Dockerfile-base

# FROM ghcr.io/biosimulators/biosimulators:latest
FROM ghcr.io/vivarium-collective/biosimulator-processes:0.0.4

LABEL authors="alexanderpatrie"

ENV DEBIAN_FRONTEND=noninteractive
ENV MONGO_URI="mongodb://mongodb/?retryWrites=true&w=majority&appName=bio-check"

# handle app creds from google
RUN mkdir /.google
COPY ./assets/.biosimulations.json /.google/.bio-check.json
# COPY ./.bio-check.json /.google/.bio-check.json

# hdf5/amici deps
RUN apt-get update \
    && apt-get install -y libatlas-base-dev libhdf5-serial-dev swig libboost-all-dev \
    && rm -rf /var/lib/apt/lists/*

# handle main content
WORKDIR /app

RUN mkdir /app/data

# copy deps
COPY ./assets/requirements.base.txt ./assets/scripts/remove_deps.sh ./assets/scripts/update_deps.sh ./assets/dropped.txt ./assets/scripts/install_deps.sh /app/assets/

# copy example files TODO: optimize this.
COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex /app/data/Elowitz-Nature-2000-Repressilator.omex
COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator /app/data/Elowitz-Nature-2000-Repressilator

RUN chmod +x /app/assets/install_deps.sh \
    && /app/assets/install_deps.sh /app/assets/requirements.base.txt

# RUN poetry add $(cat /app/assets/requirements.base.txt)

# RUN chmod +x /app/assets/remove_deps.sh \
#     && chmod +x /app/assets/update_deps.sh \
#     && pip install --upgrade pip  \
#     && /app/assets/remove_deps.sh \
#     && pip install --no-cache-dir -r /app/assets/requirements.base.txt \
#     && pip install --upgrade google-cloud-storage

# shared tooling module
# COPY ./assets/shared.py /app/shared.py