Dockerfile.build

# PyMaSC C Source Generation Dockerfile
# Purpose: Runtime source mounting with isolated build for race-condition prevention

ARG PYTHON_VERSION=3.11
FROM --platform=linux/amd64 python:${PYTHON_VERSION}-slim

# Install system dependencies
RUN apt-get update && apt-get install -y \
    gcc \
    g++ \
    make \
    && rm -rf /var/lib/apt/lists/*

# Install Python dependencies
RUN pip install --upgrade pip && \
    pip install setuptools wheel && \
    pip install numpy cython "pysam>=0.23.2" "bx-python>=0.10.0"

# Special handling for Python 3.9 - use numpy 1.x
ARG PYTHON_VERSION
RUN if [ "${PYTHON_VERSION}" = "3.9" ]; then \
        pip install --upgrade "numpy<2.0"; \
    fi

# Create working directories
WORKDIR /workspace
RUN mkdir -p /build /output

# Build command that:
# 1. Copies mounted source to isolated build directory
# 2. Builds BitArray
# 3. Generates C sources
# 4. Copies only the generated C files to /output
CMD ["bash", "-c", "\
    set -e && \
    echo '📁 Copying source to isolated build directory...' && \
    cp -r /workspace/. /build/ && \
    echo '🔨 Building BitArray library...' && \
    cd /build/external/BitArray && \
    make clean && make libbitarr.a && \
    cd /build && \
    echo '🐍 Generating C sources...' && \
    python setup.py build_ext -if && \
    echo '📦 Collecting generated C files...' && \
    find /build/PyMaSC -name '*_'${PYTHON_MAJOR_MINOR}'.c' -exec cp {} /output/ \\; && \
    echo '✅ C source generation complete. Files in /output:' && \
    ls -la /output/ \
"]