risk-network 0.0.13b5__py3-none-any.whl → 0.0.14b0__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.0"

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/_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/_io.py

@@ -18,12 +18,10 @@ 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__(
@@ -33,22 +31,16 @@ class NetworkIO:
         min_edges_per_node: int = 0,
     ):
         """
-        Initialize the NetworkIO class.
+        Initialize the NetworkAPI.
 
         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.
+            compute_sphere (bool): Whether to map nodes to a sphere. Defaults to True.
+            surface_depth (float): Surface depth for the sphere. Defaults to 0.0.
+            min_edges_per_node (int): Minimum number of edges per node. Defaults to 0.
         """
         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,
-        )
 
     def load_network_gpickle(
         self,
@@ -58,44 +50,22 @@ class NetworkIO:
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
         """
-        Load a network from a GPickle file.
+        Load a network from a GPickle file 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.
-
+            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)
-
-    def _load_network_gpickle(self, filepath: str) -> nx.Graph:
-        """
-        Private method to 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)
+        return io.load_network_gpickle(filepath=filepath)
 
     def load_network_networkx(
         self,
@@ -105,82 +75,167 @@ class NetworkIO:
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
         """
-        Load a NetworkX graph.
+        Load a NetworkX graph via NetworkIO.
 
         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.
-
+            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.
+            nx.Graph: 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_networkx(network=network)
+        return io.load_network_networkx(network=network)
 
-    def _load_network_networkx(self, network: nx.Graph) -> nx.Graph:
+    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:
         """
-        Private method to load a NetworkX graph.
+        Load a network from a Cytoscape file via NetworkIO.
 
         Args:
-            network (nx.Graph): A NetworkX graph object.
-
+            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: Processed network.
+            nx.Graph: Loaded and processed network.
         """
-        filetype = "NetworkX"
-        # Log the loading of the NetworkX graph
-        params.log_network(filetype=filetype)
-        self._log_loading_network(filetype)
-
-        # Important: Make a copy of the network to avoid modifying the original
-        network_copy = copy.deepcopy(network)
-        # Initialize the graph
-        return self._initialize_graph(network_copy)
+        io = NetworkIO(
+            compute_sphere=compute_sphere,
+            surface_depth=surface_depth,
+            min_edges_per_node=min_edges_per_node,
+        )
+        return io.load_network_cytoscape(
+            filepath=filepath,
+            source_label=source_label,
+            target_label=target_label,
+            view_name=view_name,
+        )
 
-    def load_network_cytoscape(
+    def load_network_cyjs(
         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.
+        Load a network from a Cytoscape JSON (.cyjs) file via NetworkIO.
 
         Args:
-            filepath (str): Path to the Cytoscape 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".
-            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.
-
+            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_cytoscape(
+        return io.load_network_cyjs(
             filepath=filepath,
             source_label=source_label,
             target_label=target_label,
-            view_name=view_name,
         )
 
-    def _load_network_cytoscape(
+
+class NetworkIO:
+    """
+    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.
+    """
+
+    def __init__(
+        self,
+        compute_sphere: bool = True,
+        surface_depth: float = 0.0,
+        min_edges_per_node: int = 0,
+    ):
+        """
+        Initialize the NetworkIO class.
+
+        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.
+        """
+        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,
+        )
+
+    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:
+        """
+        Load a NetworkX graph.
+
+        Args:
+            network (nx.Graph): A NetworkX graph object.
+
+        Returns:
+            nx.Graph: Processed network.
+        """
+        filetype = "NetworkX"
+        # Log the loading of the NetworkX graph
+        params.log_network(filetype=filetype)
+        self._log_loading_network(filetype)
+
+        # Important: Make a copy of the network to avoid modifying the original
+        network_copy = copy.deepcopy(network)
+        # Initialize the graph
+        return self._initialize_graph(network_copy)
+
+    def load_network_cytoscape(
         self,
         filepath: str,
         source_label: str = "source",
@@ -188,7 +243,7 @@ class NetworkIO:
         view_name: str = "",
     ) -> nx.Graph:
         """
-        Private method to load a network from a Cytoscape file.
+        Load a network from a Cytoscape file.
 
         Args:
             filepath (str): Path to the Cytoscape file.
@@ -315,44 +370,10 @@ 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/{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-0.0.14b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.13b5
+Version: 0.0.14b0
 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-0.0.14b0.dist-info}/RECORD

@@ -1,8 +1,8 @@
-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=4gUMRlMdNJ2feLptoxyeWymcTnqlyoExMrazTwzyfrs,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
@@ -17,8 +17,8 @@ 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=uiYmbKVsSRr4-TsY9KvRggDghtZv8qoxXac3QYs1lTI,28750
 risk/_network/_graph/__init__.py,sha256=SFgxgxUiZK4vvw6bdQ04DSMXEr8xjMaQV-Wne6wAIqM,104
 risk/_network/_graph/_api.py,sha256=zH7n-ulqLcbgHdAfLu1yWErdR5G4LgSqR7DcN2qApco,8520
 risk/_network/_graph/_graph.py,sha256=x2EWT_ZVwxh7m9a01yG4WMdmAxBxiaxX3CvkqP9QAXE,12486
@@ -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-0.0.14b0.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.14b0.dist-info/METADATA,sha256=rshHTAf4wXudUsCwUIQpK8VZzmb5-f_c9_fYfrYXdm0,6853
+risk_network-0.0.14b0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+risk_network-0.0.14b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.14b0.dist-info/RECORD,,

{risk_network-0.0.13b5.dist-info → risk_network-0.0.14b0.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