risk-network 0.0.12b5__py3-none-any.whl → 0.0.13__py3-none-any.whl

risk/{risk.py → _risk.py}

@@ -1,18 +1,17 @@
 """
-risk/risk
-~~~~~~~~~
+risk/_risk
+~~~~~~~~~~
 """
 
-from risk.annotation.io import AnnotationIO
-from risk.log import params, set_global_verbosity
-from risk.neighborhoods.api import NeighborhoodsAPI
-from risk.network.graph.api import GraphAPI
-from risk.network.io import NetworkIO
-from risk.network.plotter.api import PlotterAPI
+from ._annotation import AnnotationIO
+from ._log import params, set_global_verbosity
+from ._neighborhoods import NeighborhoodsAPI
+from ._network import GraphAPI, NetworkIO, PlotterAPI
 
 
 class RISK(NetworkIO, AnnotationIO, NeighborhoodsAPI, GraphAPI, PlotterAPI):
-    """RISK: A class for network analysis and visualization.
+    """
+    RISK: A class for network analysis and visualization.
 
     The RISK class integrates functionalities for loading networks, processing annotations,
     performing network-based statistical analysis to quantify neighborhood relationships,
@@ -20,7 +19,8 @@ class RISK(NetworkIO, AnnotationIO, NeighborhoodsAPI, GraphAPI, PlotterAPI):
     """
 
     def __init__(self, verbose: bool = True):
-        """Initialize the RISK class with configuration settings.
+        """
+        Initialize the RISK class with configuration settings.
 
         Args:
             verbose (bool): If False, suppresses all log messages to the console. Defaults to True.

{risk_network-0.0.12b5.dist-info → risk_network-0.0.13.dist-info}/METADATA

@@ -1,12 +1,15 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.12b5
-Summary: A Python package for biological network analysis
+Version: 0.0.13
+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
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
@@ -15,7 +18,6 @@ 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
@@ -88,9 +90,10 @@ This figure highlights RISK’s capability to detect both established and novel
 
 ## Citation
 
-If you use RISK in your research, please cite:
+If you use RISK in your research, please reference the following:
 
-**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)
+**Horecka et al.**, *"RISK: a next-generation tool for biological network annotation and visualization"*, 2025.  
+DOI: [10.1234/zenodo.xxxxxxx](https://doi.org/10.1234/zenodo.xxxxxxx)
 
 ## Software Architecture and Implementation
 

risk_network-0.0.13.dist-info/RECORD

@@ -0,0 +1,41 @@
+risk/__init__.py,sha256=Y0rk2EiC_FcwBuFYXEgu_LSMu_XyyG75UN5Rc2ZI9Dw,136
+risk/_risk.py,sha256=b8IPc45lGuzgq5tWPO6EJpuan0nvV58XOTMiL_SEOPE,1042
+risk/_annotation/__init__.py,sha256=LBLL5P_MdfwWaxkHBQHfQTPY-FF8hIGoUGKyHF1Wg4s,159
+risk/_annotation/_annotation.py,sha256=03vcnkdi4HGH5UUyokUyOdyyjXOLoKSmLFuK7VAl41c,15174
+risk/_annotation/_io.py,sha256=gEq6STSWFIFjSWoGXJfwxTME4GDJZTOgPeXZABgSdXc,12447
+risk/_annotation/_nltk_setup.py,sha256=aHHnElLOKiouVDrZ3uON0CSFmBxvzmYfjYPi07v2rJM,3584
+risk/_log/__init__.py,sha256=LX6BsfcGOH0RbAdQaUmIU-LVMmArDdKwn0jFtj45FYo,205
+risk/_log/_console.py,sha256=1jSFzY3w0-vVqIBCgc-IhyJPNT6vRg8GSGxhyw_D9MI,4653
+risk/_log/_parameters.py,sha256=8FkeeBtULDFVw3UijLArK-G3OIjy6YXyRXmPPckK7fU,5893
+risk/_neighborhoods/__init__.py,sha256=eKwjpEUKSUmAirRZ_qPTVF7MLkvhCn_fulPVq158wM8,185
+risk/_neighborhoods/_api.py,sha256=6vt25y38wSvEhMvNxy9Rl-CrQc9ARSuvGwexWagg5z0,23344
+risk/_neighborhoods/_community.py,sha256=Tr-EHO91EWbMmNr_z21UCngiqWOlWIqcjwBig_VXI8c,17850
+risk/_neighborhoods/_domains.py,sha256=He8G2-E9-yYQB8ChUtMFr51HVlfRj5EaxGu3sGVNUCo,14630
+risk/_neighborhoods/_neighborhoods.py,sha256=9H7BickJx9GdnOo5d5wpdtXkcWyvzq2w6FAy1rwLBtk,20614
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+risk/_neighborhoods/_stats/_permutation/_test_functions.py,sha256=lGI_MkdbW4UHI0jWN_T1OattRjXrq_qmzAmOfels670,3165
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+risk_network-0.0.13.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.13.dist-info/RECORD,,

{risk_network-0.0.12b5.dist-info → risk_network-0.0.13.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.0.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

risk/annotation/__init__.py

@@ -1,10 +0,0 @@
-"""
-risk/annotation
-~~~~~~~~~~~~~~~
-"""
-
-from risk.annotation.annotation import (
-    define_top_annotation,
-    get_weighted_description,
-)
-from risk.annotation.io import AnnotationIO

risk/log/__init__.py

@@ -1,11 +0,0 @@
-"""
-risk/log
-~~~~~~~~
-"""
-
-from risk.log.console import log_header, logger, set_global_verbosity
-from risk.log.parameters import Params
-
-# Initialize the global parameters logger
-params = Params()
-params.initialize()

risk/neighborhoods/__init__.py

@@ -1,7 +0,0 @@
-"""
-risk/neighborhoods
-~~~~~~~~~~~~~~~~~~
-"""
-
-from risk.neighborhoods.domains import define_domains, trim_domains
-from risk.neighborhoods.neighborhoods import process_neighborhoods

risk/neighborhoods/stats/__init__.py

@@ -1,13 +0,0 @@
-"""
-risk/neighborhoods/stats
-~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from risk.neighborhoods.stats.permutation import compute_permutation_test
-from risk.neighborhoods.stats.tests import (
-    compute_binom_test,
-    compute_chi2_test,
-    compute_hypergeom_test,
-    compute_poisson_test,
-    compute_zscore_test,
-)

risk/neighborhoods/stats/permutation/__init__.py

@@ -1,6 +0,0 @@
-"""
-risk/neighborhoods/stats/permutation
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from risk.neighborhoods.stats.permutation.permutation import compute_permutation_test

risk/network/__init__.py

@@ -1,4 +0,0 @@
-"""
-risk/network
-~~~~~~~~~~~~
-"""

risk/network/graph/__init__.py

@@ -1,4 +0,0 @@
-"""
-risk/network/graph
-~~~~~~~~~~~~~~~~~~
-"""

risk/network/plotter/__init__.py

@@ -1,4 +0,0 @@
-"""
-risk/network/plotter
-~~~~~~~~~~~~~~~~~~~~
-"""

risk_network-0.0.12b5.dist-info/RECORD

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