junifer 0.0.6.dev145__tar.gz → 0.0.6.dev154__tar.gz

junifer-0.0.6.dev154/.github/workflows/docker-ci-publish.yml

@@ -0,0 +1,103 @@
+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-latest
+    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@v4
+
+      # 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@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
+        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@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      # 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@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        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@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        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@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        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-0.0.6.dev145 → junifer-0.0.6.dev154}/.github/workflows/docs.yml

@@ -8,12 +8,16 @@ on:
     # Sequence of patterns matched against refs/tags
     tags:
       - v*
+    workflow_dispatch: {}
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
     # Use custom docs CI image
-    container: ghcr.io/juaml/junifer-docs:main
+    container:
+      image: ghcr.io/juaml/junifer-docs:main
+      # https://github.com/actions/runner/issues/2033#issuecomment-1598547465
+      options: --user 1001
     steps:
     - name: Check ANTs
       run: |

junifer-0.0.6.dev154/Dockerfile-ci

@@ -0,0 +1,71 @@
+# syntax=docker/dockerfile:1
+
+FROM python:3.12-slim
+
+LABEL org.opencontainers.image.source=https://github.com/juaml/junifer
+LABEL org.opencontainers.image.description="Junifer CI container image"
+LABEL org.opencontainers.image.licenses=AGPL-3.0-only
+
+RUN apt-get update && \
+    apt-get install -y \
+    pkg-config \
+    gcc \
+    git \
+    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
+
+# Add xfms
+COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms
+
+# 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/bin:$PATH"
+
+# Clean apt cache
+RUN apt-get autoremove --purge && apt-get clean

{junifer-0.0.6.dev145 → junifer-0.0.6.dev154}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev145
+Version: 0.0.6.dev154
 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-0.0.6.dev154/docs/changes/newsfragments/382.misc

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

junifer-0.0.6.dev154/docs/changes/newsfragments/384.misc

@@ -0,0 +1 @@
+Improve docs publishing action and add a manual trigger for it by `Synchon Mandal`_

{junifer-0.0.6.dev145 → junifer-0.0.6.dev154}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev145'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev145')
+__version__ = version = '0.0.6.dev154'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev154')

{junifer-0.0.6.dev145 → junifer-0.0.6.dev154}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev145
+Version: 0.0.6.dev154
 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-0.0.6.dev145 → junifer-0.0.6.dev154}/junifer.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@
 .gitmodules
 .pre-commit-config.yaml
 AUTHORS.rst
+Dockerfile-ci
 Dockerfile-docs
 LICENSE.md
 README.md
@@ -22,6 +23,7 @@ tox.ini
 .github/ISSUE_TEMPLATE/marker-request.yml
 .github/workflows/ci-docs.yml
 .github/workflows/ci.yml
+.github/workflows/docker-ci-publish.yml
 .github/workflows/docker-docs-publish.yml
 .github/workflows/docs-preview.yml
 .github/workflows/docs.yml
@@ -78,6 +80,8 @@ docs/changes/newsfragments/372.misc
 docs/changes/newsfragments/373.misc
 docs/changes/newsfragments/374.misc
 docs/changes/newsfragments/380.misc
+docs/changes/newsfragments/382.misc
+docs/changes/newsfragments/384.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst