Bootstrap: docker
From: debian:trixie-slim

%files
    neighbor/distance_runtime.py /opt/myst-plugin/distance_runtime.py
    neighbor/distance_engine.py /opt/myst-plugin/distance_engine.py
    neighbor/distance_input.py /opt/myst-plugin/distance_input.py
    neighbor/distance_options.json /opt/myst-plugin/distance_options.json
    neighbor/tree_output.py /opt/myst-plugin/tree_output.py

%post
    set -eu
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y --no-install-recommends phylip=1:3.697+dfsg-4 python3 python3-biopython python3-venv ca-certificates
    python3 -m venv --system-site-packages /opt/distance-env
    /opt/distance-env/bin/pip install commonnexus==2.0.0
    dpkg-query -W > /opt/myst-plugin/packages.tsv
    /opt/distance-env/bin/pip freeze > /opt/myst-plugin/python-packages.txt
    rm -rf /var/lib/apt/lists/*

%environment
    export OMP_NUM_THREADS=1
    export OPENBLAS_NUM_THREADS=1

%runscript
    exec /opt/distance-env/bin/python /opt/myst-plugin/distance_runtime.py "$@"

%test
    test -x /usr/lib/phylip/bin/neighbor
    /opt/distance-env/bin/python -c 'from Bio import AlignIO, Phylo; from commonnexus import Nexus'

%labels
    Author ATGC