Merge pull request #1 from Remi-Gau/update

[ENH] set up CI

.dockerignore

@@ -0,0 +1,8 @@
+# ignoring this might speed up build
+# by preventing passing extra content to the docker daemon
+
+.github
+tests
+
+*.simg
+*.def

.gitattributes

@@ -2,3 +2,5 @@
 **/.git* annex.largefiles=nothing
 CHANGELOG.md annex.largefiles=nothing
 README.md annex.largefiles=nothing
+.github/**/*.yml annex.largefiles=nothing
+*.def annex.largefiles=nothing

.github/dependabot.yml

@@ -0,0 +1,14 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+-   package-ecosystem: github-actions
+    directory: /
+    schedule:
+        interval: monthly
+
+-   package-ecosystem: gitsubmodule
+    directory: /
+    schedule:
+        interval: monthly

.github/workflows/apptainer.yml

@@ -0,0 +1,28 @@
+---
+name: apptainer build
+
+on:
+    push:
+        branches: [master]
+    pull_request:
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    build:
+        strategy:
+            matrix:
+                image: [Singularity_MCR.def, Singularity.def]
+            fail-fast: false
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                fetch-depth: 0
+        -   uses: eWaterCycle/setup-apptainer@v2
+            with:
+                apptainer-version: 1.3.0
+        -   name: build sif image
+            run: apptainer build cat12.sif ${{ matrix.image }}

.github/workflows/docker.yml

@@ -0,0 +1,30 @@
+---
+name: docker build
+
+on:
+    push:
+        branches: [master]
+    pull_request:
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+
+    build:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                fetch-depth: 0
+        -   name: get test data
+            run: make tests/data/MoAEpilot
+        -   name: Build the Docker image
+            run: |
+                docker build . --tag cat12
+                docker images
+        -   name: help
+            run: docker run --rm cat12 view cat_standalone_segment.m
+        -   name: test
+            run: docker run -v ${PWD}/tests/data/MoAEpilot:/data --rm cat12 /data/sub-01/anat/sub-01_T1w.nii -b cat_standalone_segment.m

.gitignore

@@ -1 +1,3 @@
-.simg
+.simg
+
+tests/data

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+---
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: check-json
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-case-conflict
+    -   id: check-merge-conflict
+    -   id: mixed-line-ending
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+    -   id: yamlfmt
+        args: [--mapping, '4', --sequence, '4', --offset, '0']
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    -   id: codespell

CHANGELOG.md

@@ -0,0 +1,22 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+-->
+
+## [Unreleased]

Dockerfile

@@ -1,58 +1,72 @@
-FROM debian:bookworm-slim
+FROM ubuntu:22.04@sha256:340d9b015b194dc6e2a13938944e0d016e57b9679963fdeb9ce021daac430221
 
-LABEL org.opencontainers.image.authors="[email protected], Malgorzata Wierzba ([email protected]), Felix Hoffstaedter ([email protected])"
+LABEL org.opencontainers.image.authors="[email protected], Malgorzata Wierzba ([email protected]), Felix Hoffstaedter ([email protected]), Remi Gau ([email protected])"
 LABEL org.opencontainers.image.source="https://gin.g-node.org/felixh/cat12-container"
-LABEL org.opencontainers.image.version="v1.1"
-
-ARG DEBIAN_FRONTEND="noninteractive"
-
-ENV CATversion="r2560"
-ENV STANDALONE="/opt/spm12/toolbox/cat12/standalone"
-
-RUN apt-get update -qq && \
-    apt-get -qq -y --no-install-recommends install \
-    build-essential \
-    ca-certificates \
-    curl \
-    unzip \
-    liboctave-dev \
-    libxext6 \
-    libxt6 \
-    moreutils \
-    octave \
-    wget \
- && apt-get clean \
- && rm -rf \
-     /tmp/hsperfdata* \
-     /var/*/apt/*/partial \
-     /var/lib/apt/lists/* \
-     /var/log/apt/term*
-
-#  install SPM12
-RUN 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
+LABEL org.opencontainers.image.version="v1.1dev"
+LABEL org.opencontainers.image.licenses="MIT"
+LABEL org.opencontainers.image.title="cat12-container"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    FORCE_SPMMCR="1" \
+    SPM_HTML_BROWSER="0" \
+    MCR_INHIBIT_CTF_LOCK="1" \
+    MCR_VERSION="2017b"
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-${MCR_VERSION}/v93/runtime/glnxa64:/opt/MCR-${MCR_VERSION}/v93/bin/glnxa64:/opt/MCR-${MCR_VERSION}/v93/sys/os/glnxa64:/opt/MCR-${MCR_VERSION}/v93/extern/bin/glnxa64" \
+    MATLABCMD="/opt/MCR-${MCR_VERSION}/v93/toolbox/matlab" \
+    XAPPLRESDIR="/opt//opt/MCR-${MCR_VERSION}/v93/x11/app-defaults" \
+    MCRROOT="/opt/MCR-${MCR_VERSION}/v93" \
+    CAT_VERSION=".8.1_r2042_R${MCR_VERSION}"
+ENV SPMROOT="/opt/CAT12${CAT_VERSION}" \
+    PATH="/opt/CAT12${CAT_VERSION}:$PATH" \
+    STANDALONE="/opt/CAT12${CAT_VERSION}/standalone"
+
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bc \
+           bzip2 \
+           ca-certificates \
+           curl \
+           dbus-x11 \
+           libncurses5 \
+           libxext6 \
+           libxmu6 \
+           libxpm-dev \
+           libxt6 \
+           locales \
+           openjdk-8-jre \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt
+
+RUN echo "Downloading MATLAB Compiler Runtime ..." \
+    && export TMPDIR="$(mktemp -d)" \
+    && curl  -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R${MCR_VERSION}/deployment_files/R${MCR_VERSION}/installers/glnxa64/MCR_R${MCR_VERSION}_glnxa64_installer.zip \
+    && unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp" \
+    && "$TMPDIR/mcrtmp/install" -destinationFolder /opt/MCR-${MCR_VERSION} -mode silent -agreeToLicense yes \
+    && rm -rf "$TMPDIR" \
+    && unset TMPDIR
+
+RUN echo "Downloading standalone CAT12 ..." \
+    && curl -fL -o /tmp/cat12.zip http://www.neuro.uni-jena.de/cat12/CAT12${CAT_VERSION}_MCR_Linux.zip \
+    && unzip -q /tmp/cat12.zip -d /tmp \
+    && rm -rf /tmp/cat12.zip \
+    && mkdir -p /opt/CAT12${CAT_VERSION} \
+    && mv /tmp/*${CAT_VERSION}*/* /opt/CAT12${CAT_VERSION}/ \
+    && chmod -R 777 /opt/CAT12${CAT_VERSION} \
+    # Test
+    && /opt/CAT12${CAT_VERSION}/spm12 function exit
 
 # transfer code and set permission
 RUN mkdir -p /code
 COPY ./code /code
 RUN ls /code && find /code -type f -print0 | xargs -0 chmod +r
 
-# install CAT12
-RUN mkdir -p /batch \
-    && mkdir -p /downloads \
-    && cd /downloads \
-    && wget http://www.neuro.uni-jena.de/cat12/cat12_${CATversion}.zip && unzip -d /opt/spm12/toolbox/ cat12_${CATversion}.zip \
-    && rm -fr /downloads \
-    && cd ${STANDALONE} && chmod +rx *.sh \
-    && cd /code && ln -s ${STANDALONE}/*.sh . \
-    && cd /batch && ln -s ${STANDALONE}/*.m .
-
-# clean
-RUN rm -f /opt/spm12/src/*.{mex,o,a}
+WORKDIR ${STANDALONE}
 
-ENTRYPOINT ['/code/main "$@"']
+ENTRYPOINT ["/code/main"]

README.md

@@ -1,7 +1,24 @@
-# Project <insert name>
+# CAT-12 container
 
-## Dataset structure
+Docker and Apptainer image for [CAT12](https://neuro-jena.github.io/cat/).
 
-- All inputs (i.e. building blocks from other sources) are located in
-  `inputs/`.
-- All custom code is located in `code/`.
+CAT12 8.1 r2042
+SPM12, version 7771 (standalone)
+MATLAB, version 9.3.0.713579 (R2017b)
+
+
+## Usage notes
+
+
+### Example
+
+```bash
+docker build . --tag cat12
+```
+
+```bash
+docker run -v ${PWD}/tests/data/MoAEpilot:/data \
+    --rm -it cat12 \
+        /data/sub-01/anat/sub-01_T1w.nii \
+        -b cat_standalone_segment.m
+```

Singularity → Singularity.def

@@ -22,15 +22,15 @@ From: debian:bookworm-slim
     DEBIAN_FRONTEND=noninteractive apt-get --yes --quiet install \
       octave \
       liboctave-dev
-    
+
     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://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
-    
+
     CATversion="r2560"
 
     cd /downloads

Singularity_MCR → Singularity_MCR.def

@@ -161,7 +161,7 @@ USAGE:
    -a2 <STRING>| --arg2 <STRING> 2nd additional argument (otherwise use defaults or batch)
    -a <STRING> | --add  <STRING> add option to batch file
 
-   The first occurance of the parameter "<UNDEFINED>" in the batch file will be replaced by the
+   The first occurrence of the parameter "<UNDEFINED>" in the batch file will be replaced by the
    list of input files. You can use the existing batch files in this folder or create your own batch
    file with the SPM12 batch editor and leave the data field undefined. Please note that for creating
    your own batch file CAT12 has to be called in expert mode because the CAT12 standalone installation

code/main

@@ -1,18 +1,15 @@
 #!/bin/bash
 
-# Help
+# Copy or view batch files
 
+# Help
 if [ "$#" = 0 ]
 then
     echo "ERROR: No arguments passed."
-    cat /.singularity.d/runscript.help
+    exec ${STANDALONE}/cat_standalone.sh
     exit 1
 fi
 
-# Copy or view batch files
-
-STANDALONE="/opt/spm12/toolbox/cat12/standalone"
-
 if [ "$1" = "copy" ]
 then
     if [ "$2" = "all" ]
@@ -22,7 +19,7 @@ then
 	exit 0
     elif [ -f ${STANDALONE}/"$2" ]
     then
-	echo "Copying batch file to:"    
+	echo "Copying batch file to:"
 	cp -vi ${STANDALONE}/"$2" "$3"
 	exit 0
     else
@@ -37,13 +34,12 @@ then
 	cat ${STANDALONE}/"$2"
 	exit 0
     else
-        echo "ERROR: batch file $2 not found. Available batch files are:"
+        echo "ERROR: batch file '$2' not found. Available batch files are:"
         find ${STANDALONE} -name "*.m" -printf "%f\n"
         exit 1
     fi
 fi
 
 # Run CAT
-
 NOW=$(date +%s)
-exec /code/cat_standalone.sh "$@" 2>&1 |tee cat_$NOW.log
+exec ${STANDALONE}/cat_standalone.sh "$@" 2>&1 | tee cat_$NOW.log