Dockerfile

FROM condaforge/miniforge3:24.9.2-0

LABEL org.opencontainers.image.title="bio-compose-server-base" \
    org.opencontainers.image.description="Base Docker image for BioCompose REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance." \
    org.opencontainers.image.url="https://compose.biosimulators.org/" \
    org.opencontainers.image.source="https://github.com/biosimulators/bio-compose-server" \
    org.opencontainers.image.authors="Alexander Patrie <apatrie@uchc.edu>, BioSimulators Team <info@biosimulators.org>" \
    org.opencontainers.image.vendor="BioSimulators Team"

# SHELL ["/usr/bin/env", "bash", "-c"]

ENV DEBIAN_FRONTEND=noninteractive

# copy assets
COPY assets/docker/config/.biosimulations.json /.google/.bio-compose.json
COPY assets/docker/config/.pys_usercfg.ini /Pysces/.pys_usercfg.ini
COPY assets/docker/config/.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini
COPY tests/test_fixtures /test_fixtures

WORKDIR /app

# copy container libs
# COPY ./gateway /bio-compose-server/gateway
# COPY ./shared /bio-compose-server/shared
# COPY ./worker /bio-compose-server/worker

# copy env configs
COPY ./environment.yml /app/environment.yml
COPY ./pyproject.toml /app/pyproject.toml
COPY ./shared/scripts/entrypoint.sh /app/entrypoint.sh

# COPY . /app

RUN echo "Server" > /app/README.md \
    && mkdir /app/config \
    && chmod +x /app/entrypoint.sh
#

RUN conda update -n base -c conda-forge conda \
    && conda env create -f /app/env.yml -y \
    && conda update -n compose-server numpy -y \
    && pip install -e .

# RUN conda update -n base -c conda-forge conda \
#     && conda env create -f /app/environment.yml -y \
#     && conda run -n server poetry self update \
#     && echo "conda activate server" >> /.bashrc \
#     && conda run -n server pip install --upgrade pip
#     # && conda run -n server pip install --no-cache-dir git+https://github.com/vivarium-collective/process-bigraph.git@main

ENTRYPOINT ["/bin/bash"]

# ENTRYPOINT ["/app/entrypoint.sh"]


# RUN apt-get update \
#     && apt-get install -y \
#         meson \
#         g++ \
#         gfortran \
#         libblas-dev \
#         liblapack-dev \
#         libgfortran5 \
#         libhdf5-dev \
#         libhdf5-serial-dev \
#         libatlas-base-dev \
#         cmake \
#         make \
#         git \
#         build-essential \
#         python3-dev \
#         swig \
#         libc6-dev \
#         libx11-dev \
#         libc6 \
#         libgl1-mesa-dev \
#         pkg-config \
#         curl \
#         tar \
#         libgl1-mesa-glx \
#         libice6 \
#         libsm6 \
#         gnupg \
#         libstdc++6
# RUN conda update -n base -c conda-forge conda \
#     && conda env create -f /bio-compose-server/environment.yml -y \
#     && conda run -n server pip install --upgrade pip \
#     && echo "conda activate server" >> /.bashrc \
#     && conda run -n server poetry config virtualenvs.create false \
#     && conda run -n server poetry lock \
#     && conda run -n server poetry install

# && conda config --env --add channels conda-forge \
# && conda config --set channel_priority strict \
# && conda install readdy \
# && conda env create -f environment.yml -y
# && conda install -c conda-forge pymem3dg -y \
# && echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:\$LD_LIBRARY_PATH' >> ~/.bashrc