Add env.sh installation script with uv support

Author: HFooladi

env.sh

@@ -0,0 +1,108 @@
+#!/bin/bash
+
+# THEMAP Environment Setup Script
+# This script sets up a Python virtual environment using uv and installs all dependencies
+#
+# Usage:
+#   source env.sh    (recommended - keeps environment activated)
+#   bash env.sh      (requires manual activation after)
+
+set -e  # Exit on error
+
+echo "=========================================="
+echo "THEMAP Environment Setup"
+echo "=========================================="
+echo ""
+
+# Check if uv is installed
+if ! command -v uv &> /dev/null; then
+    echo "📦 uv not found. Installing uv..."
+    curl -LsSf https://astral.sh/uv/install.sh | sh
+
+    # Add uv to PATH for this session
+    export PATH="$HOME/.cargo/bin:$PATH"
+
+    echo "✅ uv installed successfully"
+    echo ""
+else
+    echo "✅ uv is already installed"
+    echo ""
+fi
+
+# Check Python version
+echo "🐍 Checking Python version..."
+if command -v python3.11 &> /dev/null; then
+    PYTHON_CMD="python3.11"
+elif command -v python3.10 &> /dev/null; then
+    PYTHON_CMD="python3.10"
+elif command -v python3.9 &> /dev/null; then
+    PYTHON_CMD="python3.9"
+else
+    PYTHON_CMD="python3"
+fi
+
+PYTHON_VERSION=$($PYTHON_CMD --version 2>&1 | awk '{print $2}')
+echo "   Using Python: $PYTHON_VERSION"
+echo ""
+
+# Create virtual environment with uv
+echo "🔨 Creating virtual environment in .venv..."
+uv venv .venv --python $PYTHON_CMD
+echo "✅ Virtual environment created"
+echo ""
+
+# Activate virtual environment
+echo "🔄 Activating virtual environment..."
+source .venv/bin/activate
+echo "✅ Virtual environment activated"
+echo ""
+
+# Upgrade pip and install build tools
+echo "📦 Installing build tools..."
+uv pip install --upgrade pip setuptools wheel
+echo "✅ Build tools installed"
+echo ""
+
+# Install THEMAP with all dependencies
+echo "📚 Installing THEMAP with all dependencies..."
+echo "   This includes: core, ml, otdd, protein, dev, and test dependencies"
+echo ""
+
+# Install the package in editable mode with all optional dependencies
+uv pip install -e ".[all,dev,test]"
+
+echo ""
+echo "✅ Installation complete!"
+echo ""
+
+# Minimal verification
+echo "🔍 Verifying installation..."
+python -c "import themap; from themap.data import MoleculeDatapoint; print(f'✅ THEMAP v{themap.__version__} imported successfully')"
+
+if [ $? -eq 0 ]; then
+    echo ""
+    echo "=========================================="
+    echo "🎉 Setup Complete!"
+    echo "=========================================="
+    echo ""
+
+    # Check if script was sourced
+    if [ -n "$BASH_SOURCE" ] && [ "$0" != "$BASH_SOURCE" ]; then
+        echo "✅ Environment is ACTIVE in your current shell"
+        echo ""
+        echo "Next steps:"
+        echo "   python run_tests.py              # Run tests"
+        echo "   python examples/basic/molecule_datasets_demo.py  # Try an example"
+        echo ""
+    else
+        echo "To activate the environment, run:"
+        echo "   source .venv/bin/activate"
+        echo ""
+        echo "Or run this script with 'source' to auto-activate:"
+        echo "   source env.sh"
+        echo ""
+    fi
+else
+    echo "❌ Verification failed. Installation may be incomplete."
+    exit 1
+fi