Update documentation

Author: eliasinul

.doctrees/environment.pickle

@@ -21,6 +21,18 @@ RESource is developed to enable reproducible, adaptable assessments of VRE poten
 ## Workflow overview
 <img src="_static/workflow.jpg" alt="high_level_workflow" width="1000"/>
 
+---
+
+## 🚀 Quick Start
+
+```{include} notes/quickstart.md
+```
+
+```{tip}
+**Ready to dive deeper?** Check out the [Complete Setup Guide](notes/setup_guide.md) or explore the [BC Case Study](notes/case_BC.md) for detailed examples.
+```
+
+---
 
 ```{toctree}
 :caption: 'Contents:'

.doctrees/index.doctree

@@ -0,0 +1,264 @@
+# RESource Quickstart Guide
+
+**Get up and running with RESource** - A modular framework for renewable energy resource assessment.
+
+---
+
+## 🚀 Quick Setup (5 Minutes)
+
+### Prerequisites
+
+- **Linux environment** (Linux, macOS, or Windows WSL2)  
+- **Git** and **Conda/Miniconda** installed
+- **Python 3.12+** support
+
+### 1️⃣ Clone & Navigate
+
+```bash
+git clone https://github.com/DeltaE/RESource.git
+cd RESource
+```
+
+### 2️⃣ One-Command Setup
+
+```bash
+# Create complete conda environment
+make setupenv
+```
+
+### 3️⃣ Activate & Test
+
+```bash
+# Activate environment
+conda activate RES
+
+# Quick test
+python -c "import RES; print('✅ RESource ready!')"
+```
+
+**🎉 You're ready to go!**
+
+### 4️⃣ Download Case Study Data
+
+```bash
+# Download required data for Canadian analysis (~2GB)
+# Visit and download: https://zenodo.org/records/16658067
+# Extract to data/ directory
+
+wget https://zenodo.org/record/16658067/files/RESource_data.zip
+unzip RESource_data.zip -d data/
+```
+
+```{note}
+**Case Study Data**: Contains processed geospatial data for Canadian provinces including ERA5 weather data, exclusion zones, and land cover classifications needed for renewable energy resource assessment.
+```
+
+### 5️⃣ Setup API Access (For Custom Analysis)
+
+```{warning}
+**Required for Custom Regions**: Skip this step if only using the provided case study data.
+```
+
+For running custom analyses beyond the provided case study data, some data sources require API registration:
+
+- **ERA5 Climate Data**: Requires Copernicus Climate Data Store registration for global weather data
+- **CODERS API**: Requires registration for Canadian-specific data sources
+
+```{note}
+**Complete Setup Instructions**: For detailed API registration steps, configuration files, and data source information, see [data.md](data.md).
+```
+
+---
+
+## 🔥 First Run (2 Minutes)
+
+### Run Canadian Wind & Solar Analysis
+
+```bash
+# Run with default Canadian configuration
+make run
+
+# Or run specific region/config
+python run.py --config config/config_CAN_baseline.yaml
+```
+
+### Start Interactive Environment
+
+```bash
+# Launch Jupyter Lab
+make jupyter
+
+# Open notebooks/
+# Try: resources_playground_CAN.ipynb
+```
+
+---
+
+## 📊 What RESource Does
+
+RESource analyzes **renewable energy potential** by:
+
+1. **📍 Site Selection**: Filters suitable land using exclusion zones, slopes, land cover
+2. **🌤️ Weather Processing**: Converts ERA5 climate data to energy capacity factors  
+3. **⚡ Capacity Estimation**: Calculates wind/solar potential per grid cell
+4. **📈 Time Series Generation**: Creates hourly profiles for energy system modeling
+5. **🎯 Optimization**: Selects optimal sites based on capacity and cost criteria
+
+**Output Organization:**
+- **`data/store/`**: Primary resource data (HDF5 format) - detailed analysis results
+- **`results/Country/Region/Scenario/`**: Organized CSV files - resource clusters, timeseries, and cost-filtered sites
+- **`vis/Country/Region/`**: SVG/PNG visualizations - maps, supply curves, clustering analysis, and policy scenarios
+
+### Example Output
+
+```text
+data/store/
+├── resources_Canada_BC_BASELINE.h5     # resource data store for BASELINE
+
+results/Canada/BC/BASELINE/
+├── resource_options_wind_British Columbia.csv         # Wind resource clusters with LCOE
+├── resource_options_wind_British Columbia_timeseries.csv  # Hourly capacity factors
+├── resource_options_solar_British Columbia.csv        # Solar resource clusters with LCOE  
+├── resource_options_solar_British Columbia_timeseries.csv # Hourly capacity factors
+├── cells_aggregated_by_Region_BC_BASELINE.csv         # Regional capacity summaries
+├── wind_cells_below_50_$pMWh_BC_BASELINE.csv         # Cost-filtered wind sites
+├── solar_cells_below_57_$pMWh_BC_BASELINE.csv        # Cost-filtered solar sites
+└── Resource_options_summary.txt                       # Analysis summary report
+
+vis/Canada/BC/
+├── BC_gridcells_outline.svg                      # Grid cell boundaries
+├── BC_regions.png                                # Administrative regions
+├── supply_curve_baseline_vs_policy_BC.svg        # Supply curve comparisons
+├── Resources_proximity_to_grid_BC.svg            # Grid connectivity analysis
+├── BASELINE/
+│   ├── Resources_combined_CAPACITY.svg           # Combined capacity maps
+│   ├── Resources_combined_CF.svg                 # Capacity factor maps
+│   ├── Resources_combined_SCORE.svg              # Resource quality scores
+│   ├── wind/
+│   │   ├── Regional_cluster_Elbow_Plots/         # Clustering analysis plots
+│   │   └── lands/                                # Land availability analysis
+│   └── solar/
+│       ├── Regional_cluster_Elbow_Plots/         # Clustering analysis plots
+│       └── lands/                                # Land availability analysis
+└── strict_policy_aeroway_CPCAD_buffer/           # Alternative policy scenario
+    ├── cost_map_wind.svg                         # Cost mapping visualizations
+    ├── cost_map_solar.svg
+    └── potential_capacity_lost_*.svg             # Policy impact analysis
+```
+
+---
+
+## 📁 Key Files & Structure
+
+```text
+RESource/
+├── config/                      # Configuration files
+│   ├── config_CAN.yaml         # Canadian analysis setup
+│   └── config_WB6.yaml         # Western Balkans setup
+├── RES/                        # Core analysis modules
+├── notebooks/                  # Interactive examples
+├── run.py                      # Main analysis script
+├── data/
+│   └── store/                  # Main resource data storage (HDF5)
+├── results/                    # Downstream modeling exports (CSV)
+└── vis/                        # Visualizations & plots
+```
+
+---
+
+## 🛠️ Common Commands
+
+```bash
+make help              # Show all available commands
+make setupenv          # Create/setup conda environment  
+make updateenv         # Update existing environment
+make run              # Run main analysis
+make jupyter          # Start Jupyter Lab
+make docs             # Build documentation
+make clean            # Clean cache & build files
+```
+
+---
+
+## 🌍 Supported Regions
+
+- **🇨🇦 Canada**: Provincial analysis (BC, AB, SK, ON, QC, NS, MB)
+- **🌍 Western Balkans**: Regional analysis (6 countries)
+- **🔧 Custom**: Configure any region with your own data
+
+---
+
+## 📚 Next Steps
+
+### Explore Examples
+
+```bash
+# Try the playground notebooks
+jupyter lab notebooks/resources_playground_CAN.ipynb
+```
+
+### Build Documentation
+
+```bash
+# Generate full documentation
+make docs
+
+# Live development server
+make autobuild  # Visit http://127.0.0.1:8000
+```
+
+## 🆘 Need Help?
+
+### Quick Debugging
+
+```bash
+# Check environment
+conda activate RES && python -c "import RES"
+
+# Test all dependencies  
+python workflow/scripts/test_venv.py
+
+# Check data store (look for resources_Canada_*_BASELINE.h5)
+ls -la data/store/resources_Canada_*
+
+# View recent outputs - organized by Country/Region/Scenario
+ls -la results/Canada/BC/BASELINE/
+ls -la vis/Canada/BC/BASELINE/
+
+# Check visualization files
+find vis/Canada/BC/ -name "*.svg" -o -name "*.png" | head -10
+```
+
+### Resources
+
+- 📖 **Full Documentation**: [https://deltae.github.io/RESource/](https://deltae.github.io/RESource/)
+- 🐛 **Issues**: [GitHub Issues](https://github.com/DeltaE/RESource/issues)
+- 💬 **Discussions**: [GitHub Discussions](https://github.com/DeltaE/RESource/discussions)
+
+---
+
+## 🔍 Troubleshooting
+
+| Problem | Solution |
+|---------|----------|
+| `Environment 'RES' not found` | Run `make setupenv` |
+| `ImportError: No module named RES` | Run `conda activate RES` |
+| `FileNotFoundError: data/...` | Download case study data from [Zenodo](https://zenodo.org/records/16658067) |
+| `Permission denied` on WSL2 | Run `sudo chown -R $USER:$USER .` |
+| Slow downloads | Check internet connection, try different mirror |
+
+### Still Need Help?
+
+If you encounter issues not covered above, you can reach out to the development team:
+
+```{tip}
+**Contact the Developer**: For direct assistance, see contact information in [developers.md](developers.md) or open an issue on GitHub.
+```
+
+---
+
+**🎯 Ready to analyze renewable energy resources? Run `make run` and explore the results!**
+
+```{tip}
+For more detailed setup and development information, see the [Complete Setup Guide](setup_guide.md).
+```

.doctrees/notebooks/resource_module_runner.doctree

@@ -312,8 +312,6 @@ docs/
 
 ### Development
 
-- Use `make run` for running the main RESource script
-- Use `make jupyter` for interactive development (ensures correct kernel)
 - Use `make autobuild` for documentation development with live reload
 
 ### Collaboration