furones 0.0.1__tar.gz

furones-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Frank Vega
+
+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.

furones-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: furones
+Version: 0.0.1
+Summary: Compute the Approximate Independent Set for undirected graph encoded in DIMACS format.
+Home-page: https://github.com/frankvegadelgado/furones
+Author: Frank Vega
+Author-email: vega.frank@gmail.com
+License: MIT License
+Project-URL: Source Code, https://github.com/frankvegadelgado/furones
+Project-URL: Documentation Research, https://dev.to/frank_vega_987689489099bf/the-furones-algorithm-15lp
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Information Technology
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.2.1
+Requires-Dist: scipy>=1.15.0
+Requires-Dist: networkx[default]>=3.4.2
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# Furones: Approximate Independent Set Solver
+
+![In Loving Memory of Asia Furones (The Grandmother I Never Knew)](docs/furones.jpg)
+
+This work builds upon [A Sqrt(n)-Approximation for Independent Sets: The Furones Algorithm](https://dev.to/frank_vega_987689489099bf/the-furones-algorithm-15lp).
+
+---
+
+# Maximum Independent Set (MIS) Problem: Overview
+
+## Definition
+
+The **Maximum Independent Set (MIS)** problem is a fundamental NP-hard problem in graph theory. Given an undirected graph $G = (V, E)$, an _independent set_ is a subset of vertices $S \subseteq V$ where no two vertices in $S$ are adjacent. The MIS problem seeks the largest such subset $S$.
+
+## Key Properties
+
+- **NP-Hardness**: MIS is computationally intractable (no known polynomial-time solution unless $P = NP$).
+- **Equivalent Problems**:
+  - MIS is equivalent to finding the largest _clique_ in the complement graph $\overline{G}$.
+  - It is also related to the _Minimum Vertex Cover_ problem: $S$ is an MIS iff $V \setminus S$ is a vertex cover.
+
+## Applications
+
+1. **Scheduling**: Assigning non-conflicting tasks (e.g., scheduling exams with no shared students).
+2. **Network Design**: Selecting non-adjacent nodes for efficient resource allocation.
+3. **Bioinformatics**: Modeling protein-protein interaction networks.
+
+## Algorithms
+
+| Approach            | Description                                                            | Complexity          |
+| ------------------- | ---------------------------------------------------------------------- | ------------------- |
+| Brute-Force         | Checks all possible subsets of vertices.                               | $O(2^n)$            |
+| Greedy Heuristics   | Selects vertices with minimal degree iteratively.                      | $O(n + m)$ (approx) |
+| Dynamic Programming | Used for trees or graphs with bounded treewidth.                       | $O(3^{tw})$         |
+| Approximation       | No PTAS exists; best-known approximation ratio is $O(n / (\log n)^2)$. | NP-Hard             |
+
+## Example
+
+For a graph with vertices $\{A, B, C\}$ and edges $\{(A,B), (B,C)\}$:
+
+- **Independent Sets**: $\{A, C\}$, $\{A\}$, $\{B\}$, $\{C\}$.
+- **MIS**: $\{A, C\}$ (size 2).
+
+## Open Challenges
+
+- Finding a constant-factor approximation for general graphs.
+- Efficient quantum or parallel algorithms for large-scale graphs.
+
+---
+
+## Problem Statement
+
+Input: A Boolean Adjacency Matrix $M$.
+
+Answer: Find a Maximum Independent Set.
+
+### Example Instance: 5 x 5 matrix
+
+|        | c1  | c2  | c3  | c4  | c5  |
+| ------ | --- | --- | --- | --- | --- |
+| **r1** | 0   | 0   | 1   | 0   | 1   |
+| **r2** | 0   | 0   | 0   | 1   | 0   |
+| **r3** | 1   | 0   | 0   | 0   | 1   |
+| **r4** | 0   | 1   | 0   | 0   | 0   |
+| **r5** | 1   | 0   | 1   | 0   | 0   |
+
+The input for undirected graph is typically provided in [DIMACS](http://dimacs.rutgers.edu/Challenges) format. In this way, the previous adjacency matrix is represented in a text file using the following string representation:
+
+```
+p edge 5 4
+e 1 3
+e 1 5
+e 2 4
+e 3 5
+```
+
+This represents a 5x5 matrix in DIMACS format such that each edge $(v,w)$ appears exactly once in the input file and is not repeated as $(w,v)$. In this format, every edge appears in the form of
+
+```
+e W V
+```
+
+where the fields W and V specify the endpoints of the edge while the lower-case character `e` signifies that this is an edge descriptor line.
+
+_Example Solution:_
+
+Independent Set Found `4, 5`: Nodes `4`, and `5` constitute an optimal solution.
+
+---
+
+# Compile and Environment
+
+## Prerequisites
+
+- Python ≥ 3.10
+
+## Installation
+
+```bash
+pip install furones
+```
+
+## Execution
+
+1. Clone the repository:
+
+   ```bash
+   git clone https://github.com/frankvegadelgado/furones.git
+   cd furones
+   ```
+
+2. Run the script:
+
+   ```bash
+   asia -i ./benchmarks/testMatrix1
+   ```
+
+   utilizing the `asia` command provided by Furones's Library to execute the Boolean adjacency matrix `furones\benchmarks\testMatrix1`. The file `testMatrix1` represents the example described herein. We also support `.xz`, `.lzma`, `.bz2`, and `.bzip2` compressed text files.
+
+   **Example Output:**
+
+   ```
+   testMatrix1: Independent Set Found 4, 5
+   ```
+
+   This indicates nodes `4, 5` form a Independent Set.
+
+---
+
+## Independent Set Size
+
+Use the `-c` flag to count the nodes in the Independent Set:
+
+```bash
+asia -i ./benchmarks/testMatrix2 -c
+```
+
+**Output:**
+
+```
+testMatrix2: Independent Set Size 5
+```
+
+---
+
+# Command Options
+
+Display help and options:
+
+```bash
+asia -h
+```
+
+**Output:**
+
+```bash
+usage: asia [-h] -i INPUTFILE [-a] [-b] [-c] [-v] [-l] [--version]
+
+Compute the Approximate Independent Set for undirected graph encoded in DIMACS format.
+
+options:
+  -h, --help            show this help message and exit
+  -i INPUTFILE, --inputFile INPUTFILE
+                        input file path
+  -a, --approximation   enable comparison with a polynomial-time approximation approach within a factor of at most 2
+  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
+  -c, --count           calculate the size of the Independent Set
+  -v, --verbose         anable verbose output
+  -l, --log             enable file logging
+  --version             show program's version number and exit
+```
+
+---
+
+# Batch Execution
+
+Batch execution allows you to solve multiple graphs within a directory consecutively.
+
+To view available command-line options for the `batch_asia` command, use the following in your terminal or command prompt:
+
+```bash
+batch_asia -h
+```
+
+This will display the following help information:
+
+```bash
+usage: batch_asia [-h] -i INPUTDIRECTORY [-a] [-b] [-c] [-v] [-l] [--version]
+
+Compute the Approximate Independent Set for all undirected graphs encoded in DIMACS format and stored in a directory.
+
+options:
+  -h, --help            show this help message and exit
+  -i INPUTDIRECTORY, --inputDirectory INPUTDIRECTORY
+                        Input directory path
+  -a, --approximation   enable comparison with a polynomial-time approximation approach within a factor of at most 2
+  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
+  -c, --count           calculate the size of the Independent Set
+  -v, --verbose         anable verbose output
+  -l, --log             enable file logging
+  --version             show program's version number and exit
+```
+
+---
+
+# Testing Application
+
+A command-line utility named `test_asia` is provided for evaluating the Algorithm using randomly generated, large sparse matrices. It supports the following options:
+
+```bash
+usage: test_asia [-h] -d DIMENSION [-n NUM_TESTS] [-s SPARSITY] [-a] [-b] [-c] [-w] [-v] [-l] [--version]
+
+The Furones Testing Application using randomly generated, large sparse matrices.
+
+options:
+  -h, --help            show this help message and exit
+  -d DIMENSION, --dimension DIMENSION
+                        an integer specifying the dimensions of the square matrices
+  -n NUM_TESTS, --num_tests NUM_TESTS
+                        an integer specifying the number of tests to run
+  -s SPARSITY, --sparsity SPARSITY
+                        sparsity of the matrices (0.0 for dense, close to 1.0 for very sparse)
+  -a, --approximation   enable comparison with a polynomial-time approximation approach within a factor of at most 2
+  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
+  -c, --count           calculate the size of the Independent Set
+  -w, --write           write the generated random matrix to a file in the current directory
+  -v, --verbose         anable verbose output
+  -l, --log             enable file logging
+  --version             show program's version number and exit
+```
+
+---
+
+# Code
+
+- Python implementation by **Frank Vega**.
+
+---
+
+# Complexity
+
+```diff
++ We present a polynomial-time algorithm achieving a Sqrt(n)-approximation ratio for MIS, providing strong evidence that P = NP by efficiently solving a computationally hard problem with near-optimal solutions.
+```
+
+---
+
+# License
+
+- MIT License.

furones-0.0.1/README.md

@@ -0,0 +1,250 @@
+# Furones: Approximate Independent Set Solver
+
+![In Loving Memory of Asia Furones (The Grandmother I Never Knew)](docs/furones.jpg)
+
+This work builds upon [A Sqrt(n)-Approximation for Independent Sets: The Furones Algorithm](https://dev.to/frank_vega_987689489099bf/the-furones-algorithm-15lp).
+
+---
+
+# Maximum Independent Set (MIS) Problem: Overview
+
+## Definition
+
+The **Maximum Independent Set (MIS)** problem is a fundamental NP-hard problem in graph theory. Given an undirected graph $G = (V, E)$, an _independent set_ is a subset of vertices $S \subseteq V$ where no two vertices in $S$ are adjacent. The MIS problem seeks the largest such subset $S$.
+
+## Key Properties
+
+- **NP-Hardness**: MIS is computationally intractable (no known polynomial-time solution unless $P = NP$).
+- **Equivalent Problems**:
+  - MIS is equivalent to finding the largest _clique_ in the complement graph $\overline{G}$.
+  - It is also related to the _Minimum Vertex Cover_ problem: $S$ is an MIS iff $V \setminus S$ is a vertex cover.
+
+## Applications
+
+1. **Scheduling**: Assigning non-conflicting tasks (e.g., scheduling exams with no shared students).
+2. **Network Design**: Selecting non-adjacent nodes for efficient resource allocation.
+3. **Bioinformatics**: Modeling protein-protein interaction networks.
+
+## Algorithms
+
+| Approach            | Description                                                            | Complexity          |
+| ------------------- | ---------------------------------------------------------------------- | ------------------- |
+| Brute-Force         | Checks all possible subsets of vertices.                               | $O(2^n)$            |
+| Greedy Heuristics   | Selects vertices with minimal degree iteratively.                      | $O(n + m)$ (approx) |
+| Dynamic Programming | Used for trees or graphs with bounded treewidth.                       | $O(3^{tw})$         |
+| Approximation       | No PTAS exists; best-known approximation ratio is $O(n / (\log n)^2)$. | NP-Hard             |
+
+## Example
+
+For a graph with vertices $\{A, B, C\}$ and edges $\{(A,B), (B,C)\}$:
+
+- **Independent Sets**: $\{A, C\}$, $\{A\}$, $\{B\}$, $\{C\}$.
+- **MIS**: $\{A, C\}$ (size 2).
+
+## Open Challenges
+
+- Finding a constant-factor approximation for general graphs.
+- Efficient quantum or parallel algorithms for large-scale graphs.
+
+---
+
+## Problem Statement
+
+Input: A Boolean Adjacency Matrix $M$.
+
+Answer: Find a Maximum Independent Set.
+
+### Example Instance: 5 x 5 matrix
+
+|        | c1  | c2  | c3  | c4  | c5  |
+| ------ | --- | --- | --- | --- | --- |
+| **r1** | 0   | 0   | 1   | 0   | 1   |
+| **r2** | 0   | 0   | 0   | 1   | 0   |
+| **r3** | 1   | 0   | 0   | 0   | 1   |
+| **r4** | 0   | 1   | 0   | 0   | 0   |
+| **r5** | 1   | 0   | 1   | 0   | 0   |
+
+The input for undirected graph is typically provided in [DIMACS](http://dimacs.rutgers.edu/Challenges) format. In this way, the previous adjacency matrix is represented in a text file using the following string representation:
+
+```
+p edge 5 4
+e 1 3
+e 1 5
+e 2 4
+e 3 5
+```
+
+This represents a 5x5 matrix in DIMACS format such that each edge $(v,w)$ appears exactly once in the input file and is not repeated as $(w,v)$. In this format, every edge appears in the form of
+
+```
+e W V
+```
+
+where the fields W and V specify the endpoints of the edge while the lower-case character `e` signifies that this is an edge descriptor line.
+
+_Example Solution:_
+
+Independent Set Found `4, 5`: Nodes `4`, and `5` constitute an optimal solution.
+
+---
+
+# Compile and Environment
+
+## Prerequisites
+
+- Python ≥ 3.10
+
+## Installation
+
+```bash
+pip install furones
+```
+
+## Execution
+
+1. Clone the repository:
+
+   ```bash
+   git clone https://github.com/frankvegadelgado/furones.git
+   cd furones
+   ```
+
+2. Run the script:
+
+   ```bash
+   asia -i ./benchmarks/testMatrix1
+   ```
+
+   utilizing the `asia` command provided by Furones's Library to execute the Boolean adjacency matrix `furones\benchmarks\testMatrix1`. The file `testMatrix1` represents the example described herein. We also support `.xz`, `.lzma`, `.bz2`, and `.bzip2` compressed text files.
+
+   **Example Output:**
+
+   ```
+   testMatrix1: Independent Set Found 4, 5
+   ```
+
+   This indicates nodes `4, 5` form a Independent Set.
+
+---
+
+## Independent Set Size
+
+Use the `-c` flag to count the nodes in the Independent Set:
+
+```bash
+asia -i ./benchmarks/testMatrix2 -c
+```
+
+**Output:**
+
+```
+testMatrix2: Independent Set Size 5
+```
+
+---
+
+# Command Options
+
+Display help and options:
+
+```bash
+asia -h
+```
+
+**Output:**
+
+```bash
+usage: asia [-h] -i INPUTFILE [-a] [-b] [-c] [-v] [-l] [--version]
+
+Compute the Approximate Independent Set for undirected graph encoded in DIMACS format.
+
+options:
+  -h, --help            show this help message and exit
+  -i INPUTFILE, --inputFile INPUTFILE
+                        input file path
+  -a, --approximation   enable comparison with a polynomial-time approximation approach within a factor of at most 2
+  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
+  -c, --count           calculate the size of the Independent Set
+  -v, --verbose         anable verbose output
+  -l, --log             enable file logging
+  --version             show program's version number and exit
+```
+
+---
+
+# Batch Execution
+
+Batch execution allows you to solve multiple graphs within a directory consecutively.
+
+To view available command-line options for the `batch_asia` command, use the following in your terminal or command prompt:
+
+```bash
+batch_asia -h
+```
+
+This will display the following help information:
+
+```bash
+usage: batch_asia [-h] -i INPUTDIRECTORY [-a] [-b] [-c] [-v] [-l] [--version]
+
+Compute the Approximate Independent Set for all undirected graphs encoded in DIMACS format and stored in a directory.
+
+options:
+  -h, --help            show this help message and exit
+  -i INPUTDIRECTORY, --inputDirectory INPUTDIRECTORY
+                        Input directory path
+  -a, --approximation   enable comparison with a polynomial-time approximation approach within a factor of at most 2
+  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
+  -c, --count           calculate the size of the Independent Set
+  -v, --verbose         anable verbose output
+  -l, --log             enable file logging
+  --version             show program's version number and exit
+```
+
+---
+
+# Testing Application
+
+A command-line utility named `test_asia` is provided for evaluating the Algorithm using randomly generated, large sparse matrices. It supports the following options:
+
+```bash
+usage: test_asia [-h] -d DIMENSION [-n NUM_TESTS] [-s SPARSITY] [-a] [-b] [-c] [-w] [-v] [-l] [--version]
+
+The Furones Testing Application using randomly generated, large sparse matrices.
+
+options:
+  -h, --help            show this help message and exit
+  -d DIMENSION, --dimension DIMENSION
+                        an integer specifying the dimensions of the square matrices
+  -n NUM_TESTS, --num_tests NUM_TESTS
+                        an integer specifying the number of tests to run
+  -s SPARSITY, --sparsity SPARSITY
+                        sparsity of the matrices (0.0 for dense, close to 1.0 for very sparse)
+  -a, --approximation   enable comparison with a polynomial-time approximation approach within a factor of at most 2
+  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
+  -c, --count           calculate the size of the Independent Set
+  -w, --write           write the generated random matrix to a file in the current directory
+  -v, --verbose         anable verbose output
+  -l, --log             enable file logging
+  --version             show program's version number and exit
+```
+
+---
+
+# Code
+
+- Python implementation by **Frank Vega**.
+
+---
+
+# Complexity
+
+```diff
++ We present a polynomial-time algorithm achieving a Sqrt(n)-approximation ratio for MIS, providing strong evidence that P = NP by efficiently solving a computationally hard problem with near-optimal solutions.
+```
+
+---
+
+# License
+
+- MIT License.

furones-0.0.1/furones/__init__.py

@@ -0,0 +1,4 @@
+# Furones: Approximate Independent Set Solver https://pypi.org/project/furones
+# Author: Frank Vega
+
+__all__ = ["utils", "algorithm", "parser", "applogger", "test", "app", "batch"]