Refactor code and improve test coverage

- Updated `requirements.txt` to ensure proper package management.
- Simplified the `get_eigen_include` class in `setup.py`.
- Cleaned up comments in `rehline.h` for better readability.
- Added regression tests in `test_bugfixes.py` to cover previously fixed bugs.
- Enhanced existing tests in `test_cqr.py`, `test_elastic_net.py`, `test_fairsvm.py`, `test_mf.py`, `test_monotonic.py`, `test_multiclass.py`, `test_path_sol.py`, `test_sklearn_mixin.py`, and `test_warmstart.py` for improved assertion clarity and consistency.
- Removed unnecessary assertions and improved error messages for better debugging.

Author: statmlben

.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/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

@@ -44,4 +44,4 @@ eigen3.zip
 local/
 
 # auto API
-doc/source/autoapi/
+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:

doc/source/_static/benchmark/benchmark_FairSVM.html

@@ -22,7 +22,7 @@
   article, aside, figcaption, figure, footer, header, nav, section {
     display: block;
   }
-  
+
   /* PARAGRAPHS */
   h1, h2, h3, h4 {
     line-height: 1.25; /* Bigger text is often nicer with smaller line height */
@@ -55,7 +55,7 @@
   figure {
     margin: 1em 0; /* Default in HTML5 spec: `1em 40px` */
   }
-  
+
   /* LINKS */
   /* Default browser styles (from Firefox, similar in most browsers) */
   a {
@@ -80,7 +80,7 @@
   a img {
     border: none;
   }
-  
+
   /* MISC TEXT-LEVEL ELEMENTS */
   /* Make quotations and references more visible */
   q, cite {
@@ -95,7 +95,7 @@
   sup, sub {
     line-height: 0;
   }
-  
+
   /* FORMS */
   fieldset {
     margin: 0; /* Common default is `0 2px` */
@@ -105,7 +105,7 @@
   input, button, select {
     vertical-align: middle; /* Helps keep form elements roughly aligned */
   }
-  
+
   select {
     border: 1px solid #aaa;
     border-radius: 3px;
@@ -114,7 +114,7 @@
     padding: 4px;
     color: #333;
   }
-  
+
   /* TABLES */
   table {
     border-collapse: collapse; /* Merges cell borders together */
@@ -128,7 +128,7 @@
   td:first-child, th:first-child {
     empty-cells: hide; /* Hide empty cells when they're the first in the row */
   }
-  
+
   /* Custom stuff on top of the base style sheet */
   .status {
       font-weight: bold;
@@ -146,28 +146,28 @@
   .error {
       background-color: firebrick;
   }
-  
+
   .summary a {
       font-weight: 500;
   }
-  
+
   .highlight {
       margin: 0;
   }
-  
+
   .highlight pre {
       padding: 1em;
       border: 1px solid #eee;
       background-color: #f5f5f5;
       margin-bottom: 0.1em;
       overflow-x: auto;
   }
-  
+
   .source {
       margin: 0.3em 0 2em;
       font-size: 90%;
   }
-  
+
   .source a:visited,
   .source a:link {
       color: #666;
@@ -177,10 +177,10 @@
       color: #666;
       text-decoration: underline;
   }
-  
+
   /* Pandas dataframe css */
   /* Taken from: https://github.com/spatialaudio/nbsphinx/blob/fb3ba670fc1ba5f54d4c487573dbc1b4ecf7e9ff/src/nbsphinx.py#L587-L619 */
-  
+
   table.dataframe {
     border: none !important;
     border-collapse: collapse;
@@ -226,7 +226,7 @@
   div.dataTables_filter, div.dataTables_length {
     padding: 20px;
   }
-  
+
   .backtotop {
       text-decoration: none;
       display: flex;
@@ -240,7 +240,7 @@
       margin-left: auto;
       z-index: 999;
   }
-  
+
   .priority1 {
       color: purple;
   }
@@ -253,7 +253,7 @@
   td.number {
     text-align: right;
   }
-  
+
   /* Style buttons */
   .btn {
     background-color: DodgerBlue; /* Blue background */
@@ -879,23 +879,23 @@ <h1>
     </label>
     <select id=select_cpu onchange="change(['cpu', 'ram (GB)', 'cuda'])">
       <option value=""> Any </option>
-        
+
           <option value="<b>cpu</b>: 4"> 4 </option>
     </select>
     <label for=select_ram(GB) style="padding-left: 20px; color: #333">
        RAM (GB)
     </label>
     <select id=select_ram(GB) onchange="change(['cpu', 'ram (GB)', 'cuda'])">
       <option value=""> Any </option>
-        
+
           <option value="<b>ram (GB)</b>: 31"> 31 </option>
     </select>
     <label for=select_cuda style="padding-left: 20px; color: #333">
        CUDA
     </label>
     <select id=select_cuda onchange="change(['cpu', 'ram (GB)', 'cuda'])">
       <option value=""> Any </option>
-        
+
           <option value="<b>cuda</b>: NVIDIA GeForce RTX 4090: cuda_12.2"> NVIDIA GeForce RTX 4090: cuda_12.2 </option>
     </select>
   </div>
@@ -913,46 +913,46 @@ <h1>
   <tr>
     <td class="fname">
       <a href="benchmark_FairSVM_benchopt_run_2023-10-12_22h11m38.html">
-        
+
         FairSVM 2023-10-12 22h11m38
       </a>
       <input type="checkbox" name="checkfiles" data-result="benchopt_run_2023-10-12_22h11m38.parquet" data-html="benchmark_FairSVM_benchopt_run_2023-10-12_22h11m38.html" style="display:none;">
     </td>
     <td class="datasets">
     <ul style="list-style-type: none; margin-top: 0;">
       <div class=dataset>
-        
+
           Classification_data
           <li><span style="font-size: 80%;padding-left:15px;padding-bottom:5px;">dataset_name=steel-plates-fault </span> </li>
-        
+
       </div>
       <div class=dataset>
-        
+
           <li><span style="font-size: 80%;padding-left:15px;padding-bottom:5px;">dataset_name=philippine </span> </li>
-        
+
       </div>
       <div class=dataset>
-        
+
           <li><span style="font-size: 80%;padding-left:15px;padding-bottom:5px;">dataset_name=sylva_prior </span> </li>
-        
+
       </div>
       <div class=dataset>
-        
+
           <li><span style="font-size: 80%;padding-left:15px;padding-bottom:5px;">dataset_name=creditcard </span> </li>
-        
+
       </div>
     </ul>
 
     </td>
-    
+
     <td class="sysinfo">
       <ul style="list-style-type: none; margin-top: 0;">
           <li>
             <b>CPU</b>: 4
               <button data-idx=0 id=btn_subinfo0 class="button buttoncent" style="float:right;">
                 <i class='fas fa-plus-circle'></i>
               </button>
-              
+
           </li>
           <li>
             <b>RAM (GB)</b>: 31