Update docs, instructions and format code

CONTRIBUTING.md

@@ -6,7 +6,6 @@ Thank you for your interest in contributing to Entropice! This document provides
 
 ### Prerequisites
 
-- Python 3.13
 - CUDA 12 compatible GPU (for full functionality)
 - [Pixi package manager](https://pixi.sh/)
 
@@ -16,55 +15,36 @@ Thank you for your interest in contributing to Entropice! This document provides
 pixi install
 ```
 
-This will set up the complete environment including RAPIDS, PyTorch, and all geospatial dependencies.
+This will set up the complete environment including Python, RAPIDS, PyTorch, and all geospatial dependencies.
 
 ## Development Workflow
 
-**Important**: Always use `pixi run` to execute Python commands and scripts to ensure you're using the correct environment with all dependencies.
+> Read in the [Architecture Guide](ARCHITECTURE.md) about the code organisatoin and key modules
 
-### Code Organization
+**Important**: Always use `pixi run` to execute Python commands and scripts to ensure you're using the correct environment with all dependencies:
 
-- **`src/entropice/ingest/`**: Data ingestion modules (darts, era5, arcticdem, alphaearth)
-- **`src/entropice/spatial/`**: Spatial operations (grids, aggregators, watermask, xvec)
-- **`src/entropice/ml/`**: Machine learning components (dataset, training, inference)
-- **`src/entropice/utils/`**: Utilities (paths, codecs)
-- **`src/entropice/dashboard/`**: Streamlit visualization dashboard
-- **`scripts/`**: Data processing pipeline scripts (numbered 00-05)
-- **`notebooks/`**: Exploratory analysis and validation notebooks
-- **`tests/`**: Unit tests
+```bash
+pixi run python script.py
+pixi run python -c "import entropice"
+```
 
-### Key Modules
-
-- `spatial/grids.py`: H3/HEALPix spatial grid systems
-- `ingest/darts.py`, `ingest/era5.py`, `ingest/arcticdem.py`, `ingest/alphaearth.py`: Data source processors
-- `ml/dataset.py`: Dataset assembly and feature engineering
-- `ml/training.py`: Model training with eSPA, XGBoost, Random Forest, KNN
-- `ml/inference.py`: Prediction generation
-- `utils/paths.py`: Centralized path management
-
-## Coding Standards
-
-### Python Style
+### Python Style and Formatting
 
 - Follow PEP 8 conventions
 - Use type hints for function signatures
-- Prefer numpy-style docstrings for public functions
+- Prefer google-style docstrings for public functions
 - Keep functions focused and modular
 
-### Geospatial Best Practices
+`ty` and `ruff` are used for typing, linting and formatting.
+Ensure to check for any warnings from both of these:
 
-- Use **xarray** with XDGGS for gridded data storage
-- Store intermediate results as **Parquet** (tabular) or **Zarr** (arrays)
-- Leverage **Dask** for lazy evaluation of large datasets
-- Use **GeoPandas** for vector operations
-- Use EPSG:3413 (Arctic Stereographic) coordinate reference system (CRS) for any computation on the data and EPSG:4326 (WGS84) for data visualization and compatability with some libraries
+```sh
+pixi run ty check # For type checks
+pixi run ruff check # For linting
+pixi run ruff format # For formatting
+```
 
-### Data Pipeline
-
-- Follow the numbered script sequence: `00grids.sh` → `01darts.sh` → ... → `05train.sh`
-- Each stage should produce reproducible intermediate outputs
-- Document data dependencies in module docstrings
-- Use `utils/paths.py` for consistent path management
+Single files can be specified by just adding them to the command, e.g. `pixi run ty check src/entropice/dashboard/app.py`
 
 ## Testing
 
@@ -74,13 +54,6 @@ Run tests for specific modules:
 pixi run pytest
 ```
 
-When running Python scripts or commands, always use `pixi run`:
-
-```bash
-pixi run python script.py
-pixi run python -c "import entropice"
-```
-
 When adding features, include tests that verify:
 
 - Correct handling of geospatial coordinates and projections
@@ -100,15 +73,8 @@ When adding features, include tests that verify:
 ### Commit Messages
 
 - Use present tense: "Add feature" not "Added feature"
-- Reference issues when applicable: "Fix #123: Correct grid aggregation"
 - Keep first line under 72 characters
 
-## Working with Data
-
-### Local Development
-
-- Set `FAST_DATA_DIR` environment variable for data directory (default: `./data`)
-
 ### Notebooks
 
 - Notebooks in `notebooks/` are for exploration and validation, they are not commited to git