Bootstrap: docker
From: debian:bookworm-slim

%labels
    Author ATGC
    Tool ERaBLE
    Version 1.0
    PluginVersion 1.0.4
    InputNormalization unrooted-degree-three-root-v1
    DenseWorkloadLimit 12582912-cells
    Source https://gite.lirmm.fr/atgc/atgc_erable
    SourceCommit 4c1320614ba427c9d2649da0778ce837d002553e
    License GPL-3.0

%files
    erable/runner.py /opt/erable/runner.py
    erable/inputs.py /opt/erable/inputs.py

%post
    set -eu
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y --no-install-recommends ca-certificates curl g++ python3
    curl --fail --location --retry 3 \
        'https://gite.lirmm.fr/atgc/atgc_erable/-/raw/4c1320614ba427c9d2649da0778ce837d002553e/erable1.0_Unix_Linux.tar.gz' \
        -o /tmp/erable.tar.gz
    echo 'b03ff6f4d854a7cc064f392e428447932cdf1dba08c39712b88354d6ab1bef9a  /tmp/erable.tar.gz' | sha256sum -c -
    mkdir -p /opt/erable/source
    tar -xzf /tmp/erable.tar.gz -C /opt/erable/source --strip-components=1
    cd /opt/erable/source
    g++ -std=c++11 -O2 -Wno-deprecated-declarations -Wno-ignored-attributes src/*.cpp -o /usr/local/bin/erable
    # Retain the source, bundled Eigen and GPL text alongside the executable.
    rm /tmp/erable.tar.gz
    apt-get clean
    rm -rf /var/lib/apt/lists/*

%runscript
    exec python3 /opt/erable/runner.py "$@"

%test
    set -eu
    test -x /usr/local/bin/erable
    erable_test_dir="$(mktemp -d /tmp/erable-test.XXXXXX)"
    trap 'rm -rf "$erable_test_dir"' EXIT
    cp /opt/erable/source/Example/* "$erable_test_dir/"
    cd "$erable_test_dir"
    python3 /opt/erable/runner.py --matrices input_matrices.txt --topology input_tree_topology.nwk
    test -s erable.length.nwk
    test -s erable.rates.tsv
    # The upstream reader crashes on a degree-two root. Verify our canonicalizer
    # suppresses that artificial root without changing the scientific result.
    printf '%s\n' '((Tax10,(Tax34,(Tax20,Tax4))),(Tax14,Tax3));' > rooted.nwk
    cp erable.rates.txt expected.rates.txt
    python3 /opt/erable/runner.py --matrices input_matrices.txt --topology rooted.nwk
    cmp expected.rates.txt erable.rates.txt