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#!/usr/bin/env python3
"""
Setup script for CAI package installation in ColiFormer.
This script handles the installation of the CAI package with proper build flags
to avoid wheel naming issues that occur with standard pip install.
"""
import subprocess
import sys
import os
import importlib.util
def check_cai_installed():
"""Check if CAI package is already installed and working."""
try:
spec = importlib.util.find_spec("CAI")
if spec is None:
return False
# Try to import the specific functions we need
import CAI
from CAI import CAI as cai_func, relative_adaptiveness
print("✅ CAI package is already installed and working")
return True
except ImportError as e:
print(f"❌ CAI package not found or not working: {e}")
return False
def install_cai():
"""Install CAI package with proper build configuration."""
print("🔧 Installing CAI package...")
cai_repo = "git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git@b6e017a92c58829f6a5aec8c26a21262bc2a6610"
try:
# First ensure we have build tools
print("Installing build dependencies...")
subprocess.run([
sys.executable, "-m", "pip", "install", "--upgrade",
"setuptools>=65.0", "wheel>=0.37.0", "pip>=21.0"
], check=True, capture_output=True)
# Try installing with --no-use-pep517 flag first (preferred method)
print("Attempting CAI installation with legacy build system...")
try:
result = subprocess.run([
sys.executable, "-m", "pip", "install",
"--no-use-pep517", "--no-cache-dir", cai_repo
], check=True, capture_output=True, text=True)
print("✅ CAI installed successfully with legacy build")
return True
except subprocess.CalledProcessError:
print("⚠️ Legacy build failed, trying standard installation...")
# Fallback to standard installation
result = subprocess.run([
sys.executable, "-m", "pip", "install", "--no-cache-dir", cai_repo
], check=True, capture_output=True, text=True)
print("✅ CAI installed successfully with standard build")
return True
except subprocess.CalledProcessError as e:
print(f"❌ CAI installation failed: {e}")
if hasattr(e, 'stderr') and e.stderr:
print(f"Error output: {e.stderr}")
return False
except Exception as e:
print(f"❌ Unexpected error during CAI installation: {e}")
return False
def verify_cai_installation():
"""Verify that CAI package is working correctly."""
try:
import CAI
from CAI import CAI as cai_func, relative_adaptiveness
# Test basic functionality
test_sequences = ["ATGAAATAA", "ATGGGCTAA"]
weights = relative_adaptiveness(sequences=test_sequences)
cai_score = cai_func("ATGAAATAA", weights=weights)
print(f"✅ CAI verification successful (test score: {cai_score:.3f})")
return True
except Exception as e:
print(f"❌ CAI verification failed: {e}")
return False
def main():
"""Main setup function."""
print("ColiFormer CAI Setup")
print("=" * 50)
# Check if already installed
if check_cai_installed():
if verify_cai_installation():
print("🎉 CAI is ready to use!")
return True
else:
print("⚠️ CAI is installed but not working properly, reinstalling...")
# Install CAI
if install_cai():
# Verify installation
if verify_cai_installation():
print("🎉 CAI setup completed successfully!")
return True
else:
print("💥 CAI installation verification failed!")
return False
else:
print("💥 CAI installation failed!")
return False
if __name__ == "__main__":
success = main()
sys.exit(0 if success else 1)
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