Dockerfile

# Start from Ubuntu Noble
FROM ubuntu:noble

# Define build arguments
ARG UNAME
ARG UID
ARG ARCH
ARG AARCH
ARG VIRTUAL_ENV
ARG ALLOW_ROOT_ARG
ARG PORT_ARG
ENV ALLOW_ROOT=$ALLOW_ROOT_ARG
ENV PORT=$PORT_ARG

# Arguments for optinal packages
ARG OPTIONAL_PKGS=0
ARG INSTALL_M2=0
ARG INSTALL_SAGE=0

# Use noninteractive to avoid interactive prompts
ENV DEBIAN_FRONTEND=noninteractive

# Add Macaulay2 repo
# (MUST BE DONE BEFORE Python 3.11)
RUN if [ "$INSTALL_M2" = "1" ]; then \
        apt-get update; \
        apt-get install -y --no-install-recommends gpg-agent; \
        apt-get install -y --no-install-recommends software-properties-common apt-transport-https; \
        add-apt-repository ppa:macaulay2/macaulay2; \
        apt-get update && apt-get clean; \
    fi

# Install Python 3.11
RUN apt-get update && \
    apt-get install -y software-properties-common && \
    add-apt-repository ppa:deadsnakes/ppa && \
    apt-get update && \
    apt-get install -y python3.11 python3.11-venv python3.11-distutils python3.11-dev && \
    ln -fs /usr/share/zoneinfo/Etc/UTC /etc/localtime && \
    apt-get install -y tzdata && \
    dpkg-reconfigure --frontend noninteractive tzdata && \
    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1 && \
    update-alternatives --set python3 /usr/bin/python3.11 && \
    python3 -m ensurepip && \
    rm -rf /var/lib/apt/lists/*

# Reset DEBIAN_FRONTEND variable to its default value
ENV DEBIAN_FRONTEND=

# Set python3 as the default python
RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1

# Install dependencies
RUN apt-get -yqq update
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata
RUN apt-get -yqq install autoconf build-essential nano cmake libgmp-dev libcgal-dev\
                         libmpc-dev libsuitesparse-dev libppl-dev libeigen3-dev\
                         libc6 libcdd0d libgmp10 libgmpxx4ldbl libstdc++6 palp\
                         libflint-dev curl\
                         wget libmath-libm-perl normaliz libqsopt-ex2
RUN apt-get -yqq install nodejs

# Install Macaulay2 (optional)
RUN if [ "$INSTALL_M2" = "1" ]; then \
        apt-get -yqq install macaulay2; \
    fi

# Install Sage (optional)
RUN if [ "$INSTALL_SAGE" = "1" ]; then \
        apt-get -yqq install sagemath; \
    fi

# Make a soft link to the arb library and flint headers so that python-flint can install
#RUN ln -s /usr/lib/${AARCH}-linux-gnu/libflint-arb.so /usr/lib/${AARCH}-linux-gnu/libarb.so
RUN ln -s /usr/include/flint/* /usr/include/

# Set up non-root user
RUN if [ -z "$UID" ]; then \
        echo "Error: UID is not set. Exiting."; \
        exit 1; \
    fi

RUN set -ex && \
    echo "UID: $UID" && \
    if id -u $UID >/dev/null 2>&1; then \
        # If UID exists, check if it's root (0)
        if [ "$UID" -eq 0 ]; then \
            # If UID is 0, ensure UNAME is set to root
            if [ "$UNAME" != "root" ]; then \
                echo "Error: UID is 0, but UNAME is not root. Exiting."; \
                exit 1; \
            fi; \
        else \
            # Non-root UID exists... rename existing user to $UNAME
            USERNAME=$(getent passwd $UID | cut -d: -f1); \
            if [ "$USERNAME" != "$UNAME" ]; then \
                usermod -l $UNAME $USERNAME; \
                usermod -md /home/$UNAME $UNAME; \
                groupmod -n $UNAME $USERNAME; \
            fi; \
        fi; \
    else \
        # Create group and user $UNAME with enforced UID
        groupadd -r -g $UID $UNAME && \
        useradd -r -s /bin/bash -u $UID -g $UNAME -m $UNAME; \
    fi

# ensure we own the home directory
RUN if [ "$UNAME" != "root" ]; then \
        chown -R $UNAME:$UNAME /home/$UNAME; \
    fi

# Install Rust since there are some Python packages that now depend on it
USER $UNAME
RUN curl https://sh.rustup.rs -sSf | bash -s -- -y && \
    echo "Rust installed successfully." || \
    (echo "Rust installation failed." && exit 1)

# Update PATH for Rust
ENV PATH="/home/${UNAME}/.cargo/bin:${PATH}"

# Create python virtual environment for non-root user
RUN python3 -m venv $VIRTUAL_ENV
ENV PATH="$VIRTUAL_ENV/bin:$PATH"

# Install pip packages
ENV CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse
WORKDIR /opt/cytools/
COPY ./requirements.txt /opt/cytools/requirements.txt
COPY ./c.txt /opt/cytools/c.txt
RUN pip3 install Cython==0.29.34
RUN PIP_CONSTRAINT=c.txt pip3 install -r requirements.txt
RUN pip3 install python-flint==0.6.0
RUN pip3 install -f https://download.mosek.com/stable/wheel/index.html Mosek
ENV MOSEKLM_LICENSE_FILE=/home/$UNAME/mounted_volume/mosek/mosek.lic

# Install optional packages
USER $UNAME
RUN if [ "$OPTIONAL_PKGS" = "1" ]; then \
        export NODE_VERSION=v18.13.0 && \
        export NVM_DIR=/home/$UNAME/.nvm && \
        mkdir -p $NVM_DIR && \
        curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.3/install.sh | bash && \
        . "$NVM_DIR/nvm.sh" && nvm install ${NODE_VERSION} && \
        . "$NVM_DIR/nvm.sh" && nvm use ${NODE_VERSION} && \
        . "$NVM_DIR/nvm.sh" && nvm alias default ${NODE_VERSION} && \
        echo "export PATH=\"$NVM_DIR/versions/node/${NODE_VERSION}/bin/:$PATH\"" >> /home/$UNAME/.bashrc && \
        . /home/$UNAME/.bashrc && \
        pip3 install sympy==1.11.1 galois==0.3.3 plotly==5.13.1 plotly_express==0.4.1 ipywidgets==7.7.1 jupyterlab-widgets==1.1.1 networkx==3.0 && \
        jupyter lab build; \
    fi


# Fix cvxopt bug
USER root
RUN sed -i -e 's/mosek.solsta.near_optimal/ /g' $VIRTUAL_ENV/lib/python3.11/site-packages/cvxopt/coneprog.py

# Install TOPCOM
WORKDIR /opt/cytools/external/topcom-mod
RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v1.1.2%2Bds-1%2Bcytools-1/topcom_1.1.2+ds-1+cytools-1_${ARCH}.deb
RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v1.1.2%2Bds-1%2Bcytools-1/libtopcom0_1.1.2+ds-1+cytools-1_${ARCH}.deb
RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v1.1.2%2Bds-1%2Bcytools-1/libtopcom-dev_1.1.2+ds-1+cytools-1_${ARCH}.deb
RUN dpkg -i topcom_1.1.2+ds-1+cytools-1_${ARCH}.deb
RUN dpkg -i libtopcom0_1.1.2+ds-1+cytools-1_${ARCH}.deb
RUN dpkg -i libtopcom-dev_1.1.2+ds-1+cytools-1_${ARCH}.deb

# Download file from github to keep track of the number of downloads
RUN wget https://github.com/LiamMcAllisterGroup/cytools/releases/download/v1.0.0/download_counter.txt

# Copy code and installer
COPY . /opt/cytools/
WORKDIR /opt/cytools/
RUN pip3 install .

# Create CGAL code for different dimensions and compile
WORKDIR /opt/cytools/external/cgal
RUN for i in $(seq 2 5); do sed "27s/.*/typedef CGAL::Epick_d<CGAL::Dimension_tag<${i}> >    K;/" cgal-triangulate.cpp > "cgal-triangulate-${i}d.cpp"; done;

# Fix CGAL headers so that Eigen3 is imported correctly
RUN sed -i -e 's/Eigen\/Core/eigen3\/Eigen\/Core/g' /usr/include/CGAL/Dimension.h
RUN sed -i -e 's/Eigen\/Dense/eigen3\/Eigen\/Dense/g' /usr/include/CGAL/NewKernel_d/LA_eigen/LA.h
RUN sed -i -e 's/Eigen\/Dense/eigen3\/Eigen\/Dense/g' /usr/include/CGAL/NewKernel_d/LA_eigen/constructors.h

RUN cgal_create_CMakeLists
RUN sed -i -e 's/find_package/find_package( Eigen3 3.3 REQUIRED )\nfind_package/g' /opt/cytools/external/cgal/CMakeLists.txt
RUN cmake . -DCMAKE_BUILD_TYPE=Release
# Must be single-threaded or it crashes on macOS
RUN make -j 1
RUN for i in $(seq 2 5); do ln -s "/opt/cytools/external/cgal/cgal-triangulate-${i}d" "/usr/local/bin/cgal-triangulate-${i}d"; done
RUN ln -s "/opt/cytools/external/cgal/cgal-triangulate" "/usr/local/bin/cgal-triangulate"

# Set variables so that numpy is limited to one thread
ENV MKL_NUM_THREADS=1
ENV NUMEXPR_NUM_THREADS=1
ENV OMP_NUM_THREADS=1
ENV OPENBLAS_NUM_THREADS=1

# Set entry path
WORKDIR /home/$UNAME/mounted_volume

# Start jupyter lab by default
USER $UNAME
CMD PYDEVD_DISABLE_FILE_VALIDATION=1 jupyter-lab --ip 0.0.0.0 --port $PORT --no-browser $ALLOW_ROOT