dockerfile

# Use the Miniconda3 image as a base
FROM continuumio/miniconda3

LABEL org.opencontainers.image.source=https://github.com/suchanek/proteusPy
LABEL org.opencontainers.image.description="RCSB Disulfide Viewer"
LABEL org.opencontainers.image.licenses=BSD-3-Clause

# Set environment variables to prevent interactive prompts during package installations
ENV DEBIAN_FRONTEND=noninteractive \
    PATH="/opt/conda/envs/proteusPy/bin:$PATH" \
    PYVISTA_OFF_SCREEN=true \
    DOCKER_RUNNING=true \
    MPLCONFIGDIR=/tmp/matplotlib \
    PDB=/home/appuser


# Install system dependencies
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
        libgl1-mesa-glx \
        mesa-utils \
        libegl1-mesa \
        xvfb \
        xauth \
        libxrender1 \
        libxext6 && \
    rm -rf /var/lib/apt/lists/*

RUN useradd -m -u 1000 appuser

# Copy the environment.yml file for better caching
COPY environment.yml /tmp/environment.yml

# Create the conda environment

RUN conda env create -f /tmp/environment.yml && \
    /opt/conda/envs/proteusPy/bin/pip install --verbose proteusPy --upgrade && \
    conda clean --all --yes && \
    rm -rf /opt/conda/pkgs/*

# Set the working directory in the container
WORKDIR /app

# Copy the current directory contents into the container at /app
COPY --chown=appuser . /app

# Fix permissions and prepare Matplotlib cache
RUN mkdir -p /tmp/matplotlib && \
    chown -R appuser:appuser /tmp/matplotlib && \
    chown -R appuser:appuser /app && \
    chmod +x /app/entrypoint.sh

# Update the login bash profile to activate the environment with interactive access.
RUN echo "source activate proteusPy" >> ~/.bashrc

# Switch to the non-root user
USER appuser

# Expose port 7860 for the Bokeh server
EXPOSE 7860

# Set the entrypoint to the entrypoint script
ENTRYPOINT ["/app/entrypoint.sh"]
CMD ["panel", "serve", "--port", "7860", "--allow-websocket-origin=*", "/app/app.py"]