Merge branch 'main' into new_examples_FEI

Author: BenViolet6

.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+
+[*.{yaml,yml,toml}]
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false

.github/ISSUE_TEMPLATE/bug_report.md

@@ -21,9 +21,9 @@ assignees: ''
 ## Steps to Reproduce
 
 <!-- Steps to reproduce the bug -->
-1. 
-2. 
-3. 
+1.
+2.
+3.
 
 ## Minimal Code Example
 
@@ -37,12 +37,12 @@ from rehline import ReHLine
 
 ## Environment
 
-- OS: 
-- Python version: 
-- ReHLine version: 
-- NumPy version: 
-- SciPy version: 
-- scikit-learn version: 
+- OS:
+- Python version:
+- ReHLine version:
+- NumPy version:
+- SciPy version:
+- scikit-learn version:
 
 ## Additional Context
 

.github/workflows/ci.yml

@@ -30,10 +30,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install package and test dependencies
-        run: pip install ".[test]" pytest-cov
+        run: pip install -e ".[test]" pytest-cov
 
       - name: Run tests
-        run: pytest -v --tb=short --cov=rehline --cov-report=xml --cov-report=term
+        run: pytest -v --tb=short --cov-report=xml
 
       - name: Upload coverage to Codecov
         if: success()

.github/workflows/wheels.yml

@@ -1,6 +1,6 @@
 name: Build and upload to PyPI
 
-on: 
+on:
   push:
     paths-ignore:
       - .gitignore
@@ -27,7 +27,7 @@ jobs:
         uses: pypa/cibuildwheel@v3.3.1
         env:
           CIBW_BUILD_VERBOSITY: 1
-        
+
       - uses: actions/upload-artifact@v6
         with:
           name: rehline-wheels-${{ matrix.os }}-${{ strategy.job-index }}

.gitignore

@@ -14,6 +14,11 @@ rehline.egg-info/
 *.log
 env/
 
+# Coverage reports
+.coverage
+coverage.xml
+htmlcov/
+
 # Files during package building
 eigen-3.4.0/
 eigen-5.0.1/
@@ -41,4 +46,7 @@ eigen3.zip
 *-checkpoint.py
 
 # local
-local/
+local/
+
+# auto API
+doc/source/autoapi/

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: [--maxkb=500]
+      - id: check-merge-conflict
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies: [tomli]
+        args: [--skip, "*.so,*.cpp,*.h,*.zip,eigen-*,build,dist,.git"]

.readthedocs.yaml

@@ -29,4 +29,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
-   - requirements: ./requirements.txt
+   - requirements: ./requirements.txt

.vscode/settings.json

@@ -6,4 +6,4 @@
         "tuple": "cpp",
         "utility": "cpp"
     }
-}
+}

README.md

@@ -30,6 +30,22 @@ See more details in the [ReHLine documentation](https://rehline-python.readthedo
 pip install rehline
 ```
 
+### Development Install
+
+For contributors and developers:
+
+```bash
+git clone https://github.com/softmin/ReHLine-python.git
+cd ReHLine-python
+pip install -e ".[dev]"
+```
+
+To run tests:
+
+```bash
+pytest tests/
+```
+
 ## 🚀 Quick Start
 
 ### Scikit-Learn Style API (Recommended)
@@ -79,20 +95,27 @@ print(f"Best params: {grid_search.best_params_}")
 from rehline import ReHLine
 import numpy as np
 
+# Generate sample data
+np.random.seed(42)
+X = np.random.randn(100, 5)
+y = np.random.choice([-1, 1], size=100)
+n, d = X.shape
+C = 1.0
+
 # Define custom PLQ loss parameters
 clf = ReHLine()
 # Set custom U, V matrices for ReLU loss
 # and S, T, tau for ReHU loss
 ## U
-clf.U = -(C*y).reshape(1,-1)
+clf._U = -(C*y).reshape(1,-1)
 ## V
-clf.V = (C*np.array(np.ones(n))).reshape(1,-1)
+clf._V = (C*np.ones(n)).reshape(1,-1)
 
 # Set custom linear constraints A*beta + b >= 0
 X_sen = X[:,0]
 tol_sen = 0.1
-clf.A = np.repeat([X_sen @ X], repeats=[2], axis=0) / n
-clf.A[1] = -clf.A[1]
+clf._A = np.repeat([X_sen @ X], repeats=[2], axis=0) / n
+clf._A[1] = -clf._A[1]
 
 clf.fit(X)
 ```
@@ -113,7 +136,7 @@ ReHLine excels at solving a wide range of machine learning problems:
 | **Sparse Learning** | Feature selection with L1 regularization | Scales to high dimensions |
 | **Custom Optimization** | Any PLQ loss with linear constraints | Flexible framework for research |
 
-<!-- 
+<!--
 ## 📝 Formulation
 
 **ReHLine** is designed to address the empirical regularized ReLU-ReHU minimization problem, named *ReHLine optimization*, of the following form: