dgraph-flex 0.1.0__py3-none-any.whl

dgraph_flex/__init__.py

@@ -0,0 +1 @@
+from .dgraph_flex import DgraphFlex  # Import the DgraphFlex class

dgraph_flex/dgraph_flex.py

@@ -0,0 +1,218 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import os
+import glob
+import sys
+import json
+from pathlib import Path
+import textwrap
+from glob import glob
+import yaml
+
+from graphviz import Digraph
+import matplotlib.pyplot as plt
+# import networkx as nx
+# import pandas as pd
+# import numpy
+# import seaborn as sns
+
+
+# from dotenv import dotenv_values  # pip install python-dotenv
+# import yaml # pip install pyyaml
+
+"""
+
+
+
+"""
+
+__version_info__ = ('0', '1', '0')
+__version__ = '.'.join(__version_info__)
+
+version_history = \
+"""
+0.1.0 - initial version  
+"""
+    
+
+
+class DgraphFlex:
+    
+    def __init__(self, **kwargs):
+        
+        # initialize the graph
+        self.graph = {}
+        
+
+        # load self.config
+        self.config = {}
+        for key, value in kwargs.items():
+            self.config[key] = value
+
+        # load the graph description from the yaml file
+        # self.load_graph()
+        
+        pass
+
+
+    def read_yaml(self, yamlpath, version=1.0):
+        "read in the yaml config file"
+        with open(yamlpath, 'r') as file:
+            self.graph = yaml.safe_load(file)
+
+        if self.graph['GENERAL']['version'] > version:
+            print(f"Error: Supports up to {version}, this is version {self.graph['GENERAL']['version']}")
+            sys.exit(1)
+
+        return self.graph
+            
+    def cmd(self, cmd):
+        if cmd == 'plot':
+            self.read_yaml(self.config['yamlpath'])
+            self.load_graph()
+            
+    def load_graph(self, graph=None, index=0):
+        """
+        Load a graph definition from a yaml file into a graphviz object
+        
+        
+        set the edge attributes starting from the first character to the third character
+        
+        --> == These indicate a direct causal influence. For example, A --> B means that variable A directly causes variable B
+        o-> == Indicates that either A causes B, or there's an unobserved confounder affecting both A and B, or both.
+        <-> == Indicates the presence of an unobserved confounder affecting both variables.
+        --- == These represent a relationship between variables, but the direction of causality is uncertain.
+        o-o == Indicates that either A causes B, B causes A, or there's an unobserved confounder, or any combination of these.
+            
+        """    
+        
+        
+        # create the graph object
+        self.dot = Digraph( format='png')
+               
+        # set the node attributes
+        self.dot.attr('node', shape='oval')
+        
+        if graph is None:
+            # use the graph from the object
+            graph = self.graph
+            
+        # start with the edges in self.graph
+        for edge in graph['GRAPHS'][index]['edges']:
+
+            edge_attr = {
+                "dir": "both",
+                "label": "",
+            }
+            
+            # set default values for arrowhead and arrowtail
+            arrowhead = 'normal'
+            arrowtail = 'none'
+            
+            # set the arrowhead and arrowtail based on the edge type
+            if edge['edge_type'] == 'o->':
+                arrowtail='odot'
+            elif edge['edge_type'] == 'o-o':
+                arrowtail='odot'
+                arrowhead='odot'
+                
+            # create info structure to ease access to edge information
+            label = ''
+            color = 'black'
+            
+            if edge.get('properties',False):
+                if edge['properties'].get('strength', None) is not None:
+                    label = f"{edge['properties']['strength']}"
+                # check for pvalue
+                if edge['properties'].get('pvalue', None) is not None:
+                    label += f"\n{edge['properties']['pvalue']}"
+                if edge['properties'].get('color', None) is not None:
+                    color = edge['properties']['color']
+            # create the edge object
+            self.dot.edge(  edge['source'], edge['target'],
+                            arrowtail=arrowtail,
+                            arrowhead=arrowhead,
+                            dir='both',
+                            label=label,
+                            color=color,)
+                            #**edge_attr)
+                                    
+
+            pass
+            
+        # render
+        
+        print(self.dot.source)
+        
+        # save gv source
+        self.gv_source = self.dot.source
+        
+        self.dot.format = 'png'
+        self.dot.render(filename = 'dgflex',
+                        format='png',
+                        
+                        )
+        pass
+    
+    def modify_existing_edge(self, dot, from_node, to_node, **kwargs):
+        """Modifies the attributes of an existing edge in a Graphviz graph.
+
+        Args:
+            dot: The Graphviz Graph object.
+            from_node: The name of the starting node of the edge.
+            to_node: The name of the ending node of the edge.
+            **kwargs: The attributes to modify (e.g., color='blue', style='dotted').
+        """
+
+        for edge in dot.body:
+            if edge.tail[0] == from_node and edge.head[0] == to_node:
+                for key, value in kwargs.items():
+                    edge.attr[key] = value
+                return  # Exit after modifying the edge
+
+        print(f"Edge from '{from_node}' to '{to_node}' not found.")
+            
+if __name__ == "__main__":
+    
+    # provide a description of the program with format control
+    description = textwrap.dedent('''\
+    
+    Class to support directed graph display in support of causal structure analysis.
+    
+ 
+    ''')
+    
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawTextHelpFormatter)
+
+    # handle a single file on command line argument
+    parser.add_argument('file',  type=str,  help='input file')
+    
+
+        
+    parser.add_argument("--cmd", type = str,
+                    help="cmd - [plot], default plot",
+                    default = 'plot')
+    
+    parser.add_argument("-H", "--history", action="store_true", help="Show program history")
+     
+    # parser.add_argument("--quiet", help="Don't output results to console, default false",
+    #                     default=False, action = "store_true")  
+    
+    parser.add_argument("--verbose", type=int, help="verbose level default 2",
+                         default=2) 
+        
+    parser.add_argument('-V', '--version', action='version', version=f'%(prog)s {__version__}')
+
+    args = parser.parse_args()
+            
+    if args.history:
+        print(f"{os.path.basename(__file__) } Version: {__version__}")
+        print(version_history)
+        exit(0)
+
+    obj = DgraphFlex(  yamlpath = args.file, verbose = args.verbose)
+
+    obj.cmd('plot')

dgraph_flex-0.1.0.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Kelvin O. Lim
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dgraph_flex-0.1.0.dist-info/METADATA

@@ -0,0 +1,92 @@
+Metadata-Version: 2.2
+Name: dgraph_flex
+Version: 0.1.0
+Summary: A package for working with directed graphs
+Author-email: "Kelvin O. Lim" <lim.kelvino@gmail.com>
+Project-URL: Homepage, https://github.com/kelvinlim/dgraph_flex
+Project-URL: Bug Tracker, https://github.com/kelvinlim/dgraph_flex/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: graphviz
+Requires-Dist: pyaml
+Requires-Dist: matplotlib
+
+# dgraph_flex
+
+Package to support flexible storage of directed graphs, specifically for the support of 
+directed graphs and causal structure analysis.
+
+## unit tests
+
+```
+python -m unittest tests/*.py
+```
+
+## build
+
+```
+python -m build
+
+# upload
+twine upload dist/*
+
+```
+
+## sample usage
+
+Here is a sample yaml file describing a graph
+```yaml
+
+GENERAL:
+  version: 1.0
+  framework: dgraph_flex
+
+GRAPHS:
+  - name: graph1
+    edges:
+      - label: edge1
+        source: A
+        target: B
+        edge_type: -->
+        properties:
+          strength: 0.5
+          pvalue: 0.01
+          color: green
+      - label: edge2
+        source: B
+        target: C
+        edge_type: -->
+        properties:
+          strength: -0.5
+          pvalue: 0.001
+          color: red
+      - label: edge3
+        source: C
+        target: E
+        edge_type: o->
+        properties:
+          strength: 0.5
+          pvalue: 0.0001
+      - label: edge4
+        source: B
+        target: D
+        edge_type: o-o
+        properties:
+
+```
+Here is python code that reads in the graph and outputs a png
+
+```python
+
+from dgraph_flex import DgraphFlex
+
+obj = DgraphFlex(yamlpath='graph_sample.yaml')
+obj.cmd('plot')
+
+
+
+```

dgraph_flex-0.1.0.dist-info/RECORD

@@ -0,0 +1,7 @@
+dgraph_flex/__init__.py,sha256=eSHOSOCMDNA9Ua9MVwneyiLt26WmCXeOsD-gBeoBtH0,66
+dgraph_flex/dgraph_flex.py,sha256=BuOEIjvT2sGG0a1MlPmAy_KeBJOMl9JXFCVLvu5zhdc,6808
+dgraph_flex-0.1.0.dist-info/LICENSE,sha256=ODYZfsol95LsdE8oetDplmT53-mpZ42Cbg5wIGMYpm0,1069
+dgraph_flex-0.1.0.dist-info/METADATA,sha256=IbfnFFuHK1eQXy5q0uAduIziNdWIx9GNBa3TuB_tK6w,1807
+dgraph_flex-0.1.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+dgraph_flex-0.1.0.dist-info/top_level.txt,sha256=P0o3hBJQevidvMJDvLOxjSwXiqC_sXJ7ntqRCOZpEaY,12
+dgraph_flex-0.1.0.dist-info/RECORD,,

dgraph_flex-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (75.8.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

dgraph_flex-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+dgraph_flex