rmextract.def

Bootstrap: debootstrap
MirrorURL: http://archive.ubuntu.com/ubuntu/
OSVersion: jammy

%labels
        APPLICATION_NAME Ubuntu LTS + RMextract
        OS_VERSION 22.04
        APPLICATION_URL https://pypi.org/project/RMextract/

        SYSTEM_NAME ilifu
        SYSTEM_SINGULARITY_VERSION 3.9
        SYSTEM_URL http://www.ilifu.ac.za

        AUTHOR_NAME IDIA
        AUTHOR_EMAIL support@ilifu.ac.za

%help
        RMextract is Python software to extract TEC, vTEC, Earthmagnetic field and Rotation Measures (RM) 
        from GPS and WMM data for radio interferometry observations.

%environment
     
        export LC_ALL=C

%post

        # Create Installation Directories and export paths. This is needed as part of post.
        # %environment scriptlet does not define these paths during %post, only after.
        mkdir -p /opt
        export DEBIAN_FRONTEND=noninteractive

        # Installation of initial packages
        apt-get update -y && apt-get dist-upgrade -y
        apt-get install -y software-properties-common
        add-apt-repository -y universe
        apt-get update -y
        apt-get install -y wget vim apt-utils git build-essential bzip2 curl pkg-config python-is-python3 python3-pip gfortran

        # Install python packages 
        python -m pip install numpy scipy astropy 

        # Install RMextract
        cd /opt
        git clone https://github.com/lofar-astron/RMextract.git
        cd RMextract
        python setup.py build
        python setup.py install

        # Install IPykernel for Jupyter
        python -m pip install ipykernel

        # Fix command prompt in Singularity 3.5.2
        printf 'export PS1="\u@$SINGULARITY_NAME:\w$ "' > /.singularity.d/env/999-psvars.sh

        # Cleanup the container
        apt-get clean
        apt-get autoclean

%runscript

	python "$@"