pyrgg 1.2

Python Random Graph Generator

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Random Graph Generator

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Table of Contents

• Overview
• Installation
• Usage
• Issues & Bug Reports
• Todo
• Sample Files
• Example of Usage
• Supported Formats
• Similar Works
• Dependencies
• Contribution
• References
• Citing
• Authors
• License
• Show Your Support
• Changelog
• Code of Conduct

Overview

Pyrgg is an easy-to-use synthetic random graph generator written in Python which supports various graph file formats including DIMACS .gr files. Pyrgg has the ability to generate graphs of different sizes and is designed to provide input files for broad range of graph-based research applications, including but not limited to testing, benchmarking and performance-analysis of graph processing frameworks. Pyrgg target audiences are computer scientists who study graph algorithms and graph processing frameworks.

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Branch	master	dev
CI

Code Quality

Installation

Source Code

• Download Version 1.2 or Latest Source
• pip install -r requirements.txt or pip3 install -r requirements.txt (Need root access)
• python3 setup.py install or python setup.py install (Need root access)

PyPI

• Check Python Packaging User Guide
• pip install pyrgg==1.2 or pip3 install pyrgg==1.2 (Need root access)

Conda

• Check Conda Managing Package
• conda install -c sepandhaghighi pyrgg (Need root access)

Exe Version (Only Windows)

• Download Exe-Version 1.2
• Run PYRGG-1.2.exe

System Requirements

Pyrgg will likely run on a modern dual core PC. Typical configuration is:

• Dual Core CPU (2.0 Ghz+)
• 4GB of RAM

Note that it may run on lower end equipment though good performance is not guaranteed.

Usage

Issues & Bug Reports

Just fill an issue and describe it. We'll check it ASAP! or send an email to [e-mail].

You can also join our discord server

TODO

• Formats
  • DIMACS
  • JSON
  • YAML
  • Pickle
  • CSV
  • TSV
  • WEL
  • ASP
  • TGF
  • UCINET DL
  • GML
  • GDF
  • Matrix Market
  • Graph Line
  • GEXF
• Sizes
  • Small
  • Medium
  • Large
• Weighted Graph
  • Signed Weights
• Unweighted Graph
• Dense Graph
• Sparse Graph
• Directed Graph
• Self loop
• Parallel Arc
• Multithreading
• GUI
• Erdős–Rényi model
• Tree

Sample Files

• Sample 1-DIMACS (100 Vertices , 3KB)
• Sample 2-DIMACS (1000 Vertices , 13KB)
• Sample 3-DIMACS (1000000 Vertices , 7MB)
• Sample 4-DIMACS (5000000 Vertices , 37MB)
• Sample 1-JSON (100 Vertices , 26KB)
• Sample 2-JSON (1000 Vertices , 494KB)
• Sample 1-CSV (100 Vertices , 3KB)
• Sample 2-CSV (1000 Vertices , 51KB)
• Sample 1-TSV (100 Vertices , 29KB)
• Sample 2-TSV (1000 Vertices , 420KB)
• Sample 1-WEL (100 Vertices , 5KB)
• Sample 2-WEL (1000 Vertices , 192KB)
• Sample 1-YAML (30 Vertices , 6KB)
• Sample 2-YAML (100 Vertices , 35KB)
• Sample 1-LP (100 Vertices , 7KB)
• Sample 2-LP (1000 Vertices , 76KB)
• Sample 1-Pickle (100 Vertices , 12KB)
• Sample 2-Pickle (1000 Vertices , 340KB)
• Sample 1-TGF (100 Vertices , 4KB)
• Sample 2-TGF (1000 Vertices , 61KB)
• Sample 1-UCINET DL (100 Vertices , 8KB)
• Sample 2-UCINET DL (1000 Vertices , 729KB)
• Sample 1-MTX (100 Vertices , 59KB)
• Sample 2-MTX (1000 Vertices , 1.8MB)
• Sample 1-GL (100 Vertices , 17KB)
• Sample 2-GL (1000 Vertices , 2.4MB)
• Sample 1-GDF (100 Vertices , 21KB)
• Sample 2-GDF (1000 Vertices , 690KB)
• Sample 1-GML (100 Vertices , 120KB)
• Sample 2-GML (1000 Vertices , 2.4MB)
• Sample 1-GEXF (100 Vertices , 63KB)
• Sample 2-GEXF (1000 Vertices , 6.4MB)

Example of Usage

• Generate synthetic data for graph processing frameworks (some of them mentioned here) performance-analysis
  • Medusa
  • Totem
  • Frog
  • CuSha

Fig. 1. Rand Graph Generation

• Generate synthetic data for graph benchmark suite like GAP

Supported Formats

• DIMACS(.gr)

   	p sp <number of vertices> <number of edges>
   	a <head_1> <tail_1> <weight_1>
  
   	.
   	.
   	.
   	
   	a <head_n> <tail_n> <weight_n>
  

• CSV(.csv)

   	<head_1>,<tail_1>,<weight_1>
  
   	.
   	.
   	.
   	
   	<head_n>,<tail_n>,<weight_n>
  

• TSV(.tsv)

   	<head_1>	<tail_1>	<weight_1>
  
   	.
   	.
   	.
   	
   	<head_n>	<tail_n>	<weight_n>
  

• JSON(.json)

   {
   	"properties": {
   		"directed": true,
   		"signed": true,
   		"multigraph": true,
   		"weighted": true,
   		"self_loop": true
   	},
   	"graph": {
   		"nodes":[
   		{
   			"id": 1
   		},
  
   		.
   		.
   		.
  
   		{
   			"id": n
   		}
   		],
   		"edges":[
   		{
   			"source": head_1,
   			"target": tail_1,
   			"weight": weight_1
   		},
  
   		.
   		.
   		.
  
   		{
   			"source": head_n,
   			"target": tail_n,
   			"weight": weight_n
   		}
   		]
   	}
   }
  

• YAML(.yaml)

   	graph:
   		edges:
   		- source: head_1
   	  	target: tail_1
   	  	weight: weight_1
   	
   		.
   		.
   		.
  
   		- source: head_n
   	  	target: tail_n
   	  	weight: weight_n
   					
   		nodes:
   		- id: 1
  
   		.
   		.
   		.
  
   		- id: n
   	properties:
   		directed: true
   		multigraph: true
   		self_loop: true
   		signed: true
   		weighted: true
  
  

• Weighted Edge List(.wel)

   	<head_1> <tail_1> <weight_1>
   	
   	.
   	.
   	.
   	
   	<head_n> <tail_n> <weight_n>	
  

• ASP(.lp)

   	node(1).
   	.
   	.
   	.
   	node(n).
   	edge(head_1,tail_1,weight_1).
   	.
   	.
   	.
   	edge(head_n,tail_n,weight_n).
  

• Trivial_Graph_Format(.tgf)

   	1
   	.
   	.
   	.
   	n
   	#
   	1 2 weight_1
   	.
   	.
   	.
   	n k weight_n
  

• UCINET DL Format(.dl)

   	dl
   	format=edgelist1
   	n=<number of vertices>
   	data:
   	1 2 weight_1
   	.
   	.
   	.
   	n k weight_n	
  

• Matrix Market(.mtx)

      %%MatrixMarket matrix coordinate real general
      <number of vertices>  <number of vertices>  <number of edges>
      <head_1>    <tail_1>    <weight_1> 
      .
      .
      .
      <head_n>    <tail_n>    <weight_n> 
  

• Graph Line(.gl)

      <head_1> <tail_1>:<weight_1> <tail_2>:<weight_2>  ... <tail_n>:<weight_n>
      <head_2> <tail_1>:<weight_1> <tail_2>:<weight_2>  ... <tail_n>:<weight_n>
      .
      .
      .
      <head_n> <tail_1>:<weight_1> <tail_2>:<weight_2>  ... <tail_n>:<weight_n>
  

• GDF(.gdf)

      nodedef>name VARCHAR,label VARCHAR
      node_1,node_1_label
      node_2,node_2_label
      .
      .
      .
      node_n,node_n_label
      edgedef>node1 VARCHAR,node2 VARCHAR, weight DOUBLE
      node_1,node_2,weight_1
      node_1,node_3,weight_2
      .
      .
      .
      node_n,node_2,weight_n 
  

• GML(.gml)

      graph
      [
        multigraph 0
        directed  0
        node
        [
         id 1
         label "Node 1"
        ]
        node
        [
         id 2
         label "Node 2"
        ]
        .
        .
        .
        node
        [
         id n
         label "Node n"
        ]
        edge
        [
         source 1
         target 2
         value W1
        ]
        edge
        [
         source 2
         target 4
         value W2
        ]
        .
        .
        .
        edge
        [
         source n
         target r
         value Wn
        ]
      ]
  

• GEXF(.gexf)

      <?xml version="1.0" encoding="UTF-8"?>
      <gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
          <meta lastmodifieddate="2009-03-20">
              <creator>PyRGG</creator>
              <description>File Name</description>
          </meta>
          <graph defaultedgetype="directed">
              <nodes>
                  <node id="1" label="Node 1" />
                  <node id="2" label="Node 2" />
                  ...
              </nodes>
              <edges>
                  <edge id="1" source="1" target="2" weight="400" />
                  ...
              </edges>
          </graph>
      </gexf>
  

• Pickle(.p) (Binary Format)

Similar Works

• Random Modular Network Generator Generates random graphs with tunable strength of community structure
• randomGraph very simple random graph generator in matlab
• Graph1 Random Graph Generator with Max capacity paths (C++)

Dependencies

master	dev

Citing

If you use pyrgg in your research, please cite the JOSS paper ;-)

@article{Haghighi2017,
  doi = {10.21105/joss.00331},
  url = {https://doi.org/10.21105/joss.00331},
  year  = {2017},
  month = {sep},
  publisher = {The Open Journal},
  volume = {2},
  number = {17},
  author = {Sepand Haghighi},
  title = {Pyrgg: Python Random Graph Generator},
  journal = {The Journal of Open Source Software}
}

JOSS
Zenodo

References

1- 9th DIMACS Implementation Challenge - Shortest Paths

2- Problem Based Benchmark Suite

3- MaximalClique - ASP Competition 2013

4- Pitas, Ioannis, ed. Graph-based social media analysis. Vol. 39. CRC Press, 2016.

5- Roughan, Matthew, and Jonathan Tuke. "The hitchhikers guide to sharing graph data." 2015 3rd International Conference on Future Internet of Things and Cloud. IEEE, 2015.

6- Borgatti, Stephen P., Martin G. Everett, and Linton C. Freeman. "Ucinet for Windows: Software for social network analysis." Harvard, MA: analytic technologies 6 (2002).

7- Matrix Market: File Formats

8- Social Network Visualizer

9- Adar, Eytan. "GUESS: a language and interface for graph exploration." Proceedings of the SIGCHI conference on Human Factors in computing systems. 2006.

10- Skiena, Steven S. The algorithm design manual. Springer International Publishing, 2020.

11- Chakrabarti, Deepayan, Yiping Zhan, and Christos Faloutsos. "R-MAT: A recursive model for graph mining." Proceedings of the 2004 SIAM International Conference on Data Mining. Society for Industrial and Applied Mathematics, 2004.

12- Zhong, Jianlong, and Bingsheng He. "An overview of medusa: simplified graph processing on gpus." ACM SIGPLAN Notices 47.8 (2012): 283-284.

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# Changelog All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

1.2 - 2022-09-07

Added

• Anaconda workflow
• Discord badge

Changed

• Menu optimized
• Docstrings modified
• branch_gen function modified
• edge_gen function modified
• precision and min_edge parameters added to branch_gen function
• random_edge parameter removed from branch_gen function
• Test system modified
• AUTHORS.md updated
• License updated
• README.md modified
• Python 3.10 added to test.yml

Removed

• sign_gen function
• random_edge_limits function

1.1 - 2021-06-09

Added

• requirements-splitter.py
• is_weighted function
• _write_properties_to_json function
• PYRGG_TEST_MODE parameter

Changed

• Test system modified
• JSON, YAML and Pickle formats value changed from string to number
• properties section added to JSON, YAML and Pickle formats
• _write_to_json function renamed to _write_data_to_json
• logger function modified
• time_convert function modified
• branch_gen function modified
• References updated

1.0 - 2021-01-11

Added

• Number of files option

Changed

• All flags type changed to bool
• Menu optimized
• The logger function enhanced.
• Time format in the logger changed to %Y-%m-%d %H:%M:%S
• dl_maker function modified
• tgf_maker function modified
• gdf_maker function modified
• run function modified

0.9 - 2020-10-07

Added

• GEXF format
• Float weight support
• tox.ini

Changed

• Menu optimized
• pyrgg.py renamed to graph_gen.py
• Other functions moved to functions.py
• Test system modified
• params.py refactored
• graph_gen.py refactored
• functions.py refactored
• weight_str_to_number function renamed to convert_str_to_number
• branch_gen function bugs fixed
• input_filter function bug fixed
• gl_maker function bug fixed
• CONTRIBUTING.md updated
• AUTHORS.md updated

Removed

• print_test function
• left_justify function
• justify function
• zero_insert function

0.8 - 2020-08-19

Added

• GDF format
• GML format

Changed

• CLI snapshots updated
• AUTHORS.md updated

0.7 - 2020-08-07

Added

• Graph Line format

Changed

• Menu optimized

0.6 - 2020-07-24

Added

• Matrix Market format

Changed

• json_maker function optimized
• dl_maker function optimized
• tgf_maker function optimized
• lp_maker function optimized

0.5 - 2020-07-01

Added

• TSV format
• Multigraph control

Changed

• branch_gen function modified
• Website changed to https://www.pyrgg.ir

0.4 - 2020-06-17

Added

• Self loop control
• Github action

Changed

• appveyor.yml updated

0.3 - 2019-11-29

Added

• __version__ variable
• CHANGELOG.md
• dev-requirements.txt
• requirements.txt
• CODE_OF_CONDUCT.md
• ISSUE_TEMPLATE.md
• PULL_REQUEST_TEMPLATE.md
• CONTRIBUTING.md
• version_check.py
• pyrgg_profile.py
• Unweighted graph
• Undirected graph
• Exe version

Changed

• Test system modified
• README.md modified
• Docstrings modified
• get_input function modified
• edge_gen function modified
• Parameters moved to params.py

0.2 - 2017-09-20

Added

• CSV format
• YAML format
• Weighted edge list format (WEL)
• ASP format
• Trivial graph format (TGF)
• UCINET DL format
• Pickle format

0.1 - 2017-08-19

Added

• DIMACS format
• JSON format
• README