bidspm.def

BootStrap: docker
From: ubuntu:jammy-20240808

%files
    pyproject.toml /opt/bidspm/pyproject.toml
    requirements.txt /opt/bidspm/requirements.txt
    README.md  /opt/bidspm/README.md
    bidspm.m /opt/bidspm/bidspm.m
    src /opt/bidspm/src
    lib /opt/bidspm/lib
    .git /opt/bidspm/.git

%post
    apt-get -qq update
    DEBIAN_FRONTEND=noninteractive apt-get --yes --quiet install \
        apt-utils \
        build-essential \
        ca-certificates \
        curl \
        default-jre \
        fonts-freefont-otf \
        ghostscript \
        git \
        gnuplot-x11 \
        libcurl4-gnutls-dev \
        liboctave-dev \
        octave \
        octave-common \
        octave-io \
        octave-image \
        octave-signal \
        octave-statistics \
        python3-pip \
        python3 \
        software-properties-common \
        unzip \
        zip && \
    apt-get clean && \
    rm -rf \
        /tmp/hsperfdata* \
        /var/*/apt/*/partial \
        /var/lib/apt/lists/* \
        /var/log/apt/term*

    curl -fsSL https://deno.land/install.sh | sh
    export DENO_INSTALL="/root/.deno"
    export PATH="$DENO_INSTALL/bin:$PATH"
    deno install -Agf -n bids-validator jsr:@bids/validator@1.14.12

    mkdir /opt/spm12
    curl -fsSL --retry 5 https://github.com/spm/spm12/archive/r7771.tar.gz | tar -xzC /opt/spm12 --strip-components 1
    curl -fsSL --retry 5 https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch | patch -p0
    make -C /opt/spm12/src PLATFORM=octave distclean
    make -C /opt/spm12/src PLATFORM=octave
    make -C /opt/spm12/src PLATFORM=octave install
    ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12

    git -C /opt/bidspm restore .
    git -C /opt/bidspm/ submodule foreach --recursive 'git reset --hard'
    git -C /opt/bidspm/ submodule foreach --recursive 'git clean --force -dfx'
    git -C /opt/bidspm/ status

    pip install --upgrade pip
    pip install -r /opt/bidspm/requirements.txt
    pip install /opt/bidspm
    octave --no-gui --eval "addpath('/opt/spm12/'); savepath ('/usr/share/octave/site/m/startup/octaverc');" && \
    octave --no-gui --eval "addpath('/opt/bidspm/'); savepath('/usr/share/octave/site/m/startup/octaverc'); bidspm(); path"  && \
    octave --no-gui --eval "path"

%runscript
    bidspm "$@"

%help
    This is a bidspm container.
    Please see the documentation for more instructions:
    https://bidspm.readthedocs.io/en/latest/