risk-network 0.0.15__tar.gz → 0.0.15b0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (53) hide show
  1. {risk_network-0.0.15/src/risk_network.egg-info → risk_network-0.0.15b0}/PKG-INFO +19 -13
  2. {risk_network-0.0.15 → risk_network-0.0.15b0}/README.md +16 -10
  3. {risk_network-0.0.15 → risk_network-0.0.15b0}/pyproject.toml +2 -2
  4. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/__init__.py +1 -1
  5. {risk_network-0.0.15 → risk_network-0.0.15b0/src/risk_network.egg-info}/PKG-INFO +19 -13
  6. {risk_network-0.0.15 → risk_network-0.0.15b0}/LICENSE +0 -0
  7. {risk_network-0.0.15 → risk_network-0.0.15b0}/setup.cfg +0 -0
  8. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_annotation/__init__.py +0 -0
  9. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_annotation/_annotation.py +0 -0
  10. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_annotation/_io.py +0 -0
  11. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_annotation/_nltk_setup.py +0 -0
  12. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_log/__init__.py +0 -0
  13. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_log/_console.py +0 -0
  14. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_log/_parameters.py +0 -0
  15. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/__init__.py +0 -0
  16. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_api.py +0 -0
  17. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_community.py +0 -0
  18. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_domains.py +0 -0
  19. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_neighborhoods.py +0 -0
  20. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_stats/__init__.py +0 -0
  21. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_stats/_permutation/__init__.py +0 -0
  22. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_stats/_permutation/_permutation.py +0 -0
  23. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_stats/_permutation/_test_functions.py +0 -0
  24. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_neighborhoods/_stats/_tests.py +0 -0
  25. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/__init__.py +0 -0
  26. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_graph/__init__.py +0 -0
  27. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_graph/_api.py +0 -0
  28. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_graph/_graph.py +0 -0
  29. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_graph/_stats.py +0 -0
  30. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_graph/_summary.py +0 -0
  31. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_io.py +0 -0
  32. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/__init__.py +0 -0
  33. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_api.py +0 -0
  34. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_canvas.py +0 -0
  35. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_contour.py +0 -0
  36. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_labels.py +0 -0
  37. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_network.py +0 -0
  38. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_plotter.py +0 -0
  39. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_utils/__init__.py +0 -0
  40. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_utils/_colors.py +0 -0
  41. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_network/_plotter/_utils/_layout.py +0 -0
  42. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/_risk.py +0 -0
  43. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk_network.egg-info/SOURCES.txt +0 -0
  44. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk_network.egg-info/dependency_links.txt +0 -0
  45. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk_network.egg-info/requires.txt +0 -0
  46. {risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk_network.egg-info/top_level.txt +0 -0
  47. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_load_annotation.py +0 -0
  48. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_load_graph.py +0 -0
  49. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_load_io_combinations.py +0 -0
  50. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_load_neighborhoods.py +0 -0
  51. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_load_network.py +0 -0
  52. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_load_plotter.py +0 -0
  53. {risk_network-0.0.15 → risk_network-0.0.15b0}/tests/test_log.py +0 -0
{risk_network-0.0.15/src/risk_network.egg-info → risk_network-0.0.15b0}/PKG-INFO RENAMED
@@ -1,11 +1,11 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: risk-network
3
- Version: 0.0.15
3
+ Version: 0.0.15b0
4
4
  Summary: A Python package for scalable network analysis and high-quality visualization.
5
5
  Author-email: Ira Horecka <ira89@icloud.com>
6
6
  License: GPL-3.0-or-later
7
- Project-URL: Homepage, https://github.com/riskportal/risk
8
- Project-URL: Issues, https://github.com/riskportal/risk/issues
7
+ Project-URL: Homepage, https://github.com/riskportal/network
8
+ Project-URL: Issues, https://github.com/riskportal/network/issues
9
9
  Classifier: Development Status :: 4 - Beta
10
10
  Classifier: Intended Audience :: Developers
11
11
  Classifier: Intended Audience :: Science/Research
@@ -39,14 +39,20 @@ Requires-Dist: threadpoolctl
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  Requires-Dist: tqdm
40
40
  Dynamic: license-file
41
41
 
42
- # RISK
42
+ # RISK Network
43
+
44
+ <p align="center">
45
+ <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
46
+ </p>
47
+
48
+ <br>
43
49
 
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  ![Python](https://img.shields.io/badge/python-3.8%2B-yellow)
45
51
  [![pypiv](https://img.shields.io/pypi/v/risk-network.svg)](https://pypi.python.org/pypi/risk-network)
46
52
  ![License](https://img.shields.io/badge/license-GPLv3-purple)
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53
  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.xxxxxxx.svg)](https://doi.org/10.5281/zenodo.xxxxxxx)
48
54
  ![Downloads](https://img.shields.io/pypi/dm/risk-network)
49
- ![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
55
+ ![Tests](https://github.com/riskportal/network/actions/workflows/ci.yml/badge.svg)
50
56
 
51
57
  **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.
52
58
 
@@ -60,8 +66,8 @@ DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
60
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61
67
  Full documentation is available at:
62
68
 
63
- - **Docs:** [https://riskportal.github.io/risk-docs](https://riskportal.github.io/risk-docs)
64
- - **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/risk-docs](https://github.com/riskportal/risk-docs)
69
+ - **Docs:** [https://riskportal.github.io/network-tutorial](https://riskportal.github.io/network-tutorial)
70
+ - **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/network-tutorial](https://github.com/riskportal/network-tutorial)
65
71
 
66
72
  ## Installation
67
73
 
@@ -73,10 +79,10 @@ pip install risk-network --upgrade
73
79
 
74
80
  ## Key Features of RISK
75
81
 
76
- - **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).
82
+ - **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).
77
83
  - **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.
78
- - **Statistical Testing**: Provides permutation, hypergeometric, chi-squared, and binomial tests, balancing statistical rigor with speed.
79
- - **High-Resolution Visualization**: Generates publication-ready figures with customizable node/edge properties, contour overlays, and export to SVG, PNG, or PDF.
84
+ - **Statistical Testing**: Provides hypergeometric, chi-squared, binomial, and permutation tests, balancing speed with statistical rigor.
85
+ - **High-Resolution Visualization**: Generates publication-ready figures with contour overlays, customizable node/edge properties, and export to SVG, PNG, or PDF.
80
86
 
81
87
  ## Example Usage
82
88
 
@@ -97,12 +103,12 @@ DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
97
103
 
98
104
  We welcome contributions from the community:
99
105
 
100
- - [Issues Tracker](https://github.com/riskportal/risk/issues)
101
- - [Source Code](https://github.com/riskportal/risk/tree/main/risk)
106
+ - [Issues Tracker](https://github.com/riskportal/network/issues)
107
+ - [Source Code](https://github.com/riskportal/network/tree/main/risk)
102
108
 
103
109
  ## Support
104
110
 
105
- If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/risk/issues) on GitHub.
111
+ If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/network/issues) on GitHub.
106
112
 
107
113
  ## License
108
114
 
{risk_network-0.0.15 → risk_network-0.0.15b0}/README.md RENAMED
@@ -1,11 +1,17 @@
1
- # RISK
1
+ # RISK Network
2
+
3
+ <p align="center">
4
+ <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
5
+ </p>
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+
7
+ <br>
2
8
 
3
9
  ![Python](https://img.shields.io/badge/python-3.8%2B-yellow)
4
10
  [![pypiv](https://img.shields.io/pypi/v/risk-network.svg)](https://pypi.python.org/pypi/risk-network)
5
11
  ![License](https://img.shields.io/badge/license-GPLv3-purple)
6
12
  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.xxxxxxx.svg)](https://doi.org/10.5281/zenodo.xxxxxxx)
7
13
  ![Downloads](https://img.shields.io/pypi/dm/risk-network)
8
- ![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
14
+ ![Tests](https://github.com/riskportal/network/actions/workflows/ci.yml/badge.svg)
9
15
 
10
16
  **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.
11
17
 
@@ -19,8 +25,8 @@ DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
19
25
 
20
26
  Full documentation is available at:
21
27
 
22
- - **Docs:** [https://riskportal.github.io/risk-docs](https://riskportal.github.io/risk-docs)
23
- - **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/risk-docs](https://github.com/riskportal/risk-docs)
28
+ - **Docs:** [https://riskportal.github.io/network-tutorial](https://riskportal.github.io/network-tutorial)
29
+ - **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/network-tutorial](https://github.com/riskportal/network-tutorial)
24
30
 
25
31
  ## Installation
26
32
 
@@ -32,10 +38,10 @@ pip install risk-network --upgrade
32
38
 
33
39
  ## Key Features of RISK
34
40
 
35
- - **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).
41
+ - **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).
36
42
  - **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.
37
- - **Statistical Testing**: Provides permutation, hypergeometric, chi-squared, and binomial tests, balancing statistical rigor with speed.
38
- - **High-Resolution Visualization**: Generates publication-ready figures with customizable node/edge properties, contour overlays, and export to SVG, PNG, or PDF.
43
+ - **Statistical Testing**: Provides hypergeometric, chi-squared, binomial, and permutation tests, balancing speed with statistical rigor.
44
+ - **High-Resolution Visualization**: Generates publication-ready figures with contour overlays, customizable node/edge properties, and export to SVG, PNG, or PDF.
39
45
 
40
46
  ## Example Usage
41
47
 
@@ -56,12 +62,12 @@ DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
56
62
 
57
63
  We welcome contributions from the community:
58
64
 
59
- - [Issues Tracker](https://github.com/riskportal/risk/issues)
60
- - [Source Code](https://github.com/riskportal/risk/tree/main/risk)
65
+ - [Issues Tracker](https://github.com/riskportal/network/issues)
66
+ - [Source Code](https://github.com/riskportal/network/tree/main/risk)
61
67
 
62
68
  ## Support
63
69
 
64
- If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/risk/issues) on GitHub.
70
+ If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/network/issues) on GitHub.
65
71
 
66
72
  ## License
67
73
 
{risk_network-0.0.15 → risk_network-0.0.15b0}/pyproject.toml RENAMED
@@ -48,8 +48,8 @@ dependencies = [
48
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  text = "GPL-3.0-or-later"
49
49
 
50
50
  [project.urls]
51
- Homepage = "https://github.com/riskportal/risk"
52
- Issues = "https://github.com/riskportal/risk/issues"
51
+ Homepage = "https://github.com/riskportal/network"
52
+ Issues = "https://github.com/riskportal/network/issues"
53
53
 
54
54
  [tool.setuptools]
55
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  package-dir = {"" = "src"}
{risk_network-0.0.15 → risk_network-0.0.15b0}/src/risk/__init__.py RENAMED
@@ -8,4 +8,4 @@ RISK: Regional Inference of Significant Kinships
8
8
  from ._risk import RISK
9
9
 
10
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  __all__ = ["RISK"]
11
- __version__ = "0.0.15"
11
+ __version__ = "0.0.15-beta.0"
{risk_network-0.0.15 → risk_network-0.0.15b0/src/risk_network.egg-info}/PKG-INFO RENAMED
@@ -1,11 +1,11 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: risk-network
3
- Version: 0.0.15
3
+ Version: 0.0.15b0
4
4
  Summary: A Python package for scalable network analysis and high-quality visualization.
5
5
  Author-email: Ira Horecka <ira89@icloud.com>
6
6
  License: GPL-3.0-or-later
7
- Project-URL: Homepage, https://github.com/riskportal/risk
8
- Project-URL: Issues, https://github.com/riskportal/risk/issues
7
+ Project-URL: Homepage, https://github.com/riskportal/network
8
+ Project-URL: Issues, https://github.com/riskportal/network/issues
9
9
  Classifier: Development Status :: 4 - Beta
10
10
  Classifier: Intended Audience :: Developers
11
11
  Classifier: Intended Audience :: Science/Research
@@ -39,14 +39,20 @@ Requires-Dist: threadpoolctl
39
39
  Requires-Dist: tqdm
40
40
  Dynamic: license-file
41
41
 
42
- # RISK
42
+ # RISK Network
43
+
44
+ <p align="center">
45
+ <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
46
+ </p>
47
+
48
+ <br>
43
49
 
44
50
  ![Python](https://img.shields.io/badge/python-3.8%2B-yellow)
45
51
  [![pypiv](https://img.shields.io/pypi/v/risk-network.svg)](https://pypi.python.org/pypi/risk-network)
46
52
  ![License](https://img.shields.io/badge/license-GPLv3-purple)
47
53
  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.xxxxxxx.svg)](https://doi.org/10.5281/zenodo.xxxxxxx)
48
54
  ![Downloads](https://img.shields.io/pypi/dm/risk-network)
49
- ![Tests](https://github.com/riskportal/risk/actions/workflows/ci.yml/badge.svg)
55
+ ![Tests](https://github.com/riskportal/network/actions/workflows/ci.yml/badge.svg)
50
56
 
51
57
  **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.
52
58
 
@@ -60,8 +66,8 @@ DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
60
66
 
61
67
  Full documentation is available at:
62
68
 
63
- - **Docs:** [https://riskportal.github.io/risk-docs](https://riskportal.github.io/risk-docs)
64
- - **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/risk-docs](https://github.com/riskportal/risk-docs)
69
+ - **Docs:** [https://riskportal.github.io/network-tutorial](https://riskportal.github.io/network-tutorial)
70
+ - **Tutorial Jupyter Notebook Repository:** [https://github.com/riskportal/network-tutorial](https://github.com/riskportal/network-tutorial)
65
71
 
66
72
  ## Installation
67
73
 
@@ -73,10 +79,10 @@ pip install risk-network --upgrade
73
79
 
74
80
  ## Key Features of RISK
75
81
 
76
- - **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).
82
+ - **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).
77
83
  - **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.
78
- - **Statistical Testing**: Provides permutation, hypergeometric, chi-squared, and binomial tests, balancing statistical rigor with speed.
79
- - **High-Resolution Visualization**: Generates publication-ready figures with customizable node/edge properties, contour overlays, and export to SVG, PNG, or PDF.
84
+ - **Statistical Testing**: Provides hypergeometric, chi-squared, binomial, and permutation tests, balancing speed with statistical rigor.
85
+ - **High-Resolution Visualization**: Generates publication-ready figures with contour overlays, customizable node/edge properties, and export to SVG, PNG, or PDF.
80
86
 
81
87
  ## Example Usage
82
88
 
@@ -97,12 +103,12 @@ DOI: [10.5281/zenodo.xxxxxxx](https://doi.org/10.5281/zenodo.xxxxxxx)
97
103
 
98
104
  We welcome contributions from the community:
99
105
 
100
- - [Issues Tracker](https://github.com/riskportal/risk/issues)
101
- - [Source Code](https://github.com/riskportal/risk/tree/main/risk)
106
+ - [Issues Tracker](https://github.com/riskportal/network/issues)
107
+ - [Source Code](https://github.com/riskportal/network/tree/main/risk)
102
108
 
103
109
  ## Support
104
110
 
105
- If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/risk/issues) on GitHub.
111
+ If you encounter issues or have suggestions for new features, please use the [Issues Tracker](https://github.com/riskportal/network/issues) on GitHub.
106
112
 
107
113
  ## License
108
114
 
{risk_network-0.0.15 → risk_network-0.0.15b0}/LICENSE RENAMED
File without changes
{risk_network-0.0.15 → risk_network-0.0.15b0}/setup.cfg RENAMED
File without changes