Maintenance and documentation release.

.github/workflows/tests.yml

@@ -2,9 +2,9 @@ name: Tests
 
 on:
   push:
-    branches: [ main, dev_1.4, dev_1.7, dev_v0.2.0, dev_v0.2.1]
+    branches: [ main, dev_1.4, dev_1.7, dev_v0.2.0, dev_v0.2.1, dev_v0.2.2 ]
   pull_request:
-    branches: [ main, dev_1.4, dev_1.7, dev_v0.2.0, dev_v0.2.1 ]
+    branches: [ main, dev_1.4, dev_1.7, dev_v0.2.0, dev_v0.2.1, dev_v0.2.2 ]
 
 jobs:
   tests:
@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       # 1) Récupérer le code

.gitignore

@@ -14,6 +14,7 @@ __pycache__/
 *.pyd
 *.dll
 .pytest_tmp/
+tmp/
 *venv*/
 *.db
 *.db*
@@ -27,6 +28,9 @@ documentation/readthedocs/_build/
 # PACKAGE DATA
 # -------------------------------
 
+# Dev TODOs
+future_todos.md
+
 # Ignore everything inside OUTPUT, but keep the folder itself
 src/shinier/data/OUTPUT/*
 !src/shinier/data/OUTPUT/.gitkeep

README.md

@@ -1,4 +1,4 @@
-# 🌟 SHINIER
+# SHINIER
 ```text
    ███████╗██╗  ██╗██╗███╗  ██╗██╗███████╗██████╗
    ██╔════╝██║  ██║██║████╗ ██║██║██╔════╝██╔══██╗
@@ -15,26 +15,26 @@
 [![Tests](https://github.com/Charestlab/shinier/actions/workflows/tests.yml/badge.svg)](https://github.com/Charestlab/shinier/actions/workflows/tests.yml)
 ---
 
-## 🎯 Overview
+## Overview
 
 SHINIER is a modern Python implementation of SHINE (Spectrum, Histogram, and Intensity Normalization and Equalization), originally developed in MATLAB by Willenbockel et al., 2010. It provides precise control over luminance, contrast, histograms, and spectral content across large image sets for well-calibrated visual experiments.
 
 ### Key Features and Improvements
 
-- 🎨 **Color Processing** — New modes for color image control with modern color-space standards (Rec.601 / Rec.709 / Rec.2020).
-- 🖼️ **Dithering Support** — Reduces quantization artifacts and enhances output image quality.
-- ⚡ **Optimized Performance** — Efficient memory management and faster processing for large image sets (optional Cython/C++ convolution core).
-- 🕰 **Legacy Mode** — Ensures full backward compatibility with MATLAB’s original SHINE toolbox.
-- 🔢 **High-Precision Arithmetic** — Computations in floating-point precision rather than 8-bit integer space, minimizing rounding errors in multi-stage processing.
-- 📦 **Object-Oriented Design** — Modular, extensible architecture with a clean Python API.
-- 😀 **User-Friendly CLI** — Guided, prompt-based interface for users who prefer not to write code.
+- **Color Processing** — New modes for color image control with modern color-space standards (Rec.601 / Rec.709 / Rec.2020).
+- **Dithering Support** — Reduces quantization artifacts and enhances output image quality.
+- **Optimized Performance** — Efficient memory management and faster processing for large image sets (optional Cython/C++ convolution core).
+- **Legacy Mode** — Ensures full backward compatibility with MATLAB’s original SHINE toolbox.
+- **High-Precision Arithmetic** — Computations in floating-point precision rather than 8-bit integer space, minimizing rounding errors in multi-stage processing.
+- **Object-Oriented Design** — Modular, extensible architecture with a clean Python API.
+- **User-Friendly CLI** — Guided, prompt-based interface for users who prefer not to write code.
 
 For detailed technical documentation (algorithms, numerical choices, and MATLAB vs Python behavior), see  
 [`documentation/documentation.md`](documentation/documentation.md).
 
 ---
 
-## 🚀 Quick Start
+## Quick Start
 
 ### Installation
 
@@ -68,7 +68,7 @@ print("shinier version:", getattr(shinier, "__version__", "unknown"))
 ```
 
 
-### 😀 **User-friendly  Interface**
+### User-friendly Interface
 Call the following bash command to quickly start using the interactive CLI.  
 ```bash
 shinier --show_results --image_index=1
@@ -77,7 +77,7 @@ shinier --show_results --image_index=1
   <img src="https://raw.githubusercontent.com/Charestlab/shinier/main/assets/DEMO_INTERACTIVE_CLI.gif" width="1000" alt="CLI demo">
 </p>
 
-### 🧩 Example in Python
+### Example in Python
 Run the following python code to make sure the package is running properly.
 ```python
 from shinier import Options, ImageDataset, ImageProcessor, utils
@@ -102,15 +102,15 @@ Change the mode number (e.g. `opt = Options(mode=3)`) to change image processing
 | 6    | `hist_match → spec_match`         | Histogram, then spectrum                  |
 | 7    | `sf_match → hist_match`           | Spatial frequency, then histogram         |
 | 8    | `spec_match → hist_match` (default) | Spectrum, then histogram (recommended)  |
-| 9    | `dithering`                       | Dithering only                            |
+| 9    | `ie_methods` or `dithering`       | Standalone per-image transform (histogram-derived enhancement or dithering) |
 
 Below is an example of results obtained using mode 5 with joint histogram equalization and spatial frequency normalization.
 <p>
   <img src="https://raw.githubusercontent.com/Charestlab/shinier/main/assets/demo_cli_mode5.png" width="600" alt="CLI demo">
 </p>
 
 ---
-## 🏛️ **Technical information**
+## **Technical information**
 
 Documentation:
 1. [Package Overview](documentation/documentation.md#overview)
@@ -128,29 +128,30 @@ Documentation:
 13. [Additional Resources](documentation/documentation.md#additional-resources)
 
 ---
-## 📚 Citing
+## Citing
 If you use **SHINIER**, please cite both of these articles:
 
 ### References
-- Salvas-Hébert, M., Dupuis-Roy, N., Landry, C., Charest, I., & Gosselin, F. (2026). *SHINIER: An Open-Source Python Package for Controlling Low-Level Image Properties*
-- Willenbockel, V., Sadr, J., Fiset, D., Horne, G. O., Gosselin, F., & Tanaka, J. W. (2010). Controlling low-level image properties: The SHINE toolbox. *Behavior Research Methods, 42*(3), 671–684. https://doi.org/10.3758/BRM.42.3.671
+- Salvas-Hébert, M., Dupuis-Roy, N., Landry, C., Charest, I., & Gosselin, F. (2026). SHINIER: An open-source Python package for controlling low-level image properties. *SoftwareX*, *35*, Article 102884. https://doi.org/10.1016/j.softx.2026.102884
+- Willenbockel, V., Sadr, J., Fiset, D., Horne, G. O., Gosselin, F., & Tanaka, J. W. (2010). Controlling low-level image properties: The SHINE toolbox. *Behavior Research Methods*, *42*(3), 671–684. https://doi.org/10.3758/BRM.42.3.671
 
 ---
-## 🤝 Contributing
+## Contributing
 See [CONTRIBUTING.md](documentation/contributing.md) for guidelines (coding standards, tests, docs, and PR flow).
 
 ---
-## 📄 License
+## License
 See [LICENSE](LICENSE) for more information.
 
 ---
-## 🛠️ Troubleshooting
+## Troubleshooting
 - No compiler available: install a C/C++ toolchain or proceed with the NumPy fallback (slower).
+- Compiled extension fails to load (e.g., NumPy too old / ABI mismatch): SHINIER warns and uses the NumPy fallback; upgrade NumPy (and pip/setuptools/wheel) and reinstall to restore the compiled core.
 - Import errors after upgrade: try pip install --upgrade pip setuptools wheel and reinstall.
 - Windows build issues: ensure MSVC Build Tools are installed and on PATH.
 
 ---
 <p align="center">
   <strong>Code developed by Nicolas Dupuis-Roy and Mathias Salvas-Hébert </strong><br>
-  <em>Version 0.2.0 - Complete technical documentation</em>
+  <em>Version 0.2.2 - Complete technical documentation</em>
 </p>

documentation/contributing.md

@@ -40,7 +40,7 @@ By participating, you agree to uphold a standard of professional, inclusive, and
 
 ## Development Setup
 
-> **Python:** >=3.9, <3.13  
+> **Python:** >=3.9, <3.15  
 > **OS:** macOS / Linux / Windows  
 > **Optional:** C/C++ toolchain for the Cython-compiled `_cconvolve` extension (speeds up convolution)
 
@@ -238,6 +238,6 @@ pytest -m unit_tests
 # Validation Tests (VERY LONG AND SLOW) and markers
 pytest -q -m validation_tests
 ```
-#### 🏛️ Test README
+#### Test README
 For complete testing procedures (markers, sharding, replay/debug workflow), see the dedicated
 Testing Guide in `tests/README.md`.

documentation/demos.md

@@ -140,7 +140,7 @@ MASKS_FOLDER  = "path"
 
 ---
 
-### Mode 1 – `lum_match`
+#### Mode 1 – `lum_match`
 
 ```python
 """
@@ -168,7 +168,7 @@ opts = Options(
 
 ---
 
-### Mode 2 – `hist_match`
+#### Mode 2 – `hist_match`
 
 ```python
 """
@@ -193,7 +193,7 @@ opts = Options(
 
 ---
 
-### Mode 3 – `sf_match`
+#### Mode 3 – `sf_match`
 
 ```python
 """
@@ -216,7 +216,7 @@ opts = Options(
 
 ---
 
-### Mode 4 – `spec_match`
+#### Mode 4 – `spec_match`
 
 ```python
 """
@@ -240,7 +240,7 @@ opts = Options(
 
 ---
 
-### Mode 5 – `hist_match` → `sf_match`
+#### Mode 5 – `hist_match` → `sf_match`
 
 ```python
 """
@@ -249,7 +249,7 @@ Mode 5 (hist_match & sf_match): histogram matching followed by rotational
 
 Example use case: Histogram specification with noise is applied (legacy method),
   then rotational Fourier spectra are aligned. No rescaling is performed
-  afterwards,to preserve the luminance distribution imposed by histogram
+  afterwards, to preserve the luminance distribution imposed by histogram
   matching.
 """
 opts = Options(
@@ -264,7 +264,7 @@ opts = Options(
 
 ---
 
-### Mode 6 – `hist_match` → `spec_match`
+#### Mode 6 – `hist_match` → `spec_match`
 
 ```python
 """
@@ -285,7 +285,7 @@ opts = Options(
 
 ---
 
-### Mode 7 – `sf_match` → `hist_match`
+#### Mode 7 – `sf_match` → `hist_match`
 
 ```python
 """
@@ -308,7 +308,7 @@ opts = Options(
 
 ---
 
-### Mode 8 – `spec_match` → `hist_match`
+#### Mode 8 – `spec_match` → `hist_match`
 
 ```python
 """
@@ -332,11 +332,11 @@ opts = Options(
 
 ---
 
-### Mode 9 – Standalone Per-Image Transform
+#### Mode 9 – Standalone Per-Image Transform
 
 Mode 9 applies a standalone transform to each image independently — no inter-image target is computed. The operation is selected via `standalone_op`.
 
-#### 9a – Image Enhancement (`standalone_op="ie_methods"`)
+**9a — Image enhancement** (`standalone_op="ie_methods"`)
 
 ```python
 """
@@ -355,7 +355,7 @@ opts = Options(
 )
 ```
 
-#### 9b – Dithering only (`standalone_op="dithering"`)
+**9b — Dithering only** (`standalone_op="dithering"`)
 
 ```python
 """
@@ -373,15 +373,15 @@ opts = Options(
 
 ---
 
-### Example 10 – Mode 2 + extra parameters
+#### Example 10 – Mode 2 + extra parameters
 
 ```python
 """
 Example 10 (mode 2 + non-mode-specific parameters): to show the other parameters.
 
 Example use case: hist_matching using Coltuc, Bolon & Chassery (2006) exact
   histogram specification. Target histogram will be the average from all the
-  images (default), no SSIM optimization (Avanki, 2009).
+  images (default), no SSIM optimization (Avanaki, 2009).
 
   The masks loaded from masks_folder are used for figure-ground separation
   (whole_image = 3). The images will be transformed to grayscale (1 channel),
@@ -405,7 +405,7 @@ opts = Options(
 
 ---
 
-### Example 11 – Preserve colors with `constrain_image_chrominance`
+#### Example 11 – Preserve colors with `constrain_image_chrominance`
 
 ```python
 """