junifer 0.0.7.dev323__tar.gz → 0.0.7.dev332__tar.gz

junifer-0.0.7.dev332/.github/workflows/docker-publish.yml

@@ -0,0 +1,69 @@
+name: Docker
+
+on:
+  push:
+    branches: [ "main" ]
+    paths: [ "Dockerfile" ]
+  pull_request:
+    branches: [ "main" ]
+    paths: [ "Dockerfile" ]
+  workflow_dispatch: {}
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+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@v4.0.0
+      - 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@v3.6.0
+        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
+          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.dev332/Dockerfile

@@ -0,0 +1,82 @@
+# syntax=docker/dockerfile:1
+
+FROM python:3.12-slim-bookworm
+
+LABEL org.opencontainers.image.source=https://github.com/juaml/junifer
+LABEL org.opencontainers.image.description="Junifer container image"
+LABEL org.opencontainers.image.licenses=AGPL-3.0-only
+
+RUN apt-get update && \
+    apt-get install -y \
+    pkg-config \
+    gcc \
+    git \
+    git-annex \
+    make \
+    curl \
+    # ANTs runtime stuff
+    libhdf5-dev \
+    bc \
+    # AFNI runtime stuff
+    libf2c2-dev \
+    libglew-dev \
+    libglib2.0-dev \
+    libglu1-mesa-dev \
+    libglw1-mesa-dev \
+    libgsl-dev \
+    libgts-dev \
+    libjpeg62-turbo-dev \
+    libmotif-dev \
+    libxi-dev \
+    libxmhtml-dev \
+    libxmu-dev \
+    libxpm-dev \
+    libxt-dev \
+    netpbm \
+    libjpeg-progs \
+    qhull-bin \
+    r-base \
+    tcsh \
+    xvfb \
+    # FSL runtime stuff
+    file \
+    dc \
+    libquadmath0 \
+    libgomp1 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Add junifer-data
+COPY --from=ghcr.io/juaml/junifer-data:v7 /opt/junifer-data /root/junifer_data/v7
+
+# Add ANTs
+COPY --from=antsx/ants:latest /opt/ants /opt/ants
+# Set env vars for ANTs
+ENV PATH="/opt/ants/bin:$PATH" \
+    LD_LIBRARY_PATH="/opt/ants/lib"
+
+# Add AFNI
+COPY --from=afni/afni_make_build:latest /opt/afni/install /opt/afni/bin
+# Set env vars for AFNI
+ENV PATH="/opt/afni/bin:$PATH"
+# Patch gsl
+RUN ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.23
+
+# 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
+
+# Install Python dependencies
+RUN python -m pip install --no-cache-dir --upgrade pip setuptools wheel
+
+# Checkout latest junifer code and install
+RUN git clone --depth 1 --recurse-submodules https://github.com/juaml/junifer.git && \
+    cd junifer && \
+    python -m pip install --no-cache-dir ".[all]" && \
+    cd .. && rm -rf junifer

{junifer-0.0.7.dev323 → junifer-0.0.7.dev332}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev323
+Version: 0.0.7.dev332
 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>
@@ -153,7 +153,7 @@ If you use `junifer` in a scientific publication, we would appreciate if you cit
 ## Funding
 
 We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
-[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`.
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`. Development of this software was funded, in part, by the European Union’s Horizon Europe Framework Programme for Research infrastructures under the [specific grant agreement no. 101147319](https://cordis.europa.eu/project/id/101147319) (EBRAINS 2.0).
 (The funding sources had no role in the design, implementation and evaluation of the pipeline.)
 
 ## Contribution

{junifer-0.0.7.dev323 → junifer-0.0.7.dev332}/README.md

@@ -77,7 +77,7 @@ If you use `junifer` in a scientific publication, we would appreciate if you cit
 ## Funding
 
 We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
-[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`.
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`. Development of this software was funded, in part, by the European Union’s Horizon Europe Framework Programme for Research infrastructures under the [specific grant agreement no. 101147319](https://cordis.europa.eu/project/id/101147319) (EBRAINS 2.0).
 (The funding sources had no role in the design, implementation and evaluation of the pipeline.)
 
 ## Contribution

junifer-0.0.7.dev332/docs/changes/newsfragments/489.misc

@@ -0,0 +1 @@
+Add Dockerfile and a corresponding action for building and publishing the image by `Fede Raimondo`_ and `Synchon Mandal`_

{junifer-0.0.7.dev323 → junifer-0.0.7.dev332}/junifer/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7.dev323'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev323')
+__version__ = version = '0.0.7.dev332'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev332')
 
-__commit_id__ = commit_id = 'g6e665b143'
+__commit_id__ = commit_id = 'g52d8784c5'

{junifer-0.0.7.dev323 → junifer-0.0.7.dev332}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev323
+Version: 0.0.7.dev332
 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>
@@ -153,7 +153,7 @@ If you use `junifer` in a scientific publication, we would appreciate if you cit
 ## Funding
 
 We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
-[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`.
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`. Development of this software was funded, in part, by the European Union’s Horizon Europe Framework Programme for Research infrastructures under the [specific grant agreement no. 101147319](https://cordis.europa.eu/project/id/101147319) (EBRAINS 2.0).
 (The funding sources had no role in the design, implementation and evaluation of the pipeline.)
 
 ## Contribution

{junifer-0.0.7.dev323 → junifer-0.0.7.dev332}/junifer.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@
 .gitmodules
 .pre-commit-config.yaml
 AUTHORS.rst
+Dockerfile
 Dockerfile-ci
 Dockerfile-docs
 LICENSE.md
@@ -26,6 +27,7 @@ tox.ini
 .github/workflows/ci.yml
 .github/workflows/docker-ci-publish.yml
 .github/workflows/docker-docs-publish.yml
+.github/workflows/docker-publish.yml
 .github/workflows/docs-preview.yml
 .github/workflows/docs.yml
 .github/workflows/lint.yml
@@ -106,6 +108,7 @@ docs/changes/newsfragments/485.misc
 docs/changes/newsfragments/486.enh
 docs/changes/newsfragments/486.misc
 docs/changes/newsfragments/487.bugfix
+docs/changes/newsfragments/489.misc
 docs/extending/coordinates.rst
 docs/extending/data_dump_asset.rst
 docs/extending/data_registries.rst