skordinal 0.0.1__tar.gz

skordinal-0.0.1/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, The ORCA-python developer
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

skordinal-0.0.1/MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include skordinal/classifiers/src/libsvmrank *.h *.hpp
+recursive-include skordinal/classifiers/src/svorex *.h

skordinal-0.0.1/PKG-INFO

@@ -0,0 +1,206 @@
+Metadata-Version: 2.4
+Name: skordinal
+Version: 0.0.1
+Summary: Ordinal classification for Python, scikit-learn compatible
+Author-email: Francisco Bérchez-Moreno <fberchez@uco.es>, Víctor Manuel Vargas <vvargas@uco.es>, Javier Barbero-Gómez <jbarbero@uco.es>, Rafael Ayllón-Gavilán <rayllong@uco.es>, David Guijo-Rubio <dguijo@uco.es>, Ángel Sevilla Molina <asevilla@uco.es>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/ayrna/skordinal
+Project-URL: Repository, https://github.com/ayrna/skordinal
+Project-URL: Bug Tracker, https://github.com/ayrna/skordinal/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Python
+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 :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scikit-learn>=1.3.0
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.0.1
+Requires-Dist: scipy>=1.7
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-xdist[psutil]; extra == "dev"
+Requires-Dist: pytest-benchmark; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: mypy>=1.9; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Dynamic: license-file
+
+# skordinal
+
+| Overview  |                                                                                                                                          |
+|-----------|------------------------------------------------------------------------------------------------------------------------------------------|
+| **CI/CD** | [![Unit tests](https://github.com/ayrna/skordinal/actions/workflows/unit-tests.yml/badge.svg?branch=main)](https://github.com/ayrna/skordinal/actions/workflows/unit-tests.yml) [![!python](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)](https://www.python.org/) |
+| **Code**  | [![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) [![License - BSD 3-Clause](https://img.shields.io/pypi/l/pandas.svg)](https://github.com/ayrna/skordinal/blob/main/LICENSE) |
+
+
+## What is skordinal?
+
+**skordinal** is an experimental framework built on Python that integrates with scikit-learn to automate machine learning experiments through simple JSON configuration files. Initially designed for ordinal classification, it supports regular classification algorithms as long as they are compatible with scikit-learn, making it easy to run reproducible experiments across multiple datasets and classification methods.
+
+## Table of Contents
+
+- [Installation](#installation)
+    - [Requirements](#requirements)
+    - [Setup](#setup)
+    - [Testing Installation](#testing-installation)
+- [Quick Start](#quick-start)
+- [Configuration Files](#configuration-files)
+    - [general-conf](#general-conf)
+    - [configurations](#configurations)
+- [Running Experiments](#running-experiments)
+    - [Basic Usage](#basic-usage)
+    - [Example Output](#example-output)
+- [License](#license)
+
+## Installation
+
+### Requirements
+
+skordinal requires Python 3.9 or higher and is tested on Python 3.9, 3.10, 3.11, and 3.12.
+
+All dependencies are managed through `pyproject.toml` and include:
+- numpy (>=1.21)
+- pandas (>=1.0.1)
+- scikit-learn (>=1.3.0)
+- scipy (>=1.7)
+
+### Setup
+
+1. **Clone the repository**:
+   ```bash
+   git clone https://github.com/ayrna/skordinal
+   cd skordinal
+   ```
+
+2. **Install the framework**:
+   ```bash
+   pip install .
+   ```
+
+   For development purposes, use editable installation:
+   ```bash
+   pip install -e .
+   ```
+
+   Optional dependencies for development:
+   ```bash
+   pip install -e .[dev]
+   ```
+
+> **Note:** The editable mode is required for running tests due to automatic dependency resolution.
+
+### Testing Installation
+
+Test your installation with the provided example:
+
+```bash
+python config.py with skordinal/configurations/full_functionality_test.json
+```
+
+## Quick Start
+
+skordinal includes sample datasets with pre-partitioned train/test splits using a 30-holdout experimental design.
+
+**Basic experiment configuration:**
+
+```json
+{
+    "general_conf": {
+        "basedir": "skordinal/datasets/data",
+        "datasets": ["balance-scale", "contact-lenses", "tae"],
+        "hyperparam_cv_nfolds": 3,
+        "output_folder": "results/",
+        "metrics": ["ccr", "mae", "amae"],
+        "cv_metric": "mae"
+    },
+    "configurations": {
+        "SVM": {
+            "classifier": "SVC",
+            "parameters": {
+                "C": [0.001, 0.1, 1, 10, 100],
+                "gamma": [0.1, 1, 10]
+            }
+        },
+        "SVMOP": {
+            "classifier": "OrdinalDecomposition",
+            "parameters": {
+                "dtype": "ordered_partitions",
+                "decision_method": "frank_hall",
+                "base_classifier": "SVC",
+                "parameters": {
+                    "C": [0.01, 0.1, 1, 10],
+                    "gamma": [0.01, 0.1, 1, 10],
+                    "probability": ["True"]
+                }
+            }
+        }
+    }
+}
+```
+
+**Run the experiment:**
+```bash
+python config.py with my_experiment.json
+```
+
+Results are saved in `results/` folder with performance metrics for each dataset-classifier combination. The framework automatically performs cross-validation, hyperparameter tuning, and evaluation on test sets.
+
+## Configuration Files
+
+Experiments are defined using JSON configuration files with two main sections: general_conf for experiment settings and configurations for classifier definitions.
+
+### general-conf
+
+Controls global experiment parameters.
+
+**Required parameters:**
+- **`basedir`**: folder containing all dataset subfolders, it doesn't allow more than one folder at a time. It can be indicated using a full path, or a relative one to the framework folder.
+- **`datasets`**: name of datasets that will be experimented with. A subfolder with the same name must exist inside `basedir`.
+
+**Optional parameters:**
+- **`hyperparam_cv_folds`**: number of folds used while cross-validating.
+- **`jobs`**: number of jobs used for GridSearchCV during cross-validation.
+- **`input_preprocessing`**: data preprocessing (`"std"` for standardization, `"norm"` for normalization, `""` for none)
+- **`output_folder`**: name of the folder where all experiment results will be stored.
+- **`metrics`**: name of the accuracy metrics to measure the train and test performance of the classifier.
+- **`cv_metric`**: error measure used for GridSearchCV to find the best set of hyper-parameters.
+
+### configurations
+
+Defines classifiers and their hyperparameters for GridSearchCV. Each configuration has a name and consists of:
+
+- **`classifier`**: scikit-learn or built-in skordinal classifier
+- **`parameters`**: hyperparameters for grid search (nested for ensemble methods)
+
+## Running Experiments
+
+### Basic Usage
+
+```bash
+python config.py with experiment_file.json
+```
+
+### Example Output
+
+Results are stored in the specified output folder with detailed performance metrics and hyperparameter information for each dataset and configuration combination.
+
+## License
+[BSD 3](LICENSE)
+
+<hr>
+
+[Go to Top](#table-of-contents)

skordinal-0.0.1/README.md

@@ -0,0 +1,165 @@
+# skordinal
+
+| Overview  |                                                                                                                                          |
+|-----------|------------------------------------------------------------------------------------------------------------------------------------------|
+| **CI/CD** | [![Unit tests](https://github.com/ayrna/skordinal/actions/workflows/unit-tests.yml/badge.svg?branch=main)](https://github.com/ayrna/skordinal/actions/workflows/unit-tests.yml) [![!python](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)](https://www.python.org/) |
+| **Code**  | [![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) [![License - BSD 3-Clause](https://img.shields.io/pypi/l/pandas.svg)](https://github.com/ayrna/skordinal/blob/main/LICENSE) |
+
+
+## What is skordinal?
+
+**skordinal** is an experimental framework built on Python that integrates with scikit-learn to automate machine learning experiments through simple JSON configuration files. Initially designed for ordinal classification, it supports regular classification algorithms as long as they are compatible with scikit-learn, making it easy to run reproducible experiments across multiple datasets and classification methods.
+
+## Table of Contents
+
+- [Installation](#installation)
+    - [Requirements](#requirements)
+    - [Setup](#setup)
+    - [Testing Installation](#testing-installation)
+- [Quick Start](#quick-start)
+- [Configuration Files](#configuration-files)
+    - [general-conf](#general-conf)
+    - [configurations](#configurations)
+- [Running Experiments](#running-experiments)
+    - [Basic Usage](#basic-usage)
+    - [Example Output](#example-output)
+- [License](#license)
+
+## Installation
+
+### Requirements
+
+skordinal requires Python 3.9 or higher and is tested on Python 3.9, 3.10, 3.11, and 3.12.
+
+All dependencies are managed through `pyproject.toml` and include:
+- numpy (>=1.21)
+- pandas (>=1.0.1)
+- scikit-learn (>=1.3.0)
+- scipy (>=1.7)
+
+### Setup
+
+1. **Clone the repository**:
+   ```bash
+   git clone https://github.com/ayrna/skordinal
+   cd skordinal
+   ```
+
+2. **Install the framework**:
+   ```bash
+   pip install .
+   ```
+
+   For development purposes, use editable installation:
+   ```bash
+   pip install -e .
+   ```
+
+   Optional dependencies for development:
+   ```bash
+   pip install -e .[dev]
+   ```
+
+> **Note:** The editable mode is required for running tests due to automatic dependency resolution.
+
+### Testing Installation
+
+Test your installation with the provided example:
+
+```bash
+python config.py with skordinal/configurations/full_functionality_test.json
+```
+
+## Quick Start
+
+skordinal includes sample datasets with pre-partitioned train/test splits using a 30-holdout experimental design.
+
+**Basic experiment configuration:**
+
+```json
+{
+    "general_conf": {
+        "basedir": "skordinal/datasets/data",
+        "datasets": ["balance-scale", "contact-lenses", "tae"],
+        "hyperparam_cv_nfolds": 3,
+        "output_folder": "results/",
+        "metrics": ["ccr", "mae", "amae"],
+        "cv_metric": "mae"
+    },
+    "configurations": {
+        "SVM": {
+            "classifier": "SVC",
+            "parameters": {
+                "C": [0.001, 0.1, 1, 10, 100],
+                "gamma": [0.1, 1, 10]
+            }
+        },
+        "SVMOP": {
+            "classifier": "OrdinalDecomposition",
+            "parameters": {
+                "dtype": "ordered_partitions",
+                "decision_method": "frank_hall",
+                "base_classifier": "SVC",
+                "parameters": {
+                    "C": [0.01, 0.1, 1, 10],
+                    "gamma": [0.01, 0.1, 1, 10],
+                    "probability": ["True"]
+                }
+            }
+        }
+    }
+}
+```
+
+**Run the experiment:**
+```bash
+python config.py with my_experiment.json
+```
+
+Results are saved in `results/` folder with performance metrics for each dataset-classifier combination. The framework automatically performs cross-validation, hyperparameter tuning, and evaluation on test sets.
+
+## Configuration Files
+
+Experiments are defined using JSON configuration files with two main sections: general_conf for experiment settings and configurations for classifier definitions.
+
+### general-conf
+
+Controls global experiment parameters.
+
+**Required parameters:**
+- **`basedir`**: folder containing all dataset subfolders, it doesn't allow more than one folder at a time. It can be indicated using a full path, or a relative one to the framework folder.
+- **`datasets`**: name of datasets that will be experimented with. A subfolder with the same name must exist inside `basedir`.
+
+**Optional parameters:**
+- **`hyperparam_cv_folds`**: number of folds used while cross-validating.
+- **`jobs`**: number of jobs used for GridSearchCV during cross-validation.
+- **`input_preprocessing`**: data preprocessing (`"std"` for standardization, `"norm"` for normalization, `""` for none)
+- **`output_folder`**: name of the folder where all experiment results will be stored.
+- **`metrics`**: name of the accuracy metrics to measure the train and test performance of the classifier.
+- **`cv_metric`**: error measure used for GridSearchCV to find the best set of hyper-parameters.
+
+### configurations
+
+Defines classifiers and their hyperparameters for GridSearchCV. Each configuration has a name and consists of:
+
+- **`classifier`**: scikit-learn or built-in skordinal classifier
+- **`parameters`**: hyperparameters for grid search (nested for ensemble methods)
+
+## Running Experiments
+
+### Basic Usage
+
+```bash
+python config.py with experiment_file.json
+```
+
+### Example Output
+
+Results are stored in the specified output folder with detailed performance metrics and hyperparameter information for each dataset and configuration combination.
+
+## License
+[BSD 3](LICENSE)
+
+<hr>
+
+[Go to Top](#table-of-contents)

skordinal-0.0.1/pyproject.toml

@@ -0,0 +1,151 @@
+[build-system]
+requires = ["setuptools>=74.1.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "skordinal"
+version = "0.0.1"
+description = "Ordinal classification for Python, scikit-learn compatible"
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "BSD-3-Clause"}
+authors = [
+    {name = "Francisco Bérchez-Moreno", email = "fberchez@uco.es"},
+    {name = "Víctor Manuel Vargas", email = "vvargas@uco.es"},
+    {name = "Javier Barbero-Gómez", email = "jbarbero@uco.es"},
+    {name = "Rafael Ayllón-Gavilán", email = "rayllong@uco.es"},
+    {name = "David Guijo-Rubio", email = "dguijo@uco.es"},
+    {name = "Ángel Sevilla Molina", email = "asevilla@uco.es"},
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: C",
+    "Programming Language :: Python",
+    "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 :: Artificial Intelligence",
+    "Topic :: Software Development :: Libraries",
+]
+dependencies = [
+    "scikit-learn>=1.3.0",
+    "numpy>=1.21",
+    "pandas>=1.0.1",
+    "scipy>=1.7",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0",
+    "pytest-cov",
+    "pytest-xdist[psutil]",
+    "pytest-benchmark",
+    "ruff>=0.4",
+    "mypy>=1.9",
+    "pre-commit",
+]
+
+[project.urls]
+Homepage = "https://github.com/ayrna/skordinal"
+Repository = "https://github.com/ayrna/skordinal"
+"Bug Tracker" = "https://github.com/ayrna/skordinal/issues"
+
+[tool.setuptools.packages.find]
+include = [
+    "skordinal",
+    "skordinal.*",
+]
+exclude = ["*.tests"]
+namespaces = false
+
+[tool.setuptools.package-data]
+"skordinal.datasets" = ["data/*/*.csv"]
+
+[tool.setuptools]
+ext-modules = [
+    {name = "skordinal.classifiers._libsvmrank", language = "c++", sources = [
+            "skordinal/classifiers/src/libsvmrank/python/svm-module.cpp",
+            "skordinal/classifiers/src/libsvmrank/python/svm-train.cpp",
+            "skordinal/classifiers/src/libsvmrank/python/svm-predict.cpp",
+            "skordinal/classifiers/src/libsvmrank/python/svm-model-python.cpp",
+            "skordinal/classifiers/src/libsvmrank/python/svm.cpp",
+        ], extra-compile-args = ["-Wno-unused-result"]},
+    {name = "skordinal.classifiers._libsvorex", language = "c", sources = [
+            "skordinal/classifiers/src/svorex/svorex_module.c",
+            "skordinal/classifiers/src/svorex/svorex_train.c",
+            "skordinal/classifiers/src/svorex/svorex_predict.c",
+            "skordinal/classifiers/src/svorex/alphas.c",
+            "skordinal/classifiers/src/svorex/cachelist.c",
+            "skordinal/classifiers/src/svorex/datalist.c",
+            "skordinal/classifiers/src/svorex/def_settings.c",
+            "skordinal/classifiers/src/svorex/loadfile.c",
+            "skordinal/classifiers/src/svorex/ordinal_takestep.c",
+            "skordinal/classifiers/src/svorex/setandfi.c",
+            "skordinal/classifiers/src/svorex/smo_kernel.c",
+            "skordinal/classifiers/src/svorex/smo_routine.c",
+            "skordinal/classifiers/src/svorex/smo_settings.c",
+            "skordinal/classifiers/src/svorex/smo_timer.c",
+            "skordinal/classifiers/src/svorex/svc_predict.c",
+            "skordinal/classifiers/src/svorex/smo_model_python.c",
+            "skordinal/classifiers/src/svorex/smo_loadproblem_python.c",
+            "skordinal/classifiers/src/svorex/smo_routine_python.c",
+        ], extra-compile-args = ["-Wno-unused-result", "-ffp-contract=off"], libraries = ["m"]}
+]
+
+[tool.pytest.ini_options]
+testpaths = ["skordinal"]
+addopts = ["--color=yes", "--import-mode=importlib"]
+
+[tool.ruff]
+line-length = 88
+target-version = "py39"
+exclude = [
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    "__pycache__",
+    "build",
+    "dist",
+    "skordinal/classifiers/src/libsvmrank/",
+    "skordinal/classifiers/src/svorex/setup.py",
+]
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I"]
+ignore = ["E501"]
+
+[tool.mypy]
+ignore_missing_imports = true
+allow_redefinition = true
+exclude = ["skordinal/classifiers/src/libsvmrank/", "skordinal/classifiers/src/svorex/"]
+
+[tool.check-sdist]
+git-only = [
+    ".codecov.yml",
+    ".coveragerc",
+    ".gitignore",
+    "config.py",
+    "doc/**",
+    "skordinal/**/tests/**",
+    "skordinal/testing/**",
+    "skordinal/configurations/**",
+    "skordinal/classifiers/src/libsvmrank/grid.py",
+    "skordinal/classifiers/src/libsvmrank/svm-predict.c",
+    "skordinal/classifiers/src/libsvmrank/svm-train.c",
+    "skordinal/classifiers/src/libsvmrank/svm.cpp",
+    "skordinal/classifiers/src/libsvmrank/Makefile",
+    "skordinal/classifiers/src/libsvmrank/README",
+    "skordinal/classifiers/src/libsvmrank/python/setup.py",
+    "skordinal/classifiers/src/libsvmrank/python/makefile",
+    "skordinal/classifiers/src/svorex/main.c",
+    "skordinal/classifiers/src/svorex/Makefile",
+    "skordinal/classifiers/src/svorex/README.svorex",
+    "skordinal/classifiers/src/svorex/setup.py",
+]

skordinal-0.0.1/setup.cfg

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

skordinal-0.0.1/setup.py

@@ -0,0 +1,5 @@
+"""Setup script for skordinal."""
+
+from setuptools import setup
+
+setup()

skordinal-0.0.1/skordinal/__init__.py

@@ -0,0 +1,4 @@
+"""skordinal."""
+
+__all__: list[str] = []
+__version__ = "0.0.1"

skordinal-0.0.1/skordinal/classifiers/__init__.py

@@ -0,0 +1,15 @@
+"""Ordinal classification classifiers module."""
+
+from ._nnop import NNOP
+from ._nnpom import NNPOM
+from ._ordinal_decomposition import OrdinalDecomposition
+from ._redsvm import REDSVM
+from ._svorex import SVOREX
+
+__all__ = [
+    "NNOP",
+    "NNPOM",
+    "OrdinalDecomposition",
+    "REDSVM",
+    "SVOREX",
+]