Migrating packaging system from setup.py to pyproject.toml

.gitignore

@@ -9,4 +9,7 @@ dist
 .ipynb_checkpoints/
 
 .coverage
-htmlcov/
+htmlcov/
+
+.python-version
+uv.lock

CONTRIBUTING.md

@@ -0,0 +1,185 @@
+# Contributing to PyFastL2LiR
+
+Thank you for your interest in contributing to PyFastL2LiR! This document provides guidelines and instructions for contributing to the project.
+
+## Table of Contents
+
+- [Getting Started](#getting-started)
+- [Development Setup](#development-setup)
+- [Making Changes](#making-changes)
+- [Testing](#testing)
+- [Code Style](#code-style)
+- [Submitting Changes](#submitting-changes)
+
+## Getting Started
+
+### Prerequisites
+
+- [uv](https://github.com/astral-sh/uv)
+
+## Development Setup
+
+1. **Fork and clone the repository**
+
+   ```bash
+   git clone https://github.com/<USERNAME>/PyFastL2LiR.git
+   cd PyFastL2LiR
+   ```
+
+2. **Create a virtual environment and install dependencies**
+
+   ```bash
+   uv sync
+   ```
+
+   This will install the package in editable mode along with all development dependencies.
+
+## Making Changes
+
+1. **Create a new branch for your changes**
+
+   ```bash
+   git checkout -b feature/your-feature-name
+   ```
+
+   Use descriptive branch names:
+   - `feature/` for new features
+   - `fix/` for bug fixes
+   - `docs/` for documentation changes
+   - `refactor/` for code refactoring
+
+2. **Make your changes**
+
+   - Write clear, concise commit messages
+   - Keep commits focused and atomic
+   - Update documentation as needed
+
+## Testing
+
+We use pytest for testing. All tests should pass before submitting a pull request.
+
+### Running Tests
+
+Run all tests:
+
+```bash
+pytest
+```
+
+Run tests with coverage:
+
+```bash
+pytest --cov=fastl2lir --cov-report=term-missing
+```
+
+Run specific tests:
+
+```bash
+pytest tests/test_specific_module.py
+```
+
+### Writing Tests
+
+- Place tests in the `tests/` directory
+- Name test files with the `test_` prefix
+- Name test functions with the `test_` prefix
+- Aim for high test coverage, especially for new features
+- Include both unit tests and integration tests where appropriate
+
+## Code Style
+
+We use [Ruff](https://github.com/astral-sh/ruff) for linting and code formatting.
+
+### Running Ruff
+
+Check for linting issues:
+
+```bash
+ruff check .
+```
+
+Automatically fix issues:
+
+```bash
+ruff check --fix .
+```
+
+Format code:
+
+```bash
+ruff format .
+```
+
+### Before Committing
+
+Make sure your code passes both linting and formatting checks:
+
+```bash
+ruff check . && ruff format --check .
+```
+
+## Submitting Changes
+
+1. **Ensure all tests pass**
+
+   ```bash
+   pytest
+   ```
+
+2. **Ensure code passes linting**
+
+   ```bash
+   ruff check .
+   ruff format --check .
+   ```
+
+3. **Commit your changes**
+
+   ```bash
+   git add .
+   git commit -m "[tag] Brief description of your changes"
+   ```
+
+   Write clear commit messages following these guidelines:
+   - Use the imperative mood ("Add feature" not "Added feature")
+   - Provide additional details in the body if needed
+
+4. **Push to your fork**
+
+   ```bash
+   git push origin feature/your-feature-name
+   ```
+
+5. **Create a Pull Request**
+
+   - Go to the original repository on GitHub
+   - Click "New Pull Request"
+   - Select your fork and branch
+   - Provide a clear description of your changes
+   - Reference any related issues
+
+### Pull Request Guidelines
+
+- Provide a clear description of the problem and solution
+- Include relevant issue numbers (e.g., "Fixes #123")
+- Ensure CI checks pass
+- Respond to review comments promptly
+- Keep pull requests focused on a single feature or fix
+
+## Code Review Process
+
+- Maintainers will review your pull request
+- Address any requested changes
+- Once approved, your changes will be merged
+
+## Questions?
+
+If you have questions or need help, feel free to:
+- Open an issue on GitHub
+- Reach out to the maintainers
+
+## License
+
+By contributing to PyFastL2LiR, you agree that your contributions will be licensed under the same license as the project.
+
+Thank you for contributing!

pyproject.toml

@@ -0,0 +1,33 @@
+[project]
+name = "fastl2lir"
+version = "0.10"
+description = "Fast L2-reguralized linear regression"
+readme = "README.md"
+authors = [
+    { name = "Kei Majima", email = "[email protected]" }
+]
+maintainers = [
+    { name = "Shuntaro C. Aoki", email = "[email protected]" },
+    { name = "Yoshihiro Nagano", email = "[email protected]" }
+]
+license = { file = "LICENSE" }
+requires-python = ">=3.1"
+dependencies = [
+    "numpy>=1.16.6",
+    "threadpoolctl>=2.1.0 ; python_full_version >= '3.5'",
+    "tqdm>=4.64.1",
+]
+[project.urls]
+Homepage = "https://github.com/KamitaniLab/PyFastL2LiR"
+Repository = "https://github.com/KamitaniLab/PyFastL2LiR"
+"Bug Tracker" = "https://github.com/KamitaniLab/PyFastL2LiR/issues"
+
+[build-system]
+requires = ["uv_build>=0.8.22,<0.9.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = [
+    "pytest>=4.6.11",
+    "ruff>=0.0.17",
+]

test.py → tests/test_fastl2lir.py

@@ -16,7 +16,7 @@ class TestFastL2LiR(TestCase):
     def test_basic(self):
         '''Basic Test.'''
 
-        data = np.load('./test/testdata_basic.npz')
+        data = np.load('./tests/testdata_basic.npz')
 
         model_1d = fastl2lir.FastL2LiR()
         model_2d = fastl2lir.FastL2LiR()
@@ -38,7 +38,7 @@ def test_basic(self):
     def test_alpha(self):
         '''Test for alpha.'''
 
-        data = np.load('./test/testdata_alpha01.npz')
+        data = np.load('./tests/testdata_alpha01.npz')
 
         model_1d = fastl2lir.FastL2LiR()
         model_2d = fastl2lir.FastL2LiR()
@@ -60,7 +60,7 @@ def test_alpha(self):
     def test_nfeat(self):
         '''Test for n_feat.'''
 
-        data = np.load('./test/testdata_nfeat.npz')
+        data = np.load('./tests/testdata_nfeat.npz')
 
         model_1d = fastl2lir.FastL2LiR()
         model_2d = fastl2lir.FastL2LiR()
@@ -82,7 +82,7 @@ def test_nfeat(self):
     def test_nfeat_no_feature_selection(self):
         '''Test for n_feat when X.shape[1] < n_feat (more samples than features).'''
 
-        data = np.load('./test/testdata_basic.npz')
+        data = np.load('./tests/testdata_basic.npz')
 
         model_1d = fastl2lir.FastL2LiR()
         model_2d = fastl2lir.FastL2LiR()
@@ -104,7 +104,7 @@ def test_nfeat_no_feature_selection(self):
     def test_nfeat_no_feature_selection_wide(self):
         '''Test for n_feat when X.shape[1] < n_feat (more features than samples).'''
 
-        data = np.load('./test/testdata_wide.npz')
+        data = np.load('./tests/testdata_wide.npz')
 
         model_1d = fastl2lir.FastL2LiR()
         model_2d = fastl2lir.FastL2LiR()
@@ -126,7 +126,7 @@ def test_nfeat_no_feature_selection_wide(self):
     def test_chunk(self):
         '''Test for chunk_size.'''
 
-        data = np.load('./test/testdata_chunk.npz')
+        data = np.load('./tests/testdata_chunk.npz')
 
         model_2d = fastl2lir.FastL2LiR()