fixes

CHANGELOG.md

@@ -51,7 +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
+* [ENH] change base image in container to use Octave 9.2.0 #1308 @Remi-Gau
 
 ### Deprecated
 

Dockerfile

@@ -14,9 +14,7 @@ ARG DEBIAN_FRONTEND="noninteractive"
 ## basic OS tools install octave
 RUN apt-get update -qq && \
     apt-get -qq -y --no-install-recommends install \
-        apt-utils \
-        build-essential \
-        ca-certificates \
+        curl \
         default-jre \
         fonts-freefont-otf \
         ghostscript \
@@ -28,7 +26,6 @@ RUN apt-get update -qq && \
         octave-statistics \
         python3-pip \
         python3 \
-        software-properties-common \
         unzip && \
     apt-get clean && \
     rm -rf \
@@ -40,14 +37,16 @@ RUN apt-get update -qq && \
 # install bids validator
 # TODO find out how to pin version
 RUN curl -fsSL https://deno.land/install.sh | sh && \
+    export DENO_INSTALL="/root/.deno" && \
+    export PATH="$DENO_INSTALL/bin:$PATH" && \
     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 | \
     tar -xzC /opt/spm12 --strip-components 1 && \
     curl -SL https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch | \
-    patch -p0 && \
+    patch -p3 -d /opt/spm12 && \
     make -C /opt/spm12/src PLATFORM=octave distclean && \
     make -C /opt/spm12/src PLATFORM=octave && \
     make -C /opt/spm12/src PLATFORM=octave install && \
@@ -67,7 +66,6 @@ RUN git restore . && \
     octave --no-gui --eval "addpath(pwd); savepath('/usr/share/octave/site/m/startup/octaverc'); bidspm(); path" && \
     octave --no-gui --eval "path"
 
-
 WORKDIR /home/neuro
 
 ENTRYPOINT ["bidspm"]

bidspm.def

@@ -13,9 +13,7 @@ From: gnuoctave/octave:9.2.0
 %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 \
@@ -27,7 +25,6 @@ From: gnuoctave/octave:9.2.0
         octave-statistics \
         python3-pip \
         python3 \
-        software-properties-common \
         unzip && \
     apt-get clean && \
     rm -rf \
@@ -43,7 +40,7 @@ From: gnuoctave/octave:9.2.0
 
     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
+    curl -fsSL --retry 5 https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch | patch -p3 -d /opt/spm12
     make -C /opt/spm12/src PLATFORM=octave distclean
     make -C /opt/spm12/src PLATFORM=octave
     make -C /opt/spm12/src PLATFORM=octave install