Merge pull request #573 from Remi-Gau/infra

[INFRA] misc

Author: Remi-Gau

.all-contributorsrc

@@ -8,7 +8,7 @@
   "contributors": [
     {
       "login": "OliColli",
-      "name": "OliColli",
+      "name": "Olivier Collignon",
       "avatar_url": "https://avatars0.githubusercontent.com/u/55407947?v=4",
       "profile": "https://cpplab.be",
       "contributions": [
@@ -19,7 +19,7 @@
     },
     {
       "login": "anege",
-      "name": "anege",
+      "name": "Ane Gurtubay",
       "avatar_url": "https://avatars0.githubusercontent.com/u/50317099?v=4",
       "profile": "https://github.com/anege",
       "contributions": [
@@ -40,7 +40,7 @@
     },
     {
       "login": "marcobarilari",
-      "name": "marcobarilari",
+      "name": "Marco Barilari",
       "avatar_url": "https://avatars3.githubusercontent.com/u/38101692?v=4",
       "profile": "https://github.com/marcobarilari",
       "contributions": [
@@ -70,7 +70,7 @@
     },
     {
       "login": "fedefalag",
-      "name": "Fede F.",
+      "name": "Federica Falagiarda",
       "avatar_url": "https://avatars2.githubusercontent.com/u/50373329?v=4",
       "profile": "https://github.com/fedefalag",
       "contributions": [
@@ -80,7 +80,7 @@
     },
     {
       "login": "CerenB",
-      "name": "CerenB",
+      "name": "Ceren Battal",
       "avatar_url": "https://avatars1.githubusercontent.com/u/10451654?v=4",
       "profile": "https://github.com/CerenB",
       "contributions": [
@@ -126,6 +126,15 @@
         "review",
         "userTesting"
       ]
+    },
+    {
+      "login": "mcgnunes",
+      "name": "Márcia Nunes",
+      "avatar_url": "https://avatars.githubusercontent.com/u/98760858?v=4",
+      "profile": "https://github.com/mcgnunes",
+      "contributions": [
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.dockerignore

@@ -1,3 +1,6 @@
+# ignoring this might speed up build
+# by preventing passing extra content to the docker daemon
+
 .vscode
 .git
 .github
@@ -6,10 +9,8 @@ coverage_html
 demos/*/outputs/
 demos/*/inputs/
 demos/*/cfg/
+docs
 env
+manualTests
+templates
 tests
-
-# ignoring this might speed up build
-# by preventing passing extra content to the docker daemon
-
-# lib

.gitignore

@@ -30,6 +30,12 @@ models/*
 # jupyter notebooks
 .ipynb_checkpoints
 
+# node stuff
+
+node_modules
+package*
+yarn.lock
+
 ## MATLAB / OCTAVE gitignore template
 
 # From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore

CITATION.cff

@@ -72,6 +72,9 @@ authors:
   orcid: "https://orcid.org/0000-0002-8724-7668"
   affiliation: "Université catholique de Louvain"
 
+- family-names: "Nunes"
+  given-names: "Márcia"
+
 license: GPL-3.0
 
 keywords:

Dockerfile

@@ -1,44 +1,69 @@
-# Creates a docker image of the default branch of CPP_SPM
+# Creates a docker image of CPP_SPM with
 
 # this is mostly taken from the spm docker files: https://github.com/spm/spm-docker
-FROM ubuntu:focal
+FROM ubuntu:22.04
+
+USER root
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8"
 
 #TODO how to update this with the content of the current version
-LABEL version="1.1.2"
+LABEL version="1.1.5dev"
+
+LABEL maintainer="Rémi Gau <remi.gau@gmail.com>"
 
+## Install SPM
 # basic OS tools install and also octave
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
     build-essential \
     curl \
-    git \
     octave \
     liboctave-dev \
-    apt-get clean
+    && apt-get clean \
+    && rm -rf \
+    /tmp/hsperfdata* \
+    /var/*/apt/*/partial \
+    /var/lib/apt/lists/* \
+    /var/log/apt/term*
+
+RUN mkdir /opt/spm12 \
+    && curl -SL https://github.com/spm/spm12/archive/r7771.tar.gz \
+    | tar -xzC /opt/spm12 --strip-components 1 \
+    && curl -SL https://raw.githubusercontent.com/spm/spm-docker/main/octave/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
+
+RUN octave --no-gui --eval "addpath('/opt/spm12/'); savepath ();"
 
-RUN rm -rf \
+## Install nods and bids validator
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
+    nodejs npm \
+    && apt-get clean \
+    && rm -rf \
     /tmp/hsperfdata* \
     /var/*/apt/*/partial \
     /var/lib/apt/lists/* \
     /var/log/apt/term*
 
-RUN mkdir /opt/spm12 && \
-    curl -SL https://github.com/spm/spm12/archive/r7487.tar.gz | \
-    tar -xzC /opt/spm12 --strip-components 1 && \
-    curl -SL https://raw.githubusercontent.com/spm/spm-docker/master/octave/spm12_r7487.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
+RUN node -v && npm -v && npm install -g bids-validator
+
+## Install CPP SPM in user folder
+RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
+
+USER neuro
 
-RUN octave --no-gui --eval "addpath(\"/opt/spm12\"); savepath ();"
+WORKDIR /home/neuro
 
-RUN git clone --depth 1 --recurse-submodule https://github.com/cpp-lln-lab/CPP_SPM.git
+RUN mkdir code output cpp_spm
 
-RUN mkdir code output
+WORKDIR /home/neuro/
 
-RUN cd CPP_SPM && octave --no-gui --eval "initCppSpm(); savepath();"
+COPY [".", "/home/neuro/cpp_spm/"]
 
-WORKDIR /code
+RUN cd cpp_spm && octave --no-gui --eval "initCppSpm(false); savepath();"
 
 ENTRYPOINT ["octave"]

Dockerfile_dev

@@ -0,0 +1,139 @@
+# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
+# Latest release: Neurodocker version 0.8.0
+# Timestamp: 2022/05/17 15:29:06 UTC
+#
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+#
+#     https://github.com/ReproNim/neurodocker
+
+FROM debian:stretch-slim
+
+USER root
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    ND_ENTRYPOINT="/neurodocker/startup.sh"
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bzip2 \
+           ca-certificates \
+           curl \
+           locales \
+           unzip \
+    && apt-get clean \
+    && 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 \
+    && mkdir -p /neurodocker \
+    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
+         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
+    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
+    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
+    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+ENV FORCE_SPMMCR="1" \
+    SPM_HTML_BROWSER="0" \
+    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
+    MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
+RUN export TMPDIR="$(mktemp -d)" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           libncurses5 \
+           libxext6 \
+           libxmu6 \
+           libxpm-dev \
+           libxt6 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "Downloading MATLAB Compiler Runtime ..." \
+    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
+    && dpkg -i /tmp/toinstall.deb \
+    && rm /tmp/toinstall.deb \
+    && apt-get install -f \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
+    && chmod +x "$TMPDIR/MCRInstaller.bin" \
+    && "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
+    && rm -rf "$TMPDIR" \
+    && unset TMPDIR \
+    && echo "Downloading standalone SPM ..." \
+    && curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip \
+    && unzip -q /tmp/spm12.zip -d /tmp \
+    && mkdir -p /opt/spm12-r7771 \
+    && mv /tmp/spm12/* /opt/spm12-r7771/ \
+    && chmod -R 777 /opt/spm12-r7771 \
+    && rm -rf /tmp/spm* \
+    && /opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
+    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           nodejs \
+           npm \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN node -v && npm -v && npm install -g bids-validator
+
+RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
+USER neuro
+
+RUN mkdir code output cpp_spm
+
+COPY [".,", "/home/neuro/cpp_spm/"]
+
+RUN echo '{ \
+    \n  "pkg_manager": "apt", \
+    \n  "instructions": [ \
+    \n    [ \
+    \n      "base", \
+    \n      "debian:stretch-slim" \
+    \n    ], \
+    \n    [ \
+    \n      "spm12", \
+    \n      { \
+    \n        "version": "r7771" \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "install", \
+    \n      [ \
+    \n        "nodejs", \
+    \n        "npm" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "node -v && npm -v && npm install -g bids-validator" \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "mkdir code output cpp_spm" \
+    \n    ], \
+    \n    [ \
+    \n      "copy", \
+    \n      [ \
+    \n        ".,", \
+    \n        "/home/neuro/cpp_spm/" \
+    \n      ] \
+    \n    ] \
+    \n  ] \
+    \n}' > /neurodocker/neurodocker_specs.json