Dockerfile

FROM nvidia/cuda:11.3.1-base-ubuntu20.04

ENV DEBIAN_FRONTEND=noninteractive \
        TZ=Europe/Paris

# Remove any third-party apt sources to avoid issues with expiring keys.
# Install some basic utilities
RUN rm -f /etc/apt/sources.list.d/*.list && \
    apt-get update && apt-get install -y --no-install-recommends \
    curl \
    ca-certificates \
    sudo \
    git \
    wget \
    procps \
    git-lfs \
    zip \
    unzip \
    htop \
    vim \
    nano \
    bzip2 \
    libx11-6 \
    build-essential \
    libsndfile-dev \
    software-properties-common \
    libxrender1 \
 && rm -rf /var/lib/apt/lists/*

RUN add-apt-repository ppa:flexiondotorg/nvtop && \
    apt-get upgrade -y && \
    apt-get install -y --no-install-recommends nvtop

RUN curl -sL https://deb.nodesource.com/setup_14.x  | bash - && \
    apt-get install -y nodejs && \
    npm install -g configurable-http-proxy

# Create a working directory
WORKDIR /app

# Create a non-root user and switch to it
RUN adduser --disabled-password --gecos '' --shell /bin/bash user \
 && chown -R user:user /app
RUN echo "user ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/90-user
USER user

# All users can use /home/user as their home directory
ENV HOME=/home/user
RUN mkdir $HOME/.cache $HOME/.config \
 && chmod -R 777 $HOME

# Set up the Conda environment
ENV CONDA_AUTO_UPDATE_CONDA=false \
    PATH=$HOME/miniconda/bin:$PATH
RUN curl -sLo ~/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
 && chmod +x ~/miniconda.sh \
 && ~/miniconda.sh -b -p ~/miniconda \
 && rm ~/miniconda.sh \
 && conda clean -ya

WORKDIR $HOME/app

#######################################
# Start root user section
#######################################

USER root

# User Debian packages
## Security warning : Potential user code executed as root (build time)
RUN --mount=target=/root/packages.txt,source=packages.txt \
    apt-get update && \
    xargs -r -a /root/packages.txt apt-get install -y --no-install-recommends \
    && rm -rf /var/lib/apt/lists/*

RUN --mount=target=/root/on_startup.sh,source=on_startup.sh,readwrite \
        bash /root/on_startup.sh

RUN mkdir /data && chown user:user /data
RUN mkdir /data/chemprop_nbs && chown user:user /data/chemprop_nbs
#######################################
# End root user section
#######################################

USER user
# build jupyter env
RUN --mount=target=requirements.txt,source=requirements.txt \
    pip install --no-cache-dir --upgrade -r requirements.txt


# build an empty conda environment with appropriate Python version
RUN conda create --name chemprop_env python=3.11*

SHELL ["conda", "run", "--no-capture-output", "-n", "chemprop_env", "/bin/bash", "-c"]

# Follow the installation instructions then clear the cache
ADD chemprop chemprop
ADD jupyter_examples /data/chemprop_nbs
ADD LICENSE.txt pyproject.toml README.md ./
RUN conda install pytorch cpuonly -c pytorch && \
    conda install nb_conda_kernels && \
    conda clean --all --yes && \
    python -m pip install . && \
    python -m pip cache purge



# Python packages - should be all installed with pip install ./chemprop
#RUN --mount=target=requirements.txt,source=requirements.txt \
#    pip install --no-cache-dir --upgrade -r requirements.txt



# Copy the current directory contents into the container at $HOME/app setting the owner to the user
COPY --chown=user . $HOME/app

RUN chmod +x start_server.sh

COPY --chown=user login.html /home/user/miniconda/lib/python3.9/site-packages/jupyter_server/templates/login.html

ENV PYTHONUNBUFFERED=1 \
        GRADIO_ALLOW_FLAGGING=never \
        GRADIO_NUM_PORTS=1 \
        GRADIO_SERVER_NAME=0.0.0.0 \
        GRADIO_THEME=huggingface \
        SYSTEM=spaces \
        SHELL=/bin/bash

CMD ["./start_server.sh"]
####################################################### FROM CHEMPROP DOCKERFILE ##########################################################
# Dockerfile
#
# Builds a Docker image containing Chemprop and its required dependencies.
#
# Build this image with:
#  git clone https://github.com/chemprop/chemprop.git
#  cd chemprop
#  docker build --tag=chemprop:latest .
#
# Run the built image with:
#  docker run --name chemprop_container -it chemprop:latest
#
# Note:
# This image only runs on CPU - we do not provide a Dockerfile
# for GPU use (see installation documentation). 

# Parent Image
#FROM continuumio/miniconda3:latest

# Install libxrender1 (required by RDKit) and then clean up
#RUN apt-get update && \
#    apt-get install -y \
#    libxrender1 && \
#    apt-get autoremove -y && \
#    apt-get clean -y

#WORKDIR /opt/chemprop

# build an empty conda environment with appropriate Python version
#RUN conda create --name chemprop_env python=3.11*

# This runs all subsequent commands inside the chemprop_env conda environment
#
# Analogous to just activating the environment, which we can't actually do here
# since that requires running conda init and restarting the shell (not possible
# in a Dockerfile build script)
#SHELL ["conda", "run", "--no-capture-output", "-n", "chemprop_env", "/bin/bash", "-c"]

# Follow the installation instructions then clear the cache
#ADD chemprop chemprop
#ENV PYTHONPATH /opt/chemprop
#ADD LICENSE.txt pyproject.toml README.md ./
#RUN conda install pytorch cpuonly -c pytorch && \
#    conda clean --all --yes && \
#    python -m pip install . && \
#    python -m pip cache purge

# when running this image, open an interactive bash terminal inside the conda environment
#RUN echo "conda activate chemprop_env" > ~/.bashrc
#ENTRYPOINT ["/bin/bash", "--login"]