Fix CAI installation - remove deprecated --no-use-pep517 flag

- Remove --no-use-pep517 flag that's not supported in newer pip versions
- Use clone-and-install approach instead
- Clone CAI repo to temp directory and install from local path
- This avoids both the deprecated flag issue and wheel naming problems

app.py

@@ -11,11 +11,32 @@ def setup_cai_if_needed():
         print("CAI not found, attempting to install...")
         try:
             import subprocess
-            # Install CAI with legacy build system
-            subprocess.check_call([
-                sys.executable, "-m", "pip", "install", "--no-use-pep517", "--no-cache-dir",
-                "git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git@b6e017a92c58829f6a5aec8c26a21262bc2a6610"
-            ])
+            import tempfile
+            import shutil
+
+            # Clone the repository to a temporary directory
+            with tempfile.TemporaryDirectory() as temp_dir:
+                repo_dir = os.path.join(temp_dir, "cai")
+
+                print("Cloning CAI repository...")
+                subprocess.check_call([
+                    "git", "clone",
+                    "https://github.com/Benjamin-Lee/CodonAdaptationIndex.git",
+                    repo_dir
+                ], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+                # Checkout specific commit
+                subprocess.check_call([
+                    "git", "checkout",
+                    "b6e017a92c58829f6a5aec8c26a21262bc2a6610"
+                ], cwd=repo_dir, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+                print("Installing CAI from local directory...")
+                # Install from local directory - this avoids wheel naming issues
+                subprocess.check_call([
+                    sys.executable, "-m", "pip", "install", "--no-cache-dir", "."
+                ], cwd=repo_dir)
+
             import CAI
             print("✅ CAI installed successfully")
             return True