Merge pull request #7 from dfeen87/copilot/fix-reproducibility-and-packaging-drift

Fix reproducibility and packaging drift

Author: dfeen87

README.md

@@ -70,8 +70,8 @@ G(t) = 1{ΔΦ(t) ≥ τ}
 
 ```bash
 # Clone the repository
-git clone https://github.com/dfeen87/triadic-biosignal-monitor.git
-cd triadic-biosignal-monitor
+git clone https://github.com/dfeen87/Triadic-Biosignal-Monitor.git
+cd Triadic-Biosignal-Monitor
 
 # Install dependencies
 pip install -r requirements.txt
@@ -88,7 +88,7 @@ jupyter notebook notebooks/01_phase_extraction_demo.ipynb
 ## Repository Structure
 
 ```
-triadic-biosignal-monitor/
+Triadic-Biosignal-Monitor/
 ├── README.md                            # This file
 ├── LICENSE                              # MIT License
 ├── .github/workflows                    # CI Pipeline
@@ -417,45 +417,14 @@ pytest --cov=core tests/
 Comprehensive documentation available in `/docs/`:
 
 - **[SCOPE_AND_SAFETY.md](docs/SCOPE_AND_SAFETY.md)** - Medical-device safe language, regulatory guidance
-- **[IMPLEMENTATION_GUIDE.md](docs/IMPLEMENTATION_GUIDE.md)** - Technical implementation details
 - **[REPRODUCIBILITY.md](docs/REPRODUCIBILITY.md)** - How to reproduce paper results
-- **[API_REFERENCE.md](docs/API_REFERENCE.md)** - Function signatures and usage
 - **[VALIDATION_PROTOCOL.md](docs/VALIDATION_PROTOCOL.md)** - Prospective validation guidelines
 
 ---
 
 ## Dependencies
 
-```
-# Core numerical computing
-numpy>=1.24.0
-scipy>=1.10.0
-
-# Signal processing
-mne>=1.3.0              # EEG processing
-neurokit2>=0.2.0        # ECG/HRV analysis
-PyWavelets>=1.4.0       # Wavelet transforms
-
-# Entropy and complexity
-antropy>=0.1.6          # Entropy measures
-nolds>=0.5.2            # Nonlinear dynamics
-
-# Configuration
-pyyaml>=6.0
-h5py>=3.8.0
-
-# Visualization
-matplotlib>=3.7.0
-seaborn>=0.12.0
-
-# Testing
-pytest>=7.3.0
-pytest-cov>=4.0.0
-
-# Notebooks
-jupyter>=1.0.0
-ipywidgets>=8.0.0
-```
+See [`requirements.txt`](requirements.txt) for the full, versioned list of dependencies.
 
 ---
 
@@ -504,7 +473,7 @@ If you use this software in your research, please cite:
            Early-Warning Detection in Coupled EEG–ECG Time Series},
   year = {2026},
   publisher = {GitHub},
-  url = {https://github.com/dfeen87/triadic-biosignal-monitor}
+  url = {https://github.com/dfeen87/Triadic-Biosignal-Monitor}
 }
 
 @article{kruger2026operator,
@@ -552,8 +521,8 @@ This work builds on established signal processing and time-series analysis metho
 
 ## Contact & Support
 
-- **Issues:** [GitHub Issues](https://github.com/dfeen87/triadic-biosignal-monitor/issues)
-- **Discussions:** [GitHub Discussions](https://github.com/dfeen87/triadic-biosignal-monitor/discussions)
+- **Issues:** [GitHub Issues](https://github.com/dfeen87/Triadic-Biosignal-Monitor/issues)
+- **Discussions:** [GitHub Discussions](https://github.com/dfeen87/Triadic-Biosignal-Monitor/discussions)
 - **Email:** marcelkrueger092@gmail.com, dfeen87@gmail.com
 
 ---

requirements.txt

@@ -1,40 +1,48 @@
 # Core Scientific Computing
-numpy>=1.21.0,<2.0.0
-scipy>=1.7.0,<2.0.0
-matplotlib>=3.4.0,<4.0.0
+numpy>=1.24.0,<2.0.0
+scipy>=1.10.0,<2.0.0
+matplotlib>=3.7.0,<4.0.0
 pandas>=1.3.0,<3.0.0
 
 # Signal Processing
 scikit-learn>=1.0.0,<2.0.0
+mne>=1.3.0,<2.0.0
+neurokit2>=0.2.0,<1.0.0
+PyWavelets>=1.4.0
+
+# Entropy and Complexity
+antropy>=0.1.6
+nolds>=0.5.2
+
+# Data Storage
+h5py>=3.8.0
 
 # Jupyter and Notebooks
 jupyter>=1.0.0
 jupyterlab>=3.0.0
 notebook>=6.4.0
 ipykernel>=6.0.0
 nbconvert>=6.0.0
+ipywidgets>=8.0.0
 
 # Visualization
-seaborn>=0.11.0,<1.0.0
+seaborn>=0.12.0,<1.0.0
 plotly>=5.0.0,<6.0.0
 
-# Optional: EEG/ECG Data Loading
-mne>=1.0.0,<2.0.0  # For EEG data formats (.edf, .fif)
-
-# Optional: Additional utilities
-tqdm>=4.60.0  # Progress bars
-pyyaml>=5.4.0  # Configuration files
+# Configuration and Utilities
+tqdm>=4.60.0
+pyyaml>=6.0
 
 # Testing (optional but recommended)
-pytest>=6.2.0,<8.0.0
-pytest-cov>=2.12.0
+pytest>=7.3.0,<8.0.0
+pytest-cov>=4.0.0
 
 # Code Quality (optional)
-black>=21.0  # Code formatting
-flake8>=3.9.0  # Linting
-pylint>=2.10.0  # Static analysis
-mypy>=0.910  # Type checking
+black>=21.0
+flake8>=3.9.0
+pylint>=2.10.0
+mypy>=0.910
 
 # Documentation (optional)
-sphinx>=4.0.0  # Documentation generation
-sphinx-rtd-theme>=0.5.0  # ReadTheDocs theme
+sphinx>=4.0.0
+sphinx-rtd-theme>=0.5.0

setup.py

@@ -5,11 +5,19 @@
 
 from setuptools import setup, find_packages
 from pathlib import Path
+import re
 
 # Read the README file for long description
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text(encoding="utf-8")
 
+# Read version from the package __init__.py (single source of truth)
+init_text = (this_directory / "triadic_biosignal_monitor" / "__init__.py").read_text(encoding="utf-8")
+version_match = re.search(r'^__version__\s*=\s*["\']([^"\']+)["\']', init_text, re.MULTILINE)
+if not version_match:
+    raise RuntimeError("Unable to find version in triadic_biosignal_monitor/__init__.py")
+version = version_match.group(1)
+
 # Read requirements from requirements.txt
 requirements = []
 with open("requirements.txt", "r", encoding="utf-8") as f:
@@ -35,7 +43,7 @@
 
 setup(
     name="triadic-biosignal-monitor",
-    version="1.0.0",
+    version=version,
     author="Marcel Krüger, Don Feeney",
     author_email="marcelkrueger092@gmail.com, dfeen87@gmail.com",
     description="Operator-based heart-brain monitoring via triadic spiral-time embeddings",

triadic_biosignal_monitor/__init__.py

@@ -0,0 +1,11 @@
+"""
+Triadic Biosignal Monitor
+
+Operator-based heart-brain monitoring via triadic spiral-time embeddings.
+
+Authors: Marcel Krüger, Don Feeney
+"""
+
+__version__ = "1.0.0"
+__author__ = "Marcel Krüger, Don Feeney"
+__email__ = "marcelkrueger092@gmail.com, dfeen87@gmail.com"