Dockerfile.j2

FROM {{ parent }}
LABEL MAINTAINER="Gabriel Brammer <gabriel.brammer@nbi.ku.dk>"
ARG PACKAGE_TIMEOUT=60

USER root

# Setup default timeout of installing packages
RUN echo "[global]" > /etc/pip.conf \
    && echo "timeout=$PACKAGE_TIMEOUT" >> /etc/pip.conf

# For opencv2 and basemap geos
RUN apt-get update \
    && apt-get install -yq --no-install-recommends \
    # HDF5 and netCDF4 requirements
    libhdf5-dev \
    libhdf5-doc \
    libnetcdf-dev \
    libnetcdff-dev \
    libnetcdff-doc \
    libx11-6 \
    libsm6 \
    libxext6 \
    libgeos-dev \
    libglib2.0-0 \
    libxrender1 \
    libgl1-mesa-glx \
    graphviz \
    # Required by cartopy
    libproj-dev \
    proj-data \
    proj-bin \
    libgeos-dev \
    # JWST etc
    less \
    gfortran \
    # Used in Datf exercises
    fonts-humor-sans \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /tmp

USER $NB_UID

RUN mamba config --set remote_read_timeout_secs $PACKAGE_TIMEOUT

# Proj4 is required for cartopy
COPY environment.yml /tmp/
RUN mamba env update -n python3 -f environment.yml \
    && mamba clean --all -f -y \
    && fix-permissions $CONDA_DIR \
    && fix-permissions /home/$NB_USER

# Install packages for python3 envs
COPY requirements.txt /tmp/
RUN mamba run -n python3 pip install -r requirements.txt

#################
# Grizli
RUN git clone https://github.com/gbrammer/grizli.git

WORKDIR /tmp/grizli
RUN git checkout tags/1.7
RUN mamba env update -n python3 -f environment.yml \
    && mamba clean --all -f -y \
    && fix-permissions $CONDA_DIR \
    && fix-permissions /home/$NB_USER

WORKDIR /tmp/

# Eazy-py
RUN mamba run -n python3 pip install mpdaf
RUN git clone https://github.com/gbrammer/eazy-py.git

WORKDIR /tmp/eazy-py
RUN mamba run -n python3 pip install . -r requirements.txt

WORKDIR /tmp/
   
# Conda install hstcal
RUN mamba config --add channels http://ssb.stsci.edu/astroconda 
RUN mamba config --add channels conda-forge
RUN mamba install -n python3 hstcal \
    && mamba clean --all -f -y \
    && fix-permissions $CONDA_DIR \
    && fix-permissions /home/$NB_USER

# Patch for photutils / drizzlepac
COPY photutils.patch /tmp/
RUN mamba run -n python3 pip install drizzlepac photutils --upgrade \
    && mamba clean --all -f -y \
    && fix-permissions $CONDA_DIR \
    && fix-permissions /home/$NB_USER

RUN mamba run -n python3 python /tmp/photutils.patch \
    && mamba clean --all -f -y \
    && fix-permissions $CONDA_DIR \
    && fix-permissions /home/$NB_USER

# JWST tools
RUN mamba run -n python3 pip install jwst-backgrounds
RUN mamba run -n python3 pip install jwst-gtvt
RUN mamba run -n python3 pip install jdaviz
RUN mamba run -n python3 pip install pandeia.engine

# MIRAGE
RUN mamba run -n python3 pip install mirage grismconf nircam_gsim
    
WORKDIR "${HOME}"

# FSPS
RUN git clone https://github.com/cconroy20/fsps.git fsps_home
RUN cd fsps_home/src && make
ENV SPS_HOME /home/${NB_USER}/fsps_home

# Compile python-fsps
# Padova + lores BASEL models much faster
RUN FFLAGS="-DMIST=0 -DPADOVA=1 -DMILES=0 -DBASEL=1" mamba run -n python3 pip install fsps --no-binary fsps

# Environment variables
ENV JWST_DATA /home/${NB_USER}/work/JWST/Simulations/MirageGabe
ENV CRDS_SERVER_URL https://jwst-crds.stsci.edu 
ENV CRDS_PATH /home/${NB_USER}/crds_cache 
ENV MIRAGE_DATA ${JWST_DATA}/MIRAGE_DATA 
ENV WEBBPSF_PATH ${JWST_DATA}/webbpsf-data 
ENV GRIZLI /home/${NB_USER}/work/DAWN/Science/JWST/Software 
ENV iref ${GRIZLI}/iref/
ENV jref ${GRIZLI}/jref/

# Run container as
USER $NB_UID