update README

Author: enigne

.github/workflows/CI.yml

@@ -56,8 +56,12 @@ jobs:
         DDE_BACKEND: ${{matrix.backend}}
       run: |
         pytest --cov --junitxml=junit.xml -o junit_family=legacy
-    - name: Upload coverage reports to Codecov
+    - name: Upload coverage test results to Codecov
       if: ${{ !cancelled() }}
       uses: codecov/test-results-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

README.md

@@ -1,48 +1,149 @@
+# PINNICLE: Physics-Informed Neural Networks for Ice and CLimatE
 
-# PINNICLE
-Physics Informed Neural Networks for Ice and CLimatE
-
+![Python](https://img.shields.io/badge/python-3.9+-blue.svg)
 [![CI](https://github.com/ISSMteam/PINNICLE/actions/workflows/CI.yml/badge.svg)](https://github.com/ISSMteam/PINNICLE/actions/workflows/CI.yml)
 [![codecov](https://codecov.io/gh/ISSMteam/PINNICLE/graph/badge.svg?token=S7REK0IKJH)](https://codecov.io/gh/ISSMteam/PINNICLE)
 [![Documentation Status](https://readthedocs.org/projects/pinnicle/badge/?version=latest)](https://pinnicle.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15178900.svg)](https://doi.org/10.5281/zenodo.15178900)
+![License](https://img.shields.io/github/license/ISSMteam/PINNICLE)
+![PyPI](https://img.shields.io/pypi/v/pinnicle)
+
+**PINNICLE** (Physics-Informed Neural Networks for Ice and CLimatE) is an open-source Python library for modeling ice sheets using physics-informed neural networks.
+It is designed to integrate physical laws with observational data to solve both forward and inverse problems in glaciology.
+The library currently supports stress balance approximations, mass conservation, and time-dependent simulations, etc. Built on top of [DeepXDE](https://github.com/lululxvi/deepxde), it supports TensorFlow, PyTorch, and JAX backends.
 
-A Python library for solving ice sheet modeling problems using a unified framework with Physics Informed Neural Networks
+Developed at the Department of Earth Sciences, Dartmouth College, USA.
 
+![](docs/images/pinn.png)
 
 ---
-**NOTE**
 
-   This project is under active development.
+## 🚀 Features
 
----
+- Solve forward and inverse glaciological problems
+- Built-in support for:
+  - Shelfy-Stream Approximation (SSA)
+  - Mono-Layer Higher-Order (MOLHO) stress balance
+  - Time-dependent mass conservation
+- Support for multiple backends: TensorFlow, PyTorch, JAX
+- Integration with observational data: [ISSM](https://issm.jpl.nasa.gov) data format, MATLAB general `.mat`, HDF5, NetCDF.
+- Fourier Feature Transform for input and output
+- Fully modular and customizable architecture
 
-**Documentation**: [pinnicle.readthedocs.io](https://pinnicle.readthedocs.io)
 
-![](docs/images/pinn.png)
+## 📦 Installation
+
+### Install from PyPI (recommended)
+
+```bash
+pip install pinnicle
+```
+
+### Install from source
+
+```bash
+git clone https://github.com/ISSMteam/PINNICLE.git
+cd PINNICLE
+pip install -e .
+```
+### Dependencies
+
+PINNICLE requires:
+
+* Python ≥ 3.9
+* [DeepXDE](https://github.com/lululxvi/deepxde)
+* NumPy, SciPy, pandas, matplotlib, scikit-learn
+* mat73 (for MATLAB v7.3 files)
+
+## ⚙️ Backend Selection
+
+PINNICLE supports TensorFlow, PyTorch, and JAX backends via DeepXDE.
+
+Choose your backend:
+
+```bash
+DDE_BACKEND=tensorflow python your_script.py
+```
+
+You can also export the backend globally (Linux/macOS):
+
+```bash
+export DDE_BACKEND=pytorch
+```
+
+Alternatively, edit `~/.deepxde/config.json`:
+
+```json
+{
+  "backend": "tensorflow"
+}
+```
 
-## Physics
+## 🧪 Examples
 
-- Momentum Conservation (stress balance):
-  - Shelfy Stream Approximation (SSA)
-  - MOno-Layer Higher-Order (MOLHO) ice flow model
+Example scripts and input files are located in the [`examples/`](https://github.com/ISSMteam/PINNICLE/tree/main/examples) directory.
 
-- Mass Conservation (mass balance):
-  - Thickness evolution
+* [**Example 1**](https://github.com/ISSMteam/PINNICLE/blob/main/examples/example1_helheim_ssa_inverse.py):
+  Inverse problem on Helheim Glacier using SSA to infer basal friction
 
-- Coupuling:
-  - stress balance + mass balance
+* [**Example 2**](https://github.com/ISSMteam/PINNICLE/blob/main/examples/example2_pig_ssa_rheology.py):
+  Joint inversion of basal friction and ice rheology for Pine Island Glacier
 
-- Time dependent problems
+* [**Example 3**](https://github.com/ISSMteam/PINNICLE/blob/main/examples/example3_helheim_forward_transient.py):
+  Time-dependent forward modeling of Helheim Glacier (2008–2009)
 
-## Data format
+Each example includes a complete Python script and configuration dictionary.
 
-- [ISSM](https://issm.jpl.nasa.gov) `model()` type, directly saved from ISSM by `saveasstruct(md, filename)`
-- Scattered data
 
+## 📖 Documentation
+
+Full documentation is available in the `docs/` folder or at:
+
+📘 [pinnicle.readthedocs.io](https://pinnicle.readthedocs.io)
+
+
+## 📚 Citation
+
+If you use PINNICLE in your research, please cite:
+
+> Cheng, G., Krishna, M., and Morlighem, M.: A Python library for solving ice sheet modeling problems using Physics Informed Neural Networks, PINNICLE v1.0, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2025-1188, 2025.
+
+**BibTeX**:
+
+```bibtex
+@Article{egusphere-2025-1188,
+   AUTHOR = {Cheng, G. and Krishna, M. and Morlighem, M.},
+   TITLE = {A Python library for solving ice sheet modeling problems using Physics Informed Neural Networks, PINNICLE v1.0},
+   JOURNAL = {EGUsphere},
+   VOLUME = {2025},
+   YEAR = {2025},
+   PAGES = {1--26},
+   URL = {https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1188/},
+   DOI = {10.5194/egusphere-2025-1188}
+}
+```
+
+---
+
+## 📂 License
+
+This project is licensed under the [GNU Lesser General Public License v2.1](LICENSE).
+
+---
+
+## 🤝 Acknowledgements
+
+Supported by:
+
+* National Science Foundation \[#2118285, #2147601]
+* Novo Nordisk Foundation \[NNF23OC00807040]
+* Heising-Simons Foundation \[2019-1161, 2021-3059]
+
+---
 
-## More
+## 🔗 Links
 
-- [Install and Setup](https://pinnicle.readthedocs.io/en/latest/installation.html#installation)
-- [An example of stress balance](https://pinnicle.readthedocs.io/en/latest/examples/ssa.html)
+* 📦 PyPI: [pinnicle](https://pypi.org/project/pinnicle/)
+* 📖 Documentation: [pinnicle.readthedocs.io](https://pinnicle.readthedocs.io)
+* 📄 Zenodo Archive: [doi.org/10.5281/zenodo.15178900](https://doi.org/10.5281/zenodo.15178900)