process terms (p < 0.01).
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  ## Citation
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@@ -91,7 +90,7 @@ If you use RISK in your research, please cite the following:
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  **Horecka and Röst (2025)**, _"RISK: a next-generation tool for biological network annotation and visualization"_.
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  <br>
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- DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
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+ DOI: [10.5281/zenodo.17257418](https://doi.org/10.5281/zenodo.17257418)
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  ## Contributing
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{risk_network-0.0.15.dist-info → risk_network-0.0.16b0.dist-info}/RECORD RENAMED
@@ -1,7 +1,7 @@
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- risk/__init__.py,sha256=XXYfTIS7rMH0d7BtRqnU9BgUTlsbGb-ZDHV8bs7wekc,136
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+ risk/__init__.py,sha256=knyE98-BvAZ9sTJDMZ1TNr73YaAC-gqL_0Q1rKvwAHU,143
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  risk/_risk.py,sha256=VULCdM41BlWKM1ou4Qc579ffZ9dMZkfhAwKYgbaEeKM,1054
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  risk/_annotation/__init__.py,sha256=zr7w1DHkmvrkKFGKdPhrcvZHV-xsfd5TZOaWtFiP4Dc,164
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- risk/_annotation/_annotation.py,sha256=03vcnkdi4HGH5UUyokUyOdyyjXOLoKSmLFuK7VAl41c,15174
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+ risk/_annotation/_annotation.py,sha256=psPRC7q4DjXIvpgmE3VLzHYElLarJTJhQpclesz2W0Q,15063
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  risk/_annotation/_io.py,sha256=xic3dkEA54X82HbyWfCiXrUpAhPWFPBZ69R8jw31omQ,12457
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  risk/_annotation/_nltk_setup.py,sha256=aHHnElLOKiouVDrZ3uON0CSFmBxvzmYfjYPi07v2rJM,3584
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  risk/_log/__init__.py,sha256=LX6BsfcGOH0RbAdQaUmIU-LVMmArDdKwn0jFtj45FYo,205
@@ -34,8 +34,8 @@ risk/_network/_plotter/_plotter.py,sha256=F2hw-spUdsXjvuG36o0YFR3Pnd-CZOHYUq4vW0
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  risk/_network/_plotter/_utils/__init__.py,sha256=JXgjKiBWvXx0X2IeFnrOh5YZQGQoELbhJZ0Zh2mFEOo,211
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  risk/_network/_plotter/_utils/_colors.py,sha256=JCliSvz8_-TsjilaRHSEsqdXFBUYlzhXKOSRGdCm9Kw,19177
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  risk/_network/_plotter/_utils/_layout.py,sha256=GyGLc2U1WWUVL1Te9uPi_CLqlW_E4TImXRAL5TeA5D8,3633
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- risk_network-0.0.15.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
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- risk_network-0.0.15.dist-info/METADATA,sha256=20u6GupvvgFm16zUW2mPlYWz3V-FuxC-303GOvFxiKM,5542
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- risk_network-0.0.15.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- risk_network-0.0.15.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
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- risk_network-0.0.15.dist-info/RECORD,,
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+ risk_network-0.0.16b0.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
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+ risk_network-0.0.16b0.dist-info/METADATA,sha256=RyO3f1BZDQnREPp3my6tw6JI8Y4oFzY3gBDwEO10zL8,5390
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+ risk_network-0.0.16b0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ risk_network-0.0.16b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
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+ risk_network-0.0.16b0.dist-info/RECORD,,