use more recent octave in containers

CHANGELOG.md

@@ -51,6 +51,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [REF] Refactor and update CLI in #1096 @Remi-Gau
 * [ENH] {func}`getData` only loads anat data when requested #1257 @Remi-Gau
 * [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` #1292 @Remi-Gau
+* [ENH] change base image in container to use Octave 9.2.0 #1292 @Remi-Gau
 
 ### Deprecated
 
@@ -73,6 +74,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau
 * [FIX] rename results files (csv, tsv, png, nii) of each contrasts #1104 by @Remi-Gau
 * [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau
+* [FIX] ensure that there is a clean version number in containers #1306 @Remi-Gau
 
 ### Security
 

Dockerfile

@@ -1,4 +1,6 @@
-FROM bids/base_validator:1.13.1
+# FROM bids/base_validator:1.13.1
+# https://github.com/gnu-octave/docker/tree/main
+FROM gnuoctave/octave:9.2.0@sha256:b4cab2446a847530129fe8333a4b31eb046efb4b14bb3182e781fa2238116108
 
 LABEL org.opencontainers.image.source="https://github.com/cpp-lln-lab/bidspm"
 LABEL org.opencontainers.image.url="https://github.com/cpp-lln-lab/bidspm"
@@ -15,15 +17,10 @@ RUN apt-get update -qq && \
         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 \
@@ -32,15 +29,19 @@ RUN apt-get update -qq && \
         python3-pip \
         python3 \
         software-properties-common \
-        unzip \
-        zip && \
+        unzip && \
     apt-get clean && \
     rm -rf \
         /tmp/hsperfdata* \
         /var/*/apt/*/partial \
         /var/lib/apt/lists/* \
         /var/log/apt/term*
 
+# install bids validator
+# TODO find out how to pin version
+RUN curl -fsSL https://deno.land/install.sh | sh && \
+    deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
+
 ## Install SPM
 RUN mkdir /opt/spm12 && \
     curl -SL https://github.com/spm/spm12/archive/r7771.tar.gz | \
@@ -57,9 +58,8 @@ WORKDIR /home/neuro
 COPY . /home/neuro/bidspm
 WORKDIR /home/neuro/bidspm
 RUN git restore . && \
-    git -C lib/CPP_ROI/atlas/HCPex reset --hard && \
-    git -C lib/CPP_ROI/atlas/HCPex clean --force -dfx && \
-    git status && \
+    git submodule foreach --recursive 'git reset --hard' && \
+    git submodule foreach --recursive 'git clean --force -dfx' && \
     pip install --no-cache-dir --upgrade pip && \
     pip3 --no-cache-dir install -r requirements.txt && \
     pip3 --no-cache-dir install . && \

bidspm.def

@@ -1,5 +1,5 @@
 BootStrap: docker
-From: bids/base_validator:1.13.1
+From: gnuoctave/octave:9.2.0
 
 %files
     pyproject.toml /opt/bidspm/pyproject.toml
@@ -16,15 +16,10 @@ From: bids/base_validator:1.13.1
         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 \
@@ -33,15 +28,19 @@ From: bids/base_validator:1.13.1
         python3-pip \
         python3 \
         software-properties-common \
-        unzip \
-        zip && \
+        unzip && \
     apt-get clean && \
     rm -rf \
         /tmp/hsperfdata* \
         /var/*/apt/*/partial \
         /var/lib/apt/lists/* \
         /var/log/apt/term*
 
+    # install bids validator
+    # TODO find out how to pin version
+    curl -fsSL https://deno.land/install.sh | sh
+    deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
+
     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
@@ -53,9 +52,6 @@ From: bids/base_validator:1.13.1
     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