fast-select 0.1.3__tar.gz

fast_select-0.1.3/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Gavin Lynch
+
+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.

fast_select-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: fast-select
+Version: 0.1.3
+Summary: A Sci-Kit Learn compatible Numba and CUDA-accelerated implementation of various feature selection algorithms.
+Author-email: Gavin Lynch <gavinlynch04@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/GavinLynch04/FastSelect
+Project-URL: Documentation, https://fastselect.readthedocs.io/en/latest/
+Project-URL: Bug Tracker, https://github.com/GavinLynch04/FastSelect/issues
+Project-URL: Changelog, https://github.com/GavinLynch04/FastSelect/blob/main/CHANGELOG.md
+Keywords: bioinformatics,feature selection,relief,reliefF,machine learning,numba,cuda,gpu,SURF,MultiSURF,TuRF,SURF*,MultiSURF*, mRMR, chi2
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Utilities
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: numba>=0.56
+Requires-Dist: scikit-learn>=1.6
+Provides-Extra: gpu
+Requires-Dist: cupy-cuda11x; extra == "gpu"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0; extra == "test"
+Requires-Dist: skrebate>=0.6; extra == "test"
+Provides-Extra: docs
+Provides-Extra: dev
+Requires-Dist: fast-select[docs,gpu,test]; extra == "dev"
+Requires-Dist: black>=23.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: twine>=4.0; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: myst-parser; extra == "dev"
+Requires-Dist: sphinx-copybutton; extra == "dev"
+Dynamic: license-file
+
+# **Fast-Select: Accelerated Feature Selection for Modern Datasets**
+[![PyPI version](https://img.shields.io/pypi/v/fast-select?color=blue)](https://pypi.org/project/fast-select/)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/GavinLynch04/FastSelect/python-tests.yml?branch=main)](https://github.com/GavinLynch04/FastSelect/actions)
+[![Python Versions](https://img.shields.io/pypi/pyversions/fast-select.svg)](https://pypi.org/project/fast-select/)
+[![License](https://img.shields.io/pypi/l/fast-select.svg)](https://github.com/GavinLynch04/FastSelect/blob/main/LICENSE)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![DOI](https://zenodo.org/badge/DOI/your-zenodo-doi.svg)](https://doi.org/your-zenodo-doi)
+<!-- start-include -->
+A high-performance Python library powered by **Numba** and **CUDA**, offering accelerated algorithms for feature selection. Initially built to optimize the complete Relief family of algorithms, `fast-select` aims to expand and accelerate a wide range of feature selection methods to empower machine learning on large-scale datasets.
+
+## **Key Features**
+
+- **Blazing Fast Performance:** Leverages **Numba** for JIT compilation, **Joblib** for multi-core parallelism, and **Numba CUDA** for GPU acceleration, providing unmatched performance while scaling with modern hardware.
+  
+- **ML Pipeline Integration:** Fully compatible with **Scikit-Learn**, making it easy to fit into any machine learning pipeline with a familiar `.fit()`, `.transform()`, `.fit_transform()` interface.
+  
+- **Flexible Backends:** Offers dual execution modes for both CPU (`Joblib`) and GPU (`CUDA`). Automatically detects hardware with an easy-to-use `backend` parameter.
+  
+- **Feature-Rich Implementation:** Provides lightning-fast implementations of ReliefF, SURF, SURF*, MultiSURF, MultiSURF*, and TuRF—with plans to support additional feature selection algorithms in future releases.
+  
+- **Lightweight & Simple:** Avoids heavy dependencies like TensorFlow or PyTorch while delivering state-of-the-art acceleration for feature selection workflows.
+  
+<!-- end-include -->
+
+## **Table of Contents**
+
+1. [Installation](#installation)
+2. [Quickstart](#quickstart)
+3. [Backend Selection](#backend-selection-cpu-vs-gpu)
+4. [Benchmarking Highlights](#benchmarking-highlights)
+5. [Algorithm Implementations](#algorithm-implementations)
+6. [Future Directions](#future-directions)
+7. [Contributing](#contributing)
+8. [License](#license)
+9. [How to Cite](#how-to-cite)
+10. [Acknowledgments](#acknowledgments)
+
+## **Installation**
+<!-- start-installation-section -->
+
+Install `fast-select` directly from PyPI:
+
+```bash
+pip install fast-select
+```
+
+For development versions (with testing and documentation dependencies):
+
+```bash
+git clone https://github.com/GavinLynch04/FastSelect.git
+cd fast-select
+pip install -e .[dev]
+```
+
+<!-- end-installation-section -->
+
+
+## **Quickstart**
+<!-- start-quickstart-section -->
+
+Using `fast-select` is simple and seamless for anyone familiar with Scikit-Learn.
+
+```python
+from fast_select.estimators import MultiSURF
+from sklearn.datasets import make_classification
+from sklearn.pipeline import Pipeline
+from sklearn.preprocessing import StandardScaler
+from sklearn.linear_model import LogisticRegression  # Example classifier
+
+# 1. Generate a synthetic dataset
+X, y = make_classification(
+    n_samples=500, 
+    n_features=1000, 
+    n_informative=20, 
+    n_redundant=100, 
+    random_state=42
+)
+
+# 2. Use the MultiSURF estimator to select the top 15 features
+selector = MultiSURF(n_features_to_select=15)
+X_selected = selector.fit_transform(X, y)
+print(f"Original feature count: {X.shape[1]}")
+print(f"Selected feature count: {X_selected.shape[1]}")
+print(f"Top 15 feature indices: {selector.top_features_}")
+
+# 3. Integrate into a Scikit-Learn Pipeline
+pipeline = Pipeline([
+    ('scaler', StandardScaler()),
+    ('feature_selector', MultiSURF(n_features_to_select=10, backend='cpu')),
+    ('classifier', LogisticRegression())
+])
+
+# Fit the pipeline (now featuring fast feature selection!)
+# pipeline.fit(X, y)
+```
+<!-- end-quickstart-section -->
+
+## **Backend Selection (CPU vs. GPU)**
+
+You can control the computational backend with the `backend` parameter during initialization:
+
+- **`backend='auto'`**: Automatically detects if an NVIDIA GPU is available. Falls back to CPU if a GPU is not available.
+  
+- **`backend='gpu'`**: Explicitly runs on GPU. Will raise a `RuntimeError` if no compatible GPU is found.
+  
+- **`backend='cpu'`**: Forces CPU computations, even if a GPU is available.
+
+Example usage:
+
+```python
+# Force CPU usage
+cpu_selector = MultiSURF(n_features_to_select=10, backend='cpu')
+
+# Force GPU usage
+gpu_selector = MultiSURF(n_features_to_select=10, backend='gpu')
+```
+
+---
+
+## **Benchmarking Highlights**
+
+Fast-Select delivers groundbreaking improvements in runtime and memory efficiency. Benchmarks show **50-100x speed-ups** compared to `scikit-rebate` and R's `CORElearn` library, particularly on large datasets exceeding 10,000 samples and features. [Benchmarking scripts](./benchmarking) are available in the repository for further testing.
+
+#### Runtime vs. Number of Samples (n >> p)
+
+<p align="center">
+  <img alt="Runtime Benchmark N-Dominant" width="700" src="https://raw.githubusercontent.com/GavinLynch04/FastSelect/main/benchmarking/benchmark_n_dominant_runtime.png">
+</p>
+
+#### Runtime vs. Number of Features (p >> n)
+
+<p align="center">
+  <img alt="Memory Benchmark P-Dominant" width="700" src="https://raw.githubusercontent.com/GavinLynch04/FastSelect/main/benchmarking/benchmark_p_dominant_runtime.png">
+</p>
+
+---
+
+## **Algorithm Implementations**
+
+Currently supported:
+
+- **Relief-Family Algorithms:**
+  - ReliefF
+  - SURF
+  - SURF*
+  - MultiSURF
+  - MultiSURF*
+  - TuRF
+
+Future plans include additional feature selection algorithms, such as wrappers, embedded methods, and more filter-based approaches.
+
+
+## **Contributing**
+
+Contributions are highly encouraged. Whether you're fixing bugs, improving performance, or proposing new algorithms, your work is invaluable. Please ensure your submissions include relevant test cases and documentation updates.
+
+
+## **License**
+
+This project is licensed under the MIT License. See the [LICENSE](./LICENSE) file for full details.
+
+
+## **How to Cite**
+
+If you use `fast-select` in your research, please cite the software:
+
+### ** Citing the Software (Specific Version):**
+Use the version-specific DOI provided via Zenodo on the [GitHub Release Page](https://github.com/GavinLynch04/FastSelect/releases).
+
+## **Acknowledgments**
+
+This library builds on the exceptional work of the following:
+
+- The **Numba** team for enabling JIT compilation and GPU acceleration.
+- The **scikit-rebate** authors for their inspiring Relief-based library.
+- The original researchers behind the Relief algorithms for their foundational contributions to feature selection.

fast_select-0.1.3/README.md

@@ -0,0 +1,177 @@
+# **Fast-Select: Accelerated Feature Selection for Modern Datasets**
+[![PyPI version](https://img.shields.io/pypi/v/fast-select?color=blue)](https://pypi.org/project/fast-select/)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/GavinLynch04/FastSelect/python-tests.yml?branch=main)](https://github.com/GavinLynch04/FastSelect/actions)
+[![Python Versions](https://img.shields.io/pypi/pyversions/fast-select.svg)](https://pypi.org/project/fast-select/)
+[![License](https://img.shields.io/pypi/l/fast-select.svg)](https://github.com/GavinLynch04/FastSelect/blob/main/LICENSE)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![DOI](https://zenodo.org/badge/DOI/your-zenodo-doi.svg)](https://doi.org/your-zenodo-doi)
+<!-- start-include -->
+A high-performance Python library powered by **Numba** and **CUDA**, offering accelerated algorithms for feature selection. Initially built to optimize the complete Relief family of algorithms, `fast-select` aims to expand and accelerate a wide range of feature selection methods to empower machine learning on large-scale datasets.
+
+## **Key Features**
+
+- **Blazing Fast Performance:** Leverages **Numba** for JIT compilation, **Joblib** for multi-core parallelism, and **Numba CUDA** for GPU acceleration, providing unmatched performance while scaling with modern hardware.
+  
+- **ML Pipeline Integration:** Fully compatible with **Scikit-Learn**, making it easy to fit into any machine learning pipeline with a familiar `.fit()`, `.transform()`, `.fit_transform()` interface.
+  
+- **Flexible Backends:** Offers dual execution modes for both CPU (`Joblib`) and GPU (`CUDA`). Automatically detects hardware with an easy-to-use `backend` parameter.
+  
+- **Feature-Rich Implementation:** Provides lightning-fast implementations of ReliefF, SURF, SURF*, MultiSURF, MultiSURF*, and TuRF—with plans to support additional feature selection algorithms in future releases.
+  
+- **Lightweight & Simple:** Avoids heavy dependencies like TensorFlow or PyTorch while delivering state-of-the-art acceleration for feature selection workflows.
+  
+<!-- end-include -->
+
+## **Table of Contents**
+
+1. [Installation](#installation)
+2. [Quickstart](#quickstart)
+3. [Backend Selection](#backend-selection-cpu-vs-gpu)
+4. [Benchmarking Highlights](#benchmarking-highlights)
+5. [Algorithm Implementations](#algorithm-implementations)
+6. [Future Directions](#future-directions)
+7. [Contributing](#contributing)
+8. [License](#license)
+9. [How to Cite](#how-to-cite)
+10. [Acknowledgments](#acknowledgments)
+
+## **Installation**
+<!-- start-installation-section -->
+
+Install `fast-select` directly from PyPI:
+
+```bash
+pip install fast-select
+```
+
+For development versions (with testing and documentation dependencies):
+
+```bash
+git clone https://github.com/GavinLynch04/FastSelect.git
+cd fast-select
+pip install -e .[dev]
+```
+
+<!-- end-installation-section -->
+
+
+## **Quickstart**
+<!-- start-quickstart-section -->
+
+Using `fast-select` is simple and seamless for anyone familiar with Scikit-Learn.
+
+```python
+from fast_select.estimators import MultiSURF
+from sklearn.datasets import make_classification
+from sklearn.pipeline import Pipeline
+from sklearn.preprocessing import StandardScaler
+from sklearn.linear_model import LogisticRegression  # Example classifier
+
+# 1. Generate a synthetic dataset
+X, y = make_classification(
+    n_samples=500, 
+    n_features=1000, 
+    n_informative=20, 
+    n_redundant=100, 
+    random_state=42
+)
+
+# 2. Use the MultiSURF estimator to select the top 15 features
+selector = MultiSURF(n_features_to_select=15)
+X_selected = selector.fit_transform(X, y)
+print(f"Original feature count: {X.shape[1]}")
+print(f"Selected feature count: {X_selected.shape[1]}")
+print(f"Top 15 feature indices: {selector.top_features_}")
+
+# 3. Integrate into a Scikit-Learn Pipeline
+pipeline = Pipeline([
+    ('scaler', StandardScaler()),
+    ('feature_selector', MultiSURF(n_features_to_select=10, backend='cpu')),
+    ('classifier', LogisticRegression())
+])
+
+# Fit the pipeline (now featuring fast feature selection!)
+# pipeline.fit(X, y)
+```
+<!-- end-quickstart-section -->
+
+## **Backend Selection (CPU vs. GPU)**
+
+You can control the computational backend with the `backend` parameter during initialization:
+
+- **`backend='auto'`**: Automatically detects if an NVIDIA GPU is available. Falls back to CPU if a GPU is not available.
+  
+- **`backend='gpu'`**: Explicitly runs on GPU. Will raise a `RuntimeError` if no compatible GPU is found.
+  
+- **`backend='cpu'`**: Forces CPU computations, even if a GPU is available.
+
+Example usage:
+
+```python
+# Force CPU usage
+cpu_selector = MultiSURF(n_features_to_select=10, backend='cpu')
+
+# Force GPU usage
+gpu_selector = MultiSURF(n_features_to_select=10, backend='gpu')
+```
+
+---
+
+## **Benchmarking Highlights**
+
+Fast-Select delivers groundbreaking improvements in runtime and memory efficiency. Benchmarks show **50-100x speed-ups** compared to `scikit-rebate` and R's `CORElearn` library, particularly on large datasets exceeding 10,000 samples and features. [Benchmarking scripts](./benchmarking) are available in the repository for further testing.
+
+#### Runtime vs. Number of Samples (n >> p)
+
+<p align="center">
+  <img alt="Runtime Benchmark N-Dominant" width="700" src="https://raw.githubusercontent.com/GavinLynch04/FastSelect/main/benchmarking/benchmark_n_dominant_runtime.png">
+</p>
+
+#### Runtime vs. Number of Features (p >> n)
+
+<p align="center">
+  <img alt="Memory Benchmark P-Dominant" width="700" src="https://raw.githubusercontent.com/GavinLynch04/FastSelect/main/benchmarking/benchmark_p_dominant_runtime.png">
+</p>
+
+---
+
+## **Algorithm Implementations**
+
+Currently supported:
+
+- **Relief-Family Algorithms:**
+  - ReliefF
+  - SURF
+  - SURF*
+  - MultiSURF
+  - MultiSURF*
+  - TuRF
+
+Future plans include additional feature selection algorithms, such as wrappers, embedded methods, and more filter-based approaches.
+
+
+## **Contributing**
+
+Contributions are highly encouraged. Whether you're fixing bugs, improving performance, or proposing new algorithms, your work is invaluable. Please ensure your submissions include relevant test cases and documentation updates.
+
+
+## **License**
+
+This project is licensed under the MIT License. See the [LICENSE](./LICENSE) file for full details.
+
+
+## **How to Cite**
+
+If you use `fast-select` in your research, please cite the software:
+
+### ** Citing the Software (Specific Version):**
+Use the version-specific DOI provided via Zenodo on the [GitHub Release Page](https://github.com/GavinLynch04/FastSelect/releases).
+
+## **Acknowledgments**
+
+This library builds on the exceptional work of the following:
+
+- The **Numba** team for enabling JIT compilation and GPU acceleration.
+- The **scikit-rebate** authors for their inspiring Relief-based library.
+- The original researchers behind the Relief algorithms for their foundational contributions to feature selection.

fast_select-0.1.3/pyproject.toml

@@ -0,0 +1,102 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "fast-select"
+version = "0.1.3"
+
+authors = [
+  { name="Gavin Lynch", email="gavinlynch04@gmail.com" },
+]
+
+description = "A Sci-Kit Learn compatible Numba and CUDA-accelerated implementation of various feature selection algorithms."
+
+readme = "README.md"
+
+requires-python = ">=3.9"
+
+license = "MIT"
+license-files = ["LICENSE"]
+
+keywords = ["bioinformatics", "feature selection", "relief", "reliefF", "machine learning", "numba", "cuda", "gpu", "SURF", "MultiSURF", "TuRF", "SURF*", "MultiSURF*, mRMR, chi2"]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Utilities",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+
+dependencies = [
+    "numpy>=1.21",
+    "numba>=0.56",
+    "scikit-learn>=1.6",
+]
+
+
+[project.urls]
+"Homepage" = "https://github.com/GavinLynch04/FastSelect"
+"Documentation" = "https://fastselect.readthedocs.io/en/latest/"
+"Bug Tracker" = "https://github.com/GavinLynch04/FastSelect/issues"
+"Changelog" = "https://github.com/GavinLynch04/FastSelect/blob/main/CHANGELOG.md"
+
+
+[project.optional-dependencies]
+gpu = [
+    "cupy-cuda11x",
+]
+
+test = [
+    "pytest>=7.0",
+    "pytest-cov>=4.0",
+    "skrebate>=0.6",
+]
+
+docs = [
+]
+
+dev = [
+    "fast-select[gpu, test, docs]",
+    "black>=23.0",
+    "ruff>=0.1.0",
+    "twine>=4.0",
+    "sphinx",
+    "furo",
+    "myst-parser",
+    "sphinx-copybutton",
+]
+
+
+
+[tool.setuptools.packages]
+find = { where = ["src"] }
+
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+addopts = "-ra -q --cov=fast_relief --cov-report=term-missing"
+testpaths = ["tests"]
+
+
+[tool.black]
+line-length = 120
+
+
+[tool.ruff]
+line-length = 120
+ignore = ["N811", "N803", "N806", "E731"]
+select = ["E", "F", "W", "I", "N", "UP"]
+
+[tool.ruff.isort]
+known-first-party = ["fast_select"]

fast_select-0.1.3/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+