File size: 2,378 Bytes
54cd552 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | #!/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 "========================================================================"
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