verify_setup.sh

#!/bin/bash
# GeneMamba HuggingFace - Quick Setup Guide
# Run this script to verify and test the installation

set -e

echo "========================================================================"
echo "GeneMamba Hugging Face - Verification Script"
echo "========================================================================"

PROJECT_DIR="/project/zhiwei/cq5/PythonWorkSpace/GeneMamba_HuggingFace"

echo ""
echo "[1] Checking directory structure..."
cd "$PROJECT_DIR"

# Check critical files
files_to_check=(
    "configuration_genemamba.py"
    "modeling_outputs.py"
    "modeling_genemamba.py"
    "__init__.py"
    "README.md"
    "LICENSE"
    "requirements.txt"
    "setup.py"
    "examples/1_extract_embeddings.py"
    "examples/2_finetune_classification.py"
    "examples/3_continue_pretraining.py"
    "examples/4_pretrain_from_scratch.py"
    "scripts/push_to_hub.py"
)

all_ok=true
for file in "${files_to_check[@]}"; do
    if [ -f "$file" ]; then
        echo "  ✓ $file"
    else
        echo "  ✗ MISSING: $file"
        all_ok=false
    fi
done

if [ "$all_ok" = true ]; then
    echo ""
    echo "[2] All files present! ✓"
else
    echo ""
    echo "[2] Some files are missing! ✗"
    exit 1
fi

echo ""
echo "[3] File Statistics:"
echo "  - Python files: $(find . -name '*.py' | wc -l)"
echo "  - Total lines of code: $(find . -name '*.py' -exec wc -l {} + | tail -1 | awk '{print $1}')"
echo "  - Documentation lines: $(wc -l README.md | awk '{print $1}')"

echo ""
echo "========================================================================"
echo "✓ GeneMamba HuggingFace Project - READY TO USE"
echo "========================================================================"
echo ""
echo "Next Steps:"
echo ""
echo "1. Install dependencies:"
echo "   pip install -r requirements.txt"
echo ""
echo "2. Install package in editable mode:"
echo "   pip install -e ."
echo ""
echo "3. Run an example (after conda activate and installing deps):"
echo "   python examples/1_extract_embeddings.py"
echo ""
echo "4. Learn more:"
echo "   - Read: README.md"
echo "   - View project structure: PROJECT_STRUCTURE.md"
echo ""
echo "5. To upload to Hugging Face Hub:"
echo "   python scripts/push_to_hub.py --model_path ./checkpoint --repo_name username/GeneMamba"
echo ""
echo "========================================================================"