Fix CAI installation with Dockerfile approach

- Create custom Dockerfile that installs CAI with --no-use-pep517 flag
- Remove CAI from requirements.txt since it's handled in Dockerfile
- Add install_cai.py script for local testing
- This avoids the wheel naming issue that was causing build failures

Dockerfile

@@ -0,0 +1,68 @@
+FROM python:3.10
+
+WORKDIR /app
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    git \
+    git-lfs \
+    ffmpeg \
+    libsm6 \
+    libxext6 \
+    cmake \
+    rsync \
+    libgl1 \
+    && rm -rf /var/lib/apt/lists/* \
+    && git lfs install
+
+# Upgrade pip and install base packages
+RUN pip install --no-cache-dir pip -U && \
+    pip install --no-cache-dir \
+        setuptools \
+        wheel \
+        datasets \
+        "huggingface-hub>=0.30" \
+        "hf-transfer>=0.1.4" \
+        "protobuf<4" \
+        "click<8.1" \
+        "pydantic~=1.0"
+
+# Install CAI package first with legacy build system to avoid wheel naming issues
+RUN pip install --no-use-pep517 --no-cache-dir \
+    git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git@b6e017a92c58829f6a5aec8c26a21262bc2a6610
+
+# Copy requirements file and install remaining dependencies
+COPY requirements.txt /tmp/requirements.txt
+RUN pip install --no-cache-dir -r /tmp/requirements.txt
+
+# Install additional streamlit dependencies
+RUN pip install --no-cache-dir \
+    streamlit==1.28.1 \
+    "uvicorn>=0.14.0" \
+    spaces
+
+# Create user directory structure
+RUN mkdir -p .streamlit && \
+    git config --global core.excludesfile ~/.gitignore && \
+    echo ".streamlit" > ~/.gitignore
+
+RUN mkdir -p /home/user && \
+    ( [ -e /home/user/app ] || ln -s /app/ /home/user/app ) || true
+
+# Copy application files
+COPY --link ./ /app
+
+# Set up environment
+ENV PYTHONPATH=/app
+ENV STREAMLIT_SERVER_HEADLESS=true
+ENV STREAMLIT_SERVER_PORT=7860
+ENV STREAMLIT_SERVER_ADDRESS=0.0.0.0
+
+# Expose port
+EXPOSE 7860
+
+# Health check
+HEALTHCHECK CMD curl --fail http://localhost:7860/_stcore/health
+
+# Run the application
+CMD ["streamlit", "run", "app.py", "--server.port=7860", "--server.address=0.0.0.0"]

install_cai.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+"""
+Install CAI package with workaround for wheel naming issues.
+This script installs the CAI package using --no-use-pep517 to avoid
+the dynamic wheel naming problem that occurs with pyproject.toml builds.
+"""
+
+import subprocess
+import sys
+import os
+
+def install_cai():
+    """Install CAI package with legacy setup.py build system."""
+    print("Installing CAI package...")
+
+    # CAI repository URL and commit
+    cai_url = "git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git@b6e017a92c58829f6a5aec8c26a21262bc2a6610"
+
+    try:
+        # Install with --no-use-pep517 to force legacy setup.py build
+        cmd = [
+            sys.executable, "-m", "pip", "install",
+            "--no-use-pep517",
+            "--no-cache-dir",
+            cai_url
+        ]
+
+        print(f"Running: {' '.join(cmd)}")
+        result = subprocess.run(cmd, check=True, capture_output=True, text=True)
+
+        print("CAI installation successful!")
+        print(result.stdout)
+        return True
+
+    except subprocess.CalledProcessError as e:
+        print(f"CAI installation failed: {e}")
+        print(f"STDOUT: {e.stdout}")
+        print(f"STDERR: {e.stderr}")
+        return False
+
+def verify_installation():
+    """Verify CAI package can be imported."""
+    try:
+        import CAI
+        from CAI import CAI as cai_func, relative_adaptiveness
+        print("✅ CAI package imported successfully")
+        return True
+    except ImportError as e:
+        print(f"❌ Failed to import CAI: {e}")
+        return False
+
+if __name__ == "__main__":
+    print("ColiFormer CAI Package Installer")
+    print("=" * 40)
+
+    # Install CAI
+    if install_cai():
+        # Verify installation
+        if verify_installation():
+            print("🎉 CAI installation completed successfully!")
+            sys.exit(0)
+        else:
+            print("💥 CAI installation verification failed!")
+            sys.exit(1)
+    else:
+        print("💥 CAI installation failed!")
+        sys.exit(1)

requirements.txt

@@ -17,9 +17,3 @@ requests>=2.25.0
 ipywidgets>=7.6.0
 huggingface-hub>=0.20.0
 datasets>=2.0.0
-# Install CAI (CodonAdaptationIndex) from GitHub. Pin to master branch.
-# If this still fails, try installing this dependency separately with:
-#   pip install git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git@master
-# or clone the repo and run `pip install .` inside it.
-
-git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git@master