junifer 0.0.7.dev192__tar.gz → 0.0.7.dev206__tar.gz

junifer-0.0.7.dev206/.github/workflows/ci.yml

@@ -0,0 +1,86 @@
+name: Run Tests
+
+on:
+  push:
+    paths:
+      - 'junifer/**'
+      - '.github/workflows/**'
+      - 'tox.ini'
+      - 'pyproject.toml'
+  pull_request:
+    paths:
+      - 'junifer/**'
+      - '.github/workflows/**'
+      - 'tox.ini'
+      - 'pyproject.toml'
+  workflow_dispatch: {}
+
+jobs:
+  run-tests:
+    # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
+    runs-on: ubuntu-22.04
+    # Use custom CI image
+    container: ghcr.io/juaml/junifer-ci:main
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+      - run: df -h
+      - name: Clean runner
+        run: |
+          rm -rf /usr/share/dotnet \
+                 /usr/local/lib/android \
+                 /opt/ghc \
+                 /opt/hostedtoolcache
+      - run: df -h
+      - name: Check ANTs
+        run: |
+          echo "Using ANTs : $(antsRegistration --version)"
+      - name: Check AFNI
+        run: |
+          echo "Using AFNI : $(afni --version)"
+      - name: Check FSL
+        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: |
+          apt-get -qq update
+          apt-get -qq install -y \
+          git \
+          git-annex \
+          make \
+          jq
+      - name: Copy junifer-data directory
+        run: |
+          mkdir -p $HOME/junifer_data/v4
+          cp -ar /root/junifer_data/v4/. $HOME/junifer_data/v4/
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          submodules: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install tox tox-gh-actions
+      - name: Configure Git for DataLad
+        run: |
+          git config --global user.email "junifer-runner@github.com"
+          git config --global user.name "GitHub Runner"
+      - name: Test with tox
+        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
+        run: |
+          git config --system --add safe.directory $(pwd)
+          tox
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          flags: junifer
+        if: success() && matrix.python-version == 3.12

junifer-0.0.7.dev206/.github/workflows/docker-ci-publish.yml

@@ -0,0 +1,69 @@
+name: Docker for CI
+
+on:
+  push:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-ci" ]
+  pull_request:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-ci" ]
+  workflow_dispatch: {}
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}-ci
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+    steps:
+      - run: df -h
+      - name: Clean runner
+        run: |
+          sudo rm -rf /usr/share/dotnet \
+                 /usr/local/lib/android \
+                 /opt/ghc \
+                 /opt/hostedtoolcache
+          sudo docker image prune --all --force
+          sudo docker builder prune -a
+      - run: df -h
+      - name: Checkout repository
+        uses: actions/checkout@v5
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3.10.0
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3.11.1
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3.5.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5.8.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v6.18.0
+        with:
+          context: .
+          file: Dockerfile-ci
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

junifer-0.0.7.dev206/.github/workflows/docker-docs-publish.yml

@@ -0,0 +1,69 @@
+name: Docker for docs
+
+on:
+  push:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-docs" ]
+  pull_request:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-docs" ]
+  workflow_dispatch: {}
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}-docs
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+    steps:
+      - run: df -h
+      - name: Clean runner
+        run: |
+          rm -rf /usr/share/dotnet \
+                 /usr/local/lib/android \
+                 /opt/ghc \
+                 /opt/hostedtoolcache
+          docker image prune --all --force
+          docker builder prune -a
+      - run: df -h
+      - name: Checkout repository
+        uses: actions/checkout@v5
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3.10.0
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3.11.1
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3.5.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5.8.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v6.18.0
+        with:
+          context: .
+          file: Dockerfile-docs
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

{junifer-0.0.7.dev192 → junifer-0.0.7.dev206}/Dockerfile-ci

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1
 
-FROM python:3.12-slim
+FROM python:3.12-slim-bookworm
 
 LABEL org.opencontainers.image.source=https://github.com/juaml/junifer
 LABEL org.opencontainers.image.description="Junifer CI container image"
@@ -60,14 +60,13 @@ ENV PATH="/opt/afni/bin:$PATH"
 # Patch gsl
 RUN ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.23
 
-# disabled as standard github runner fails to install due to insufficient space on device
-# # Add FSL
-# RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | \
-#     python - -d /opt/fsl/ --skip_registration
-# # Set env vars for FSL
-# ENV FSLDIR=/opt/fsl \
-#     FSLOUTPUTTYPE=NIFTI_GZ \
-#     PATH="/opt/fsl/share/fsl/bin:$PATH"
+# Add FSL
+RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | \
+    python - -d /opt/fsl/ --skip_registration
+# Set env vars for FSL
+ENV FSLDIR=/opt/fsl \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    PATH="/opt/fsl/share/fsl/bin:$PATH"
 
 # Clean apt cache
 RUN apt-get autoremove --purge && apt-get clean

{junifer-0.0.7.dev192 → junifer-0.0.7.dev206}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev192
+Version: 0.0.7.dev206
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.7.dev206/docs/changes/newsfragments/467.misc

@@ -0,0 +1 @@
+Disable FSL installation for ``junifer-ci`` Docker image build with ``junifer-data`` v4 by `Synchon Mandal`_

junifer-0.0.7.dev206/docs/changes/newsfragments/468.misc

@@ -0,0 +1 @@
+Pin ``junifer-ci`` Docker image to ``python:3.12-slim-bookworm`` and re-enable FSL installation by `Synchon Mandal`_

{junifer-0.0.7.dev192 → junifer-0.0.7.dev206}/junifer/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7.dev192'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev192')
+__version__ = version = '0.0.7.dev206'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev206')
 
-__commit_id__ = commit_id = 'g61f12e356'
+__commit_id__ = commit_id = 'g151631cf7'

{junifer-0.0.7.dev192 → junifer-0.0.7.dev206}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev192
+Version: 0.0.7.dev206
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.7.dev192 → junifer-0.0.7.dev206}/junifer.egg-info/SOURCES.txt

@@ -88,6 +88,7 @@ docs/changes/newsfragments/464.misc
 docs/changes/newsfragments/465.misc
 docs/changes/newsfragments/466.misc
 docs/changes/newsfragments/467.misc
+docs/changes/newsfragments/468.misc
 docs/extending/coordinates.rst
 docs/extending/data_dump_asset.rst
 docs/extending/data_registries.rst

junifer-0.0.7.dev192/.github/workflows/ci.yml

@@ -1,86 +0,0 @@
-name: Run Tests
-
-on:
-  push:
-    paths:
-      - 'junifer/**'
-      - '.github/workflows/**'
-      - 'tox.ini'
-      - 'pyproject.toml'
-  pull_request:
-    paths:
-      - 'junifer/**'
-      - '.github/workflows/**'
-      - 'tox.ini'
-      - 'pyproject.toml'
-
-jobs:
-  run-tests:
-    # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
-    runs-on: ubuntu-22.04
-    # Use custom CI image
-    container: ghcr.io/juaml/junifer-ci:main
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-
-    steps:
-    - run: df -h
-    - name: Clean runner
-      run: |
-        rm -rf /usr/share/dotnet \
-                    /usr/local/lib/android \
-                    /opt/ghc \
-                    /opt/hostedtoolcache/CodeQL
-    - run: df -h
-    - name: Check ANTs
-      run: |
-        echo "Using ANTs : $(antsRegistration --version)"
-    - name: Check AFNI
-      run: |
-        echo "Using AFNI : $(afni --version)"
-    - name: Check FSL
-      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: |
-        apt-get -qq update
-        apt-get -qq install -y \
-        git \
-        git-annex \
-        make \
-        jq
-    - name: Copy junifer-data directory
-      run: |
-        mkdir -p $HOME/junifer_data/v4
-        cp -ar /root/junifer_data/v4/. $HOME/junifer_data/v4/
-    - name: Checkout repository
-      uses: actions/checkout@v5
-      with:
-        submodules: true
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tox tox-gh-actions
-    - name: Configure Git for DataLad
-      run: |
-        git config --global user.email "junifer-runner@github.com"
-        git config --global user.name "GitHub Runner"
-    - name: Test with tox
-      # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
-      run: |
-        git config --system --add safe.directory $(pwd)
-        tox
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v5
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: true
-        flags: junifer
-      if: success() && matrix.python-version == 3.12

junifer-0.0.7.dev192/.github/workflows/docker-ci-publish.yml

@@ -1,103 +0,0 @@
-name: Docker for CI
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-on:
-  push:
-    # Only run when the file is edited on main
-    branches: [ "main" ]
-    paths: [ "Dockerfile-ci" ]
-  pull_request:
-    # Only run when the file is edited on main
-    branches: [ "main" ]
-    paths: [ "Dockerfile-ci" ]
-  workflow_dispatch: {}
-
-env:
-  # Use docker.io for Docker Hub if empty
-  REGISTRY: ghcr.io
-  # github.repository as <account>/<repo>
-  IMAGE_NAME: ${{ github.repository }}-ci
-
-
-jobs:
-  build:
-
-    runs-on: ubuntu-24.04
-    permissions:
-      contents: read
-      packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
-      id-token: write
-
-    steps:
-      # Taken from https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
-      - name: Delete huge unnecessary tools folder
-        run: rm -rf /opt/hostedtoolcache
-      - name: Checkout repository
-        uses: actions/checkout@v5
-
-      # Install the cosign tool except on PR
-      # https://github.com/sigstore/cosign-installer
-      - name: Install cosign
-        if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@d7543c93d881b35a8faa02e8e3605f69b7a1ce62 #v3.10.0
-        with:
-          cosign-release: 'v2.2.4'
-
-      # Set up BuildKit Docker container builder to be able to build
-      # multi-platform images and export cache
-      # https://github.com/docker/setup-buildx-action
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3.11.1
-
-      # Login against a Docker registry except on PR
-      # https://github.com/docker/login-action
-      - name: Log into registry ${{ env.REGISTRY }}
-        if: github.event_name != 'pull_request'
-        uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      # Extract metadata (tags, labels) for Docker
-      # https://github.com/docker/metadata-action
-      - name: Extract Docker metadata
-        id: meta
-        uses: docker/metadata-action@c1e51972afc2121e065aed6d45c65596fe445f3f # v5.8.0
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      # Build and push Docker image with Buildx (don't push on PR)
-      # https://github.com/docker/build-push-action
-      - name: Build and push Docker image
-        id: build-and-push
-        uses: docker/build-push-action@263435318d21b8e681c14492fe198d362a7d2c83 # v6.18.0
-        with:
-          context: .
-          file: Dockerfile-ci
-          push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-
-      # Sign the resulting Docker image digest except on PRs.
-      # This will only write to the public Rekor transparency log when the Docker
-      # repository is public to avoid leaking data.  If you would like to publish
-      # transparency data even for private images, pass --force to cosign below.
-      # https://github.com/sigstore/cosign
-      - name: Sign the published Docker image
-        if: ${{ github.event_name != 'pull_request' }}
-        env:
-          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
-          TAGS: ${{ steps.meta.outputs.tags }}
-          DIGEST: ${{ steps.build-and-push.outputs.digest }}
-        # This step uses the identity token to provision an ephemeral certificate
-        # against the sigstore community Fulcio instance.
-        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

junifer-0.0.7.dev192/.github/workflows/docker-docs-publish.yml

@@ -1,100 +0,0 @@
-name: Docker for docs
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-on:
-  push:
-    # Only run when the file is edited on main
-    branches: [ "main" ]
-    paths: [ "Dockerfile-docs" ]
-  pull_request:
-    # Only run when the file is edited on main
-    branches: [ "main" ]
-    paths: [ "Dockerfile-docs" ]
-  workflow_dispatch: {}
-
-env:
-  # Use docker.io for Docker Hub if empty
-  REGISTRY: ghcr.io
-  # github.repository as <account>/<repo>
-  IMAGE_NAME: ${{ github.repository }}-docs
-
-
-jobs:
-  build:
-
-    runs-on: ubuntu-24.04
-    permissions:
-      contents: read
-      packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
-      id-token: write
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v5
-
-      # Install the cosign tool except on PR
-      # https://github.com/sigstore/cosign-installer
-      - name: Install cosign
-        if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@d7543c93d881b35a8faa02e8e3605f69b7a1ce62 #v3.10.0
-        with:
-          cosign-release: 'v2.2.4'
-
-      # Set up BuildKit Docker container builder to be able to build
-      # multi-platform images and export cache
-      # https://github.com/docker/setup-buildx-action
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3.11.1
-
-      # Login against a Docker registry except on PR
-      # https://github.com/docker/login-action
-      - name: Log into registry ${{ env.REGISTRY }}
-        if: github.event_name != 'pull_request'
-        uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      # Extract metadata (tags, labels) for Docker
-      # https://github.com/docker/metadata-action
-      - name: Extract Docker metadata
-        id: meta
-        uses: docker/metadata-action@c1e51972afc2121e065aed6d45c65596fe445f3f # v5.8.0
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      # Build and push Docker image with Buildx (don't push on PR)
-      # https://github.com/docker/build-push-action
-      - name: Build and push Docker image
-        id: build-and-push
-        uses: docker/build-push-action@263435318d21b8e681c14492fe198d362a7d2c83 # v6.18.0
-        with:
-          context: .
-          file: Dockerfile-docs
-          push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-
-      # Sign the resulting Docker image digest except on PRs.
-      # This will only write to the public Rekor transparency log when the Docker
-      # repository is public to avoid leaking data.  If you would like to publish
-      # transparency data even for private images, pass --force to cosign below.
-      # https://github.com/sigstore/cosign
-      - name: Sign the published Docker image
-        if: ${{ github.event_name != 'pull_request' }}
-        env:
-          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
-          TAGS: ${{ steps.meta.outputs.tags }}
-          DIGEST: ${{ steps.build-and-push.outputs.digest }}
-        # This step uses the identity token to provision an ephemeral certificate
-        # against the sigstore community Fulcio instance.
-        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

junifer-0.0.7.dev192/docs/changes/newsfragments/467.misc

@@ -1 +0,0 @@
-Disable FSL installation for `junifer-ci` Docker image build with `junifer-data` v4 by `Synchon Mandal`_