Update README.md

Author: geopayme

README.md

@@ -8,47 +8,106 @@
 https://colab.research.google.com/github/geopayme/AstroPhysics/blob/main/DLSFH_Entropy_Diagnostic_NOAA.ipynb
 )
 
-This release package accompanies the paper:
+This repository accompanies the paper:
 
 **_Entropy Rings and Fragmented Suns: A New Approach to Flare and CME Risk Detection_**  
 Antonios Valamontes, Kapodistrian Academy of Science
 
 It contains the computational materials required for **transparent, auditable reproduction** of the paper’s diagnostic framework: a 20-node DLSFH partition of solar magnetograms, localized Shannon entropy estimation, coherence amplitude $\psi^\star_s = \exp(-S)$, SGCV fragmentation detection, entropy-ring identification via the DLSFH adjacency graph, and the composite flare/CME risk score $\(R_{\mathrm{flare}}\)$.
 
-The repository is intended to support **method verification and qualitative robustness assessment**, not operational deployment.
+The repository supports **method verification, qualitative robustness assessment, and exploratory interpretation**. It is not an operational forecasting system.
 
 ---
 
 ## Contents
 
 ### Notebooks (source of truth)
 
-In this repository, “source of truth” denotes the authoritative computational implementations from which the figures, diagnostics, and numerical results reported in the paper are generated. All analyses shown in the manuscript can be reproduced directly by executing these notebooks; derived figures or summaries should be treated as secondary to the notebook outputs.
+In this repository, **“source of truth”** denotes the authoritative computational implementations from which the figures, diagnostics, and numerical results reported in the paper are generated.
 
-The canonical analysis notebooks are hosted in the associated GitHub repository:
+#### Core reproducibility and analysis
 
-1. `DLSFH_Entropy_Diagnostic_NOAA.ipynb` — **Primary reproducibility pipeline**  
-2. `DLSFH_PhysicsEntropy_Enhanced.ipynb` — **Sensitivity / robustness exploration**  
-3. `DLSFH_PhysicsEntropy_AdvancedFinal_FINAL_5.ipynb` — **Extended physics interpretation (exploratory)**
+1. `DLSFH_Entropy_Diagnostic_NOAA.ipynb`  
+   **Canonical end-to-end pipeline**: magnetogram partitioning, entropy extraction, coherence computation, fragmentation detection, entropy-ring identification, and risk scoring.
 
-Because this ZIP is designed to be portable, it includes a **manifest** and a **fetch script** to retrieve the latest notebook copies from GitHub when internet access is available:
+2. `DLSFH_Entropy_AutoAnalysis_Patched.ipynb`  
+   Automated batch-style execution of the entropy–coherence pipeline with patched robustness handling. Used for repeated frame analysis and consistency checks.
 
-- `manifest/notebooks.json`  
-- `tools/fetch_notebooks.py`
+3. `Complete_DLSFH_Dual_Overlay_Test.ipynb`  
+   Validation notebook demonstrating geometric alignment between DLSFH node placement and NOAA active-region overlays.
+
+#### Sensitivity, robustness, and interpretation
+
+4. `DLSFH_PhysicsEntropy_Enhanced.ipynb`  
+   Sensitivity and robustness exploration (coherence threshold variation, entropy binning effects, node-level trend stability).
+
+5. `DLSFH_PhysicsEntropy_AdvancedFinal_FINAL.ipynb`  
+   Exploratory and interpretive analysis motivated by the DLSFH/SGCV framework. Not required to reproduce operational diagnostics.
 
 ---
 
 ## Execution order
 
-- **Reproduce the paper’s core results:** `DLSFH_Entropy_Diagnostic_NOAA.ipynb`  
-- **Sensitivity & robustness:** `DLSFH_PhysicsEntropy_Enhanced.ipynb`  
-- **Exploratory theory (optional):** `DLSFH_PhysicsEntropy_AdvancedFinal_FINAL_5.ipynb`
+Recommended execution order depends on intent:
+
+### Reproduce the paper’s core results
+1. `DLSFH_Entropy_Diagnostic_NOAA.ipynb`
+
+### Validate geometry and overlays
+2. `Complete_DLSFH_Dual_Overlay_Test.ipynb`
+
+### Automated or repeated analyses
+3. `DLSFH_Entropy_AutoAnalysis_Patched.ipynb`
+
+### Sensitivity and robustness
+4. `DLSFH_PhysicsEntropy_Enhanced.ipynb`
 
-See `RUN_ORDER.md` for details.
+### Exploratory theoretical interpretation (optional)
+5. `DLSFH_PhysicsEntropy_AdvancedFinal_FINAL.ipynb`
+
+See `RUN_ORDER.md` for concise guidance.
 
 ---
 
 ## Environment requirements
 
 - Python 3.10+  
-- Jupyter Notebook or JupyterLa
+- Jupyter Notebook or JupyterLab  
+- Standard scientific Python stack
+
+Environment specifications:
+- `requirements.txt` (pip)
+- `environment.yml` (conda, optional)
+
+Step-by-step instructions and expected outputs are documented in `REPRODUCIBILITY.md`.
+
+---
+
+## Data sources
+
+All analyses rely on **publicly available solar magnetogram data**, including NOAA and NSO/GONG products. No proprietary datasets are required.
+
+---
+
+## Citation and archiving
+
+Formal citation metadata and archival information are provided in:
+
+- `CITATION.cff`
+- `zenodo.json`
+
+A versioned Zenodo DOI is minted upon release to ensure long-term traceability.
+
+---
+
+## License
+
+See `LICENSE`.
+
+---
+
+## Contact
+
+Antonios Valamontes  
+Kapodistrian Academy of Science  
+Email: avalamontes@Kapodistrian.edu.gr