risk-network 0.0.13b5__py3-none-any.whl → 0.0.14b1__py3-none-any.whl

risk/__init__.py

@@ -5,7 +5,7 @@ risk
 RISK: Regional Inference of Significant Kinships
 """
 
-from .risk import RISK
+from ._risk import RISK
 
 __all__ = ["RISK"]
-__version__ = "0.0.13-beta.5"
+__version__ = "0.0.14-beta.1"

risk/_annotation/__init__.py

@@ -7,4 +7,4 @@ from ._annotation import (
     define_top_annotation,
     get_weighted_description,
 )
-from ._io import AnnotationIO
+from ._io import AnnotationHandler

risk/_annotation/_io.py

@@ -13,11 +13,11 @@ from .._log import log_header, logger, params
 from ._annotation import load_annotation
 
 
-class AnnotationIO:
+class AnnotationHandler:
     """
     Handles the loading and exporting of annotation in various file formats.
 
-    The AnnotationIO class provides methods to load annotation from different file types (JSON, CSV, Excel, etc.)
+    The AnnotationHandler class provides methods to load annotation from different file types (JSON, CSV, Excel, etc.)
     and to export parameter data to various formats like JSON, CSV, and text files.
     """
 

risk/_neighborhoods/_api.py

@@ -29,9 +29,6 @@ class NeighborhoodsAPI:
     The NeighborhoodsAPI class provides methods to load neighborhood results from statistical tests.
     """
 
-    def __init__(self) -> None:
-        pass
-
     def load_neighborhoods_binom(
         self,
         network: nx.Graph,

risk/_network/__init__.py

@@ -4,5 +4,5 @@ risk/_network
 """
 
 from ._graph import GraphAPI
-from ._io import NetworkIO
+from ._io import NetworkAPI
 from ._plotter import PlotterAPI

risk/_network/_graph/_api.py

@@ -27,9 +27,6 @@ class GraphAPI:
     The GraphAPI class provides methods to load and process network graphs, annotations, and neighborhoods.
     """
 
-    def __init__(self) -> None:
-        pass
-
     def load_graph(
         self,
         network: nx.Graph,

risk/_network/_io.py

@@ -18,114 +18,188 @@ import pandas as pd
 from .._log import log_header, logger, params
 
 
-class NetworkIO:
+class NetworkAPI:
     """
-    A class for loading, processing, and managing network data.
-
-    The NetworkIO class provides methods to load network data from various formats (e.g., GPickle, NetworkX)
-    and process the network by adjusting node coordinates, calculating edge lengths, and validating graph structure.
+    Public-facing interface for loading and initializing network data.
+    Delegates to the NetworkIO worker class for actual I/O and processing.
     """
 
-    def __init__(
+    def load_network_gpickle(
         self,
+        filepath: str,
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-    ):
+    ) -> nx.Graph:
         """
-        Initialize the NetworkIO class.
+        Load a network from a GPickle file via NetworkIO.
 
         Args:
-            compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
-            surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
-            min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
+            filepath (str): Path to the GPickle file.
+            compute_sphere (bool, optional): Override or use API default. Defaults to True.
+            surface_depth (float, optional): Override or use API default. Defaults to 0.0.
+            min_edges_per_node (int, optional): Override or use API default. Defaults to 0.
+        Returns:
+            nx.Graph: Loaded and processed network.
         """
-        self.compute_sphere = compute_sphere
-        self.surface_depth = surface_depth
-        self.min_edges_per_node = min_edges_per_node
-        # Log the initialization of the NetworkIO class
-        params.log_network(
+        io = NetworkIO(
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
         )
+        return io.load_network_gpickle(filepath=filepath)
 
-    def load_network_gpickle(
+    def load_network_networkx(
         self,
-        filepath: str,
+        network: nx.Graph,
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
         """
-        Load a network from a GPickle file.
+        Load a NetworkX graph via NetworkIO.
 
         Args:
-            filepath (str): Path to the GPickle file.
-            compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
-            surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
-            min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
+            network (nx.Graph): A NetworkX graph object.
+            compute_sphere (bool, optional): Override or use API default. Defaults to True.
+            surface_depth (float, optional): Override or use API default. Defaults to 0.0.
+            min_edges_per_node (int, optional): Override or use API default. Defaults to 0.
+        Returns:
+            nx.Graph: Processed network.
+        """
+        io = NetworkIO(
+            compute_sphere=compute_sphere,
+            surface_depth=surface_depth,
+            min_edges_per_node=min_edges_per_node,
+        )
+        return io.load_network_networkx(network=network)
+
+    def load_network_cytoscape(
+        self,
+        filepath: str,
+        source_label: str = "source",
+        target_label: str = "target",
+        view_name: str = "",
+        compute_sphere: bool = True,
+        surface_depth: float = 0.0,
+        min_edges_per_node: int = 0,
+    ) -> nx.Graph:
+        """
+        Load a network from a Cytoscape file via NetworkIO.
 
+        Args:
+            filepath (str): Path to the Cytoscape file.
+            source_label (str, optional): Source node label. Defaults to "source".
+            target_label (str, optional): Target node label. Defaults to "target".
+            view_name (str, optional): Specific view name to load. Defaults to "".
+            compute_sphere (bool, optional): Override or use API default. Defaults to True.
+            surface_depth (float, optional): Override or use API default. Defaults to 0.0.
+            min_edges_per_node (int, optional): Override or use API default. Defaults to 0.
         Returns:
             nx.Graph: Loaded and processed network.
         """
-        networkio = NetworkIO(
+        io = NetworkIO(
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
         )
-        return networkio._load_network_gpickle(filepath=filepath)
+        return io.load_network_cytoscape(
+            filepath=filepath,
+            source_label=source_label,
+            target_label=target_label,
+            view_name=view_name,
+        )
 
-    def _load_network_gpickle(self, filepath: str) -> nx.Graph:
+    def load_network_cyjs(
+        self,
+        filepath: str,
+        source_label: str = "source",
+        target_label: str = "target",
+        compute_sphere: bool = True,
+        surface_depth: float = 0.0,
+        min_edges_per_node: int = 0,
+    ) -> nx.Graph:
         """
-        Private method to load a network from a GPickle file.
+        Load a network from a Cytoscape JSON (.cyjs) file via NetworkIO.
 
         Args:
-            filepath (str): Path to the GPickle file.
-
+            filepath (str): Path to the Cytoscape JSON file.
+            source_label (str, optional): Source node label. Defaults to "source".
+            target_label (str, optional): Target node label. Defaults to "target".
+            compute_sphere (bool, optional): Override or use API default. Defaults to True.
+            surface_depth (float, optional): Override or use API default. Defaults to 0.0.
+            min_edges_per_node (int, optional): Override or use API default. Defaults to 0.
         Returns:
             nx.Graph: Loaded and processed network.
         """
-        filetype = "GPickle"
-        # Log the loading of the GPickle file
-        params.log_network(filetype=filetype, filepath=filepath)
-        self._log_loading_network(filetype, filepath=filepath)
+        io = NetworkIO(
+            compute_sphere=compute_sphere,
+            surface_depth=surface_depth,
+            min_edges_per_node=min_edges_per_node,
+        )
+        return io.load_network_cyjs(
+            filepath=filepath,
+            source_label=source_label,
+            target_label=target_label,
+        )
 
-        with open(filepath, "rb") as f:
-            G = pickle.load(f)
 
-        # Initialize the graph
-        return self._initialize_graph(G)
+class NetworkIO:
+    """
+    A class for loading, processing, and managing network data.
 
-    def load_network_networkx(
+    The NetworkIO class provides methods to load network data from various formats (e.g., GPickle, NetworkX)
+    and process the network by adjusting node coordinates, calculating edge lengths, and validating graph structure.
+    """
+
+    def __init__(
         self,
-        network: nx.Graph,
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-    ) -> nx.Graph:
+    ):
         """
-        Load a NetworkX graph.
+        Initialize the NetworkIO class.
 
         Args:
-            network (nx.Graph): A NetworkX graph object.
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
             min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-
-        Returns:
-            nx.Graph: Loaded and processed network.
         """
-        networkio = NetworkIO(
+        self.compute_sphere = compute_sphere
+        self.surface_depth = surface_depth
+        self.min_edges_per_node = min_edges_per_node
+        # Log the initialization of the NetworkIO class
+        params.log_network(
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
         )
-        return networkio._load_network_networkx(network=network)
 
-    def _load_network_networkx(self, network: nx.Graph) -> nx.Graph:
+    def load_network_gpickle(self, filepath: str) -> nx.Graph:
+        """
+        Load a network from a GPickle file.
+
+        Args:
+            filepath (str): Path to the GPickle file.
+
+        Returns:
+            nx.Graph: Loaded and processed network.
+        """
+        filetype = "GPickle"
+        # Log the loading of the GPickle file
+        params.log_network(filetype=filetype, filepath=filepath)
+        self._log_loading_network(filetype, filepath=filepath)
+
+        with open(filepath, "rb") as f:
+            G = pickle.load(f)
+
+        # Initialize the graph
+        return self._initialize_graph(G)
+
+    def load_network_networkx(self, network: nx.Graph) -> nx.Graph:
         """
-        Private method to load a NetworkX graph.
+        Load a NetworkX graph.
 
         Args:
             network (nx.Graph): A NetworkX graph object.
@@ -149,47 +223,10 @@ class NetworkIO:
         source_label: str = "source",
         target_label: str = "target",
         view_name: str = "",
-        compute_sphere: bool = True,
-        surface_depth: float = 0.0,
-        min_edges_per_node: int = 0,
     ) -> nx.Graph:
         """
         Load a network from a Cytoscape file.
 
-        Args:
-            filepath (str): Path to the Cytoscape file.
-            source_label (str, optional): Source node label. Defaults to "source".
-            target_label (str, optional): Target node label. Defaults to "target".
-            view_name (str, optional): Specific view name to load. Defaults to "".
-            compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
-            surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
-            min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-
-        Returns:
-            nx.Graph: Loaded and processed network.
-        """
-        networkio = NetworkIO(
-            compute_sphere=compute_sphere,
-            surface_depth=surface_depth,
-            min_edges_per_node=min_edges_per_node,
-        )
-        return networkio._load_network_cytoscape(
-            filepath=filepath,
-            source_label=source_label,
-            target_label=target_label,
-            view_name=view_name,
-        )
-
-    def _load_network_cytoscape(
-        self,
-        filepath: str,
-        source_label: str = "source",
-        target_label: str = "target",
-        view_name: str = "",
-    ) -> nx.Graph:
-        """
-        Private method to load a network from a Cytoscape file.
-
         Args:
             filepath (str): Path to the Cytoscape file.
             source_label (str, optional): Source node label. Defaults to "source".
@@ -315,44 +352,10 @@ class NetworkIO:
             if os.path.exists(tmp_dir):
                 shutil.rmtree(tmp_dir)
 
-    def load_network_cyjs(
-        self,
-        filepath: str,
-        source_label: str = "source",
-        target_label: str = "target",
-        compute_sphere: bool = True,
-        surface_depth: float = 0.0,
-        min_edges_per_node: int = 0,
-    ) -> nx.Graph:
+    def load_network_cyjs(self, filepath, source_label="source", target_label="target"):
         """
         Load a network from a Cytoscape JSON (.cyjs) file.
 
-        Args:
-            filepath (str): Path to the Cytoscape JSON file.
-            source_label (str, optional): Source node label. Default is "source".
-            target_label (str, optional): Target node label. Default is "target".
-            compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
-            surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
-            min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-
-        Returns:
-            NetworkX graph: Loaded and processed network.
-        """
-        networkio = NetworkIO(
-            compute_sphere=compute_sphere,
-            surface_depth=surface_depth,
-            min_edges_per_node=min_edges_per_node,
-        )
-        return networkio._load_network_cyjs(
-            filepath=filepath,
-            source_label=source_label,
-            target_label=target_label,
-        )
-
-    def _load_network_cyjs(self, filepath, source_label="source", target_label="target"):
-        """
-        Private method to load a network from a Cytoscape JSON (.cyjs) file.
-
         Args:
             filepath (str): Path to the Cytoscape JSON file.
             source_label (str, optional): Source node label. Default is "source".

risk/_network/_plotter/_api.py

@@ -19,9 +19,6 @@ class PlotterAPI:
     The PlotterAPI class provides methods to load and configure Plotter objects for plotting network graphs.
     """
 
-    def __init__(self) -> None:
-        pass
-
     def load_plotter(
         self,
         graph: Graph,

risk/{risk.py → _risk.py}

@@ -1,15 +1,15 @@
 """
-risk/risk
-~~~~~~~~~
+risk/_risk
+~~~~~~~~~~
 """
 
-from ._annotation import AnnotationIO
+from ._annotation import AnnotationHandler
 from ._log import params, set_global_verbosity
 from ._neighborhoods import NeighborhoodsAPI
-from ._network import GraphAPI, NetworkIO, PlotterAPI
+from ._network import GraphAPI, NetworkAPI, PlotterAPI
 
 
-class RISK(NetworkIO, AnnotationIO, NeighborhoodsAPI, GraphAPI, PlotterAPI):
+class RISK(NetworkAPI, AnnotationHandler, NeighborhoodsAPI, GraphAPI, PlotterAPI):
     """
     RISK: A class for network analysis and visualization.
 

{risk_network-0.0.13b5.dist-info → risk_network-0.0.14b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.13b5
+Version: 0.0.14b1
 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

{risk_network-0.0.13b5.dist-info → risk_network-0.0.14b1.dist-info}/RECORD

@@ -1,14 +1,14 @@
-risk/__init__.py,sha256=lyhdzjETYJ9Jg8da35gncJ_u2_QrElRsW5t1c69OIJY,142
-risk/risk.py,sha256=l7Btltgd-K00rmUV4_jTgJTwikSmMb-9A2IUQN5PnY8,1040
-risk/_annotation/__init__.py,sha256=LBLL5P_MdfwWaxkHBQHfQTPY-FF8hIGoUGKyHF1Wg4s,159
+risk/__init__.py,sha256=EhZWpNfkex4HOMUEdfleuQ78CzIktejWJnpn8TdWr6Q,143
+risk/_risk.py,sha256=VULCdM41BlWKM1ou4Qc579ffZ9dMZkfhAwKYgbaEeKM,1054
+risk/_annotation/__init__.py,sha256=zr7w1DHkmvrkKFGKdPhrcvZHV-xsfd5TZOaWtFiP4Dc,164
 risk/_annotation/_annotation.py,sha256=03vcnkdi4HGH5UUyokUyOdyyjXOLoKSmLFuK7VAl41c,15174
-risk/_annotation/_io.py,sha256=gEq6STSWFIFjSWoGXJfwxTME4GDJZTOgPeXZABgSdXc,12447
+risk/_annotation/_io.py,sha256=xic3dkEA54X82HbyWfCiXrUpAhPWFPBZ69R8jw31omQ,12457
 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/_api.py,sha256=s1f4d_nEPWc66KDmOUUpRNXzp6dfoevw45ewOg9eMNo,23298
 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
@@ -17,15 +17,15 @@ risk/_neighborhoods/_stats/_tests.py,sha256=-ioHdyrsgW63YnypKFpanatauuKrF3LT7aMZ
 risk/_neighborhoods/_stats/_permutation/__init__.py,sha256=nfTaW29CK8OZCdFnpMVlHnFaqr1E4AZp6mvhlUazHXM,140
 risk/_neighborhoods/_stats/_permutation/_permutation.py,sha256=e5qVuYWGhiAn5Jv8VILk-WYMOO4km48cGdRYTOl355M,10661
 risk/_neighborhoods/_stats/_permutation/_test_functions.py,sha256=lGI_MkdbW4UHI0jWN_T1OattRjXrq_qmzAmOfels670,3165
-risk/_network/__init__.py,sha256=LbXsJGU2-ydDMw5_qgwizE6YHMljGDuOGc6TO-jk4Pk,126
-risk/_network/_io.py,sha256=vOSfAWnj1Q4jQSVo9BqY-nwQIoEG-CYZ_Cv2clopVw0,28090
+risk/_network/__init__.py,sha256=YrAMfhL0CMWQb3sY-mn1VxK44zZAWeFAvHrBONH9I-A,127
+risk/_network/_io.py,sha256=wjy_wkQkRO4sI_U6Xvheu7x_Jd8mXyBnXAhtZSjqJHY,28129
 risk/_network/_graph/__init__.py,sha256=SFgxgxUiZK4vvw6bdQ04DSMXEr8xjMaQV-Wne6wAIqM,104
-risk/_network/_graph/_api.py,sha256=zH7n-ulqLcbgHdAfLu1yWErdR5G4LgSqR7DcN2qApco,8520
+risk/_network/_graph/_api.py,sha256=sp3_mLJDP_xQexYBjyM17iyzLb2oGmiC050kcw-jVho,8474
 risk/_network/_graph/_graph.py,sha256=x2EWT_ZVwxh7m9a01yG4WMdmAxBxiaxX3CvkqP9QAXE,12486
 risk/_network/_graph/_stats.py,sha256=6mxZkuL6LJlwKDsBbP22DAVkNUEhq-JZwYMKhFKD08k,7359
 risk/_network/_graph/_summary.py,sha256=4eGhCArssePDg4LXr3sg5bUpNn7KFK9oPZcCz5lJKEQ,10334
 risk/_network/_plotter/__init__.py,sha256=qFRtQKSBGIqmUGwmA7VPL7hTHBb9yvRIt0nLISXnwkY,84
-risk/_network/_plotter/_api.py,sha256=MHZIMTlul2u-Ve5m9r-eUljI2oC3IRklNn7AVlfmzGs,1773
+risk/_network/_plotter/_api.py,sha256=OaV1CCRGsz98wEEzyEhaq2CqEuZh6t2qS7g_rY6HJJs,1727
 risk/_network/_plotter/_canvas.py,sha256=H7rPz4Gv7ED3bDHMif4cf2usdU4ifmxzXeug5A_no68,13599
 risk/_network/_plotter/_contour.py,sha256=E3ILjlv-VBSbK3ClwObB84TvP1D48_B47ODXwtApjIE,15557
 risk/_network/_plotter/_labels.py,sha256=8JXzEOIBQefwr1ngF-2ZYCnYLZXs2Erz-R1c28NnsL0,46915
@@ -34,8 +34,8 @@ risk/_network/_plotter/_plotter.py,sha256=F2hw-spUdsXjvuG36o0YFR3Pnd-CZOHYUq4vW0
 risk/_network/_plotter/_utils/__init__.py,sha256=JXgjKiBWvXx0X2IeFnrOh5YZQGQoELbhJZ0Zh2mFEOo,211
 risk/_network/_plotter/_utils/_colors.py,sha256=JCliSvz8_-TsjilaRHSEsqdXFBUYlzhXKOSRGdCm9Kw,19177
 risk/_network/_plotter/_utils/_layout.py,sha256=GyGLc2U1WWUVL1Te9uPi_CLqlW_E4TImXRAL5TeA5D8,3633
-risk_network-0.0.13b5.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.13b5.dist-info/METADATA,sha256=dkYs8JCdMr945DZ-7bJ95MX0zuxfbkw1VpOhuLtCE_U,6853
-risk_network-0.0.13b5.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
-risk_network-0.0.13b5.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.13b5.dist-info/RECORD,,
+risk_network-0.0.14b1.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.14b1.dist-info/METADATA,sha256=82-RZi0eyLscZ5PG64zxheyTSVCb36LkV2GXE7Kmf44,6853
+risk_network-0.0.14b1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+risk_network-0.0.14b1.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.14b1.dist-info/RECORD,,

{risk_network-0.0.13b5.dist-info → risk_network-0.0.14b1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.3.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any