[CI]: Upgrade Docker images and workflows

.github/workflows/ci.yml

@@ -31,16 +31,16 @@ jobs:
       run: |
         echo "Using FSL : $(flirt -version)"
     - name: Install system dependencies
+      # actions/checkout fails to identify Git as it's not in the CI image
       run: |
-        # actions/checkout fails to identify Git as it's not in the CI image
-        apt-get -qq update && \
-        apt-get -qq install -y \
+        sudo apt-get update
+        sudo apt-get install -y \
         git \
         git-annex \
         make \
         jq
-        # Copy xfms directory
-        mkdir -p $HOME/junifer/data/xfms && \
+    - name: Copy xfms directory
+        mkdir -p $HOME/junifer/data/xfms
         cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -59,8 +59,8 @@ jobs:
         git config --global user.email "[email protected]"
         git config --global user.name "GitHub Runner"
     - name: Test with tox
+      # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
       run: |
-        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
         git config --system --add safe.directory $(pwd)
         tox
     - name: Upload coverage to Codecov

.github/workflows/docker-ci-publish.yml

@@ -26,7 +26,7 @@ env:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     permissions:
       contents: read
       packages: write

.github/workflows/docker-docs-publish.yml

@@ -26,7 +26,7 @@ env:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     permissions:
       contents: read
       packages: write

.github/workflows/docs.yml

@@ -20,18 +20,18 @@ jobs:
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
     - name: Install system dependencies
+      # actions/checkout fails to identify Git as it's not in the CI image
       run: |
-        # actions/checkout fails to identify Git as it's not in the CI image
-        apt-get -qq update && \
-        apt-get -qq install -y \
+        sudo apt-get update
+        sudo apt-get install -y \
         git \
         git-annex \
         make \
         jq
-        # Copy xfms directory
-        mkdir -p $HOME/junifer/data/xfms && \
+    - name: Copy xfms directory
+        mkdir -p $HOME/junifer/data/xfms
         cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
-    - name: Checkout source
+    - name: Checkout repository
       uses: actions/checkout@v4
       with:
         # require all of history to see all tagged versions' docs
@@ -59,8 +59,8 @@ jobs:
           path: docs/_build
     - name: Build docs
       # Use the args we normally pass to sphinx-build, but run sphinx-multiversion
+      # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
       run: |
-        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
         git config --system --add safe.directory $(pwd)
         make -C docs/ html
         touch docs/_build/.nojekyll

Dockerfile-ci

@@ -41,7 +41,8 @@ RUN apt-get update && \
     file \
     dc \
     libquadmath0 \
-    libgomp1
+    libgomp1 \
+    && rm -rf /var/lib/apt/lists/*
 
 # Add xfms
 COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms

Dockerfile-docs

@@ -10,7 +10,8 @@ RUN apt-get update && \
     apt-get install -y \
     # ANTs runtime stuff
     libhdf5-dev \
-    bc
+    bc \
+    && rm -rf /var/lib/apt/lists/*
 
 # Add xfms
 COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms