junifer 0.0.8.dev211__tar.gz → 0.0.8.dev249__tar.gz

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/.dockerignore

@@ -17,3 +17,6 @@ __pycache__
 
 # Compiled Documentation
 docs/_build
+
+# Local environments
+.venv

junifer-0.0.8.dev249/.github/workflows/ci.yml

@@ -0,0 +1,157 @@
+name: Run Tests
+
+on:
+  push:
+    # Branches are tested through their pull requests
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch: {}
+
+# Cancel superseded runs of the same branch / PR, except on main
+concurrency:
+  group: tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  # Check whether the library changed, to skip the tests otherwise
+  # (e.g. on docs-only changes)
+  changes:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+    outputs:
+      code: ${{ steps.filter.outputs.code }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v7
+        if: github.event_name != 'pull_request'
+      - name: Check for library changes
+        uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          filters: |
+            code:
+              - 'junifer/**'
+              - '.github/workflows/ci.yml'
+              - 'tox.ini'
+              - 'pyproject.toml'
+              - 'uv.lock'
+              - 'codecov.yml'
+
+  # Tests that need testing datasets, junifer-data or AFNI / ANTs / FSL
+  run-tests-external:
+    needs: changes
+    if: needs.changes.outputs.code == 'true' || github.event_name == 'workflow_dispatch'
+    runs-on: [self-hosted, linux, x64, data-v7]
+    strategy:
+      fail-fast: false
+      matrix:
+        # Only the version used for coverage; all versions run on the rest
+        python-version: ['3.13']
+        # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
+    steps:
+      - 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 : $(flirt -version)"
+      - name: Check tooling
+        run: |
+          echo "HOME=$HOME"
+          which git-annex && git annex version | head -1
+          ls -d "$HOME"/junifer_data/* && cat "$HOME/junifer-data-version"
+      - name: Checkout repository
+        uses: actions/checkout@v7
+        with:
+          submodules: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.2.0
+      - name: Install tox
+        # tox-uv makes tox create the test environments with uv
+        run: |
+          uv tool install tox --with tox-uv --with 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 --global --add safe.directory $(pwd)
+          tox -- -m external
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v7
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          flags: junifer
+        if: success() && matrix.python-version == '3.13'
+
+  # All the other tests
+  run-tests:
+    needs: changes
+    if: needs.changes.outputs.code == 'true' || github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v7
+        with:
+          submodules: true
+      - name: Install git-annex
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y git-annex
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.2.0
+      - name: Install tox
+        # tox-uv makes tox create the test environments with uv
+        run: |
+          uv tool install tox --with tox-uv --with 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
+        run: |
+          tox -- -m "not external"
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v7
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          flags: junifer
+        if: success() && matrix.python-version == '3.13'
+
+  # Single status to require in branch protection: passes when the tests
+  # passed or were skipped because the library did not change
+  tests:
+    needs: [changes, run-tests-external, run-tests]
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check test results
+        if: >-
+          contains(needs.*.result, 'failure') ||
+          contains(needs.*.result, 'cancelled')
+        run: |
+          echo "Some test jobs failed or were cancelled"
+          exit 1
+      - run: echo "Tests passed or were not needed"

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/.github/workflows/docker-publish.yml

@@ -1,12 +1,14 @@
 name: Docker
 
 on:
+  # Publish an image for every release
   push:
-    branches: [ "main" ]
-    paths: [ "Dockerfile" ]
+    tags:
+      - v*
+  # Only test that the image builds
   pull_request:
     branches: [ "main" ]
-    paths: [ "Dockerfile" ]
+    paths: [ "Dockerfile", ".github/workflows/docker-publish.yml" ]
   workflow_dispatch: {}
 
 env:
@@ -33,6 +35,10 @@ jobs:
       - run: df -h
       - name: Checkout repository
         uses: actions/checkout@v7
+        with:
+          # Tags are needed for the junifer version (setuptools-scm)
+          fetch-depth: 0
+          submodules: true
       - name: Install cosign
         if: github.event_name != 'pull_request'
         uses: sigstore/cosign-installer@v4.1.2
@@ -50,6 +56,12 @@ jobs:
         uses: docker/metadata-action@v6.2.0
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          # vX.Y.Z -> X.Y.Z, X.Y and latest; branch name for manual runs
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=ref,event=branch
+            type=ref,event=pr
       - name: Build and push Docker image
         id: build-and-push
         uses: docker/build-push-action@v7.3.0

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/.github/workflows/docs-preview.yml

@@ -1,11 +1,7 @@
 name: Build and preview docs
 
 on:
-  push:
-    branches-ignore:
-      - 'main'
-    tags-ignore:
-      - v*
+  # Docs for main and tags are built by docs.yml
   pull_request:
     types:
       - opened
@@ -13,35 +9,25 @@ on:
       - synchronize
       - closed
 
-concurrency: preview-${{ github.ref }}
+concurrency:
+  group: preview-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build-docs:
-    # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
-    runs-on: ubuntu-22.04
+    runs-on: [self-hosted, linux, x64, data-v7]
     permissions:
       # Needed for preview deploy
       pull-requests: write
       contents: write
-    # Use custom docs CI image
-    container: ghcr.io/juaml/junifer-docs:main
     steps:
     - name: Check ANTs
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
-    - name: Install system dependencies
-      # actions/checkout fails to identify Git as it's not in the CI image
+    - name: Check tooling
       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/v7
-        cp -ar /root/junifer_data/v7/. $HOME/junifer_data/v7/
+        which make git-annex jq
+        ls -d "$HOME"/junifer_data/v7
     - name: Checkout repository
       uses: actions/checkout@v7
       with:
@@ -51,10 +37,11 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: "3.12"
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.2.0
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -e ".[docs,neurokit2]"
+        uv pip install --system -e ".[docs,neurokit2]"
     - name: Configure Git for DataLad
       run: |
         git config --global user.email "junifer-runner@github.com"

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/.github/workflows/docs.yml

@@ -12,27 +12,15 @@ on:
 
 jobs:
   build-docs:
-    # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
-    runs-on: ubuntu-22.04
-    # Use custom docs CI image
-    container: ghcr.io/juaml/junifer-docs:main
+    runs-on: [self-hosted, linux, x64, data-v7]
     steps:
     - name: Check ANTs
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
-    - name: Install system dependencies
-      # actions/checkout fails to identify Git as it's not in the CI image
+    - name: Check tooling
       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/v7
-        cp -ar /root/junifer_data/v7/. $HOME/junifer_data/v7/
+        which make git-annex jq
+        ls -d "$HOME"/junifer_data/v7
     - name: Checkout repository
       uses: actions/checkout@v7
       with:
@@ -43,11 +31,12 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: "3.12"
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.2.0
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -e ".[docs,neurokit2]"
-        python -m pip install git+https://github.com/dls-controls/sphinx-multiversion@only-arg
+        uv pip install --system -e ".[docs,neurokit2]"
+        uv pip install --system git+https://github.com/dls-controls/sphinx-multiversion@only-arg
     - name: Configure Git for DataLad
       run: |
         git config --global user.email "junifer-runner@github.com"
@@ -63,7 +52,7 @@ jobs:
       # Use the args we normally pass to sphinx-build, but run sphinx-multiversion
       # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
       run: |
-        git config --system --add safe.directory $(pwd)
+        git config --global --add safe.directory $(pwd)
         make -C docs/ html
         touch docs/_build/.nojekyll
         cp docs/redirect.html docs/_build/index.html

junifer-0.0.8.dev249/.github/workflows/lint.yml

@@ -0,0 +1,29 @@
+name: Lint
+
+on:
+  - push
+  - pull_request
+
+# Cancel superseded runs of the same branch / PR, except on main
+concurrency:
+  group: lint-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - name: Install Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.x"
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.2.0
+      - name: Install tox
+        run: |
+          uv tool install tox --with tox-uv
+      - name: Run ruff
+        run: uvx "ruff>=0.1.0" check --output-format=github .
+      - name: Run codespell
+        run: tox -e codespell

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/.github/workflows/publish.yml

@@ -26,13 +26,11 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: "3.x"
-    - name: Install build
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install build
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.2.0
     - name: Build package
       run:
-        python -m build
+        uv build
     - name: Publish package to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
     - name: Make release on GitHub

junifer-0.0.8.dev249/Dockerfile

@@ -0,0 +1,82 @@
+# syntax=docker/dockerfile:1
+
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+LABEL org.opencontainers.image.source=https://github.com/juaml/junifer \
+      org.opencontainers.image.description="Junifer container image" \
+      org.opencontainers.image.licenses=AGPL-3.0-only \
+      BaseImage="ubuntu:24.04"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    # Base tooling
+    ca-certificates curl git file make build-essential \
+    python3 python3-venv python3-dev python-is-python3 \
+    # Data
+    git-annex \
+    # ANTs runtime
+    bc \
+    # AFNI runtime (non-GUI subset of AFNI's Ubuntu 24 list)
+    tcsh gsl-bin libgsl27 libglu1-mesa libglw1-mesa libxm4 libjpeg62 \
+    libxmu6 libxpm4 libxi6 libxext6 libglib2.0-0t64 libgomp1 \
+    netpbm xvfb xfonts-base python3-numpy python3-matplotlib r-base \
+    # FSL runtime
+    dc libquadmath0 \
+    && rm -rf /var/lib/apt/lists/*
+
+# --- Heavy, rarely-changing neuroimaging tools ---
+
+# ANTs
+COPY --from=antsx/ants:latest /opt/ants /opt/ants
+ENV PATH="/opt/ants/bin:$PATH" \
+    LD_LIBRARY_PATH="/opt/ants/lib"
+
+# AFNI — native Ubuntu 24.04 build
+RUN mkdir -p /opt/afni \
+    && curl -fsSL https://afni.nimh.nih.gov/pub/dist/tgz/linux_ubuntu_24_64.tgz \
+       | tar -xz -C /opt/afni --strip-components=1
+ENV PATH="/opt/afni:$PATH"
+
+# FSL
+RUN curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -o /tmp/fslinstaller.py \
+    && (python3 /tmp/fslinstaller.py -d /opt/fsl/ --skip_registration \
+        || { cat /root/fsl_installation_*.log; exit 1; }) \
+    && rm -rf /opt/fsl/pkgs /tmp/fslinstaller.py /root/fsl_installation_*.log \
+    && find /opt/fsl -name '__pycache__' -prune -exec rm -rf {} +
+ENV FSLDIR=/opt/fsl \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    PATH="/opt/fsl/share/fsl/bin:$PATH"
+
+# --- Python environment (the system Python is externally managed) ---
+RUN python3 -m venv /opt/junifer \
+    && /opt/junifer/bin/pip install --no-cache-dir --upgrade pip setuptools wheel \
+    && /opt/junifer/bin/pip install --no-cache-dir datalad
+ENV PATH="/opt/junifer/bin:$PATH"
+
+# --- junifer-data, version and commit taken from junifer itself ---
+COPY junifer/data/utils.py /tmp/junifer_data_utils.py
+RUN set -eux; \
+    version="v$(sed -n 's/^JUNIFER_DATA_VERSION = "\(.*\)"/\1/p' /tmp/junifer_data_utils.py)"; \
+    hexsha="$(sed -n 's/^JUNIFER_DATA_HEXSHA = "\(.*\)"/\1/p' /tmp/junifer_data_utils.py)"; \
+    test "$version" != "v" && test -n "$hexsha"; \
+    git config --global user.name "junifer"; \
+    git config --global user.email "junifer@localhost"; \
+    datalad clone https://cerebra.fz-juelich.de/junifer/junifer-data.git "$HOME/junifer_data/${version}"; \
+    cd "$HOME/junifer_data/${version}"; \
+    git checkout -q "${version}"; \
+    test "$(git rev-parse HEAD)" = "$hexsha"; \
+    datalad get -r -J 4 .; \
+    test -z "$(git status --porcelain)"; \
+    git log -1 --format='junifer-data %D @ %H'; \
+    echo "${version}" > "$HOME/junifer-data-version"; \
+    rm /tmp/junifer_data_utils.py
+
+# --- junifer from the build context (changes most often → last) ---
+# The build context must include .git so the version matches the release tag
+COPY . /tmp/junifer
+RUN python -m pip install --no-cache-dir "/tmp/junifer[all]" \
+    && rm -rf /tmp/junifer \
+    && junifer --version

junifer-0.0.8.dev249/Dockerfile-ci

@@ -0,0 +1,134 @@
+# syntax=docker/dockerfile:1
+
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+LABEL org.opencontainers.image.source=https://github.com/juaml/junifer \
+      org.opencontainers.image.description="Junifer CI container image" \
+      org.opencontainers.image.licenses=AGPL-3.0-only \
+      Author="Fede Raimondo" \
+      Email="f.raimondo@fz-juelich.de" \
+      GitHub="https://github.com/fraimondo" \
+      BaseImage="ubuntu:24.04"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    # Base / runner tooling
+    ca-certificates curl wget git jq sudo unzip vim file make gnupg \
+    xz-utils bzip2 zstd \
+    python3 python3-venv python-is-python3 \
+    # Data
+    git-annex \
+    # ANTs runtime
+    bc \
+    # AFNI runtime (non-GUI subset of AFNI's Ubuntu 24 list)
+    tcsh gsl-bin libgsl27 libglu1-mesa libglw1-mesa libxm4 libjpeg62 \
+    libxmu6 libxpm4 libxi6 libxext6 libglib2.0-0t64 libgomp1 \
+    netpbm xvfb xfonts-base python3-numpy python3-matplotlib r-base \
+    # FSL runtime
+    dc libquadmath0 \
+    && rm -rf /var/lib/apt/lists/*
+
+# DataLad (not packaged for Ubuntu 24.04) in its own venv
+RUN python3 -m venv /opt/datalad \
+    && /opt/datalad/bin/pip install --no-cache-dir datalad \
+    && ln -s /opt/datalad/bin/datalad /usr/local/bin/datalad \
+    && datalad --version
+
+# Ubuntu 24.04 ships a default 'ubuntu' user (uid 1000); give that uid to our user
+RUN userdel -r ubuntu 2>/dev/null || true; \
+    useradd -m -u 1000 -s /bin/bash docker
+
+# --- Heavy, rarely-changing neuroimaging tools ---
+
+# ANTs
+COPY --from=antsx/ants:latest /opt/ants /opt/ants
+ENV PATH="/opt/ants/bin:$PATH" \
+    LD_LIBRARY_PATH="/opt/ants/lib"
+
+# AFNI — native Ubuntu 24.04 build
+RUN mkdir -p /opt/afni \
+    && curl -fsSL https://afni.nimh.nih.gov/pub/dist/tgz/linux_ubuntu_24_64.tgz \
+       | tar -xz -C /opt/afni --strip-components=1
+ENV PATH="/opt/afni:$PATH"
+
+# FSL
+RUN curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -o /tmp/fslinstaller.py \
+    && (python3 /tmp/fslinstaller.py -d /opt/fsl/ --skip_registration \
+        || { cat /root/fsl_installation_*.log; exit 1; }) \
+    && rm -rf /opt/fsl/pkgs /tmp/fslinstaller.py /root/fsl_installation_*.log \
+    && find /opt/fsl -name '__pycache__' -prune -exec rm -rf {} +
+ENV FSLDIR=/opt/fsl \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    PATH="/opt/fsl/share/fsl/bin:$PATH"
+
+# --- Hosted tool cache, pre-populated (no downloads at job time) ---
+ARG PYTHON_VERSIONS="3.10 3.11 3.12 3.13 3.14"
+ARG UBUNTU_TAG=24.04
+ENV AGENT_TOOLSDIRECTORY=/opt/hostedtoolcache
+RUN set -eux; \
+    mkdir -p "$AGENT_TOOLSDIRECTORY"; \
+    curl -fsSL https://raw.githubusercontent.com/actions/python-versions/main/versions-manifest.json -o /tmp/manifest.json; \
+    filter='[ .[] | select(.stable and (.version | startswith($v + "."))) | .files[] | select(.platform=="linux" and .platform_version==$os and .arch=="x64") ][0].download_url'; \
+    for v in $PYTHON_VERSIONS; do \
+      url=$(jq -r --arg v "$v" --arg os "$UBUNTU_TAG" "$filter" /tmp/manifest.json); \
+      [ "$url" != "null" ] || { echo "No $v build for Ubuntu $UBUNTU_TAG"; exit 1; }; \
+      tmp=$(mktemp -d); \
+      curl -fsSL "$url" | tar -xz -C "$tmp"; \
+      (cd "$tmp" && bash ./setup.sh); \
+      rm -rf "$tmp"; \
+    done; \
+    rm /tmp/manifest.json; \
+    find "$AGENT_TOOLSDIRECTORY" -name '__pycache__' -prune -exec rm -rf {} +; \
+    chown -R docker:docker "$AGENT_TOOLSDIRECTORY"; \
+    ls "$AGENT_TOOLSDIRECTORY/Python"
+
+# --- GitHub Actions runner ---
+ARG RUNNER_VERSION
+LABEL RunnerVersion=${RUNNER_VERSION}
+RUN mkdir -p /home/docker/actions-runner && cd /home/docker/actions-runner \
+    && curl -fsSL -o runner.tar.gz \
+       https://github.com/actions/runner/releases/download/v${RUNNER_VERSION}/actions-runner-linux-x64-${RUNNER_VERSION}.tar.gz \
+    && tar xzf runner.tar.gz && rm runner.tar.gz \
+    && ./bin/installdependencies.sh \
+    && rm -rf /var/lib/apt/lists/* \
+    && chown -R docker:docker /home/docker
+
+COPY --chmod=755 scripts/start.sh /start.sh
+
+USER docker
+WORKDIR /home/docker
+
+# --- Test data (changes most often → last), cloned as the runner user ---
+ARG DATA_VERSION
+RUN set -eux; \
+    git config --global user.name "junifer-ci"; \
+    git config --global user.email "junifer-ci@localhost"; \
+    datalad clone https://cerebra.fz-juelich.de/junifer/junifer-data.git "$HOME/junifer_data/${DATA_VERSION}"; \
+    cd "$HOME/junifer_data/${DATA_VERSION}"; \
+    git checkout -q "${DATA_VERSION}"; \
+    datalad get -r -J 4 .; \
+    test -z "$(git status --porcelain)"; \
+    git log -1 --format='junifer-data %D @ %H'; \
+    echo "${DATA_VERSION}" > "$HOME/junifer-data-version"
+
+# --- nilearn datasets used by junifer.testing (no downloads at test time) ---
+ARG NILEARN_VERSION=0.10.4
+RUN <<'EOF'
+set -eux
+python3 -m venv /tmp/nilearn-venv
+/tmp/nilearn-venv/bin/pip install --no-cache-dir -q "nilearn==${NILEARN_VERSION}" "numpy<2.4"
+/tmp/nilearn-venv/bin/python - <<'PY'
+from nilearn import datasets
+datasets.fetch_oasis_vbm(n_subjects=10)
+datasets.fetch_development_fmri(n_subjects=10, reduce_confounds=True, age_group="both")
+datasets.fetch_spm_auditory()
+datasets.fetch_adhd(n_subjects=10)
+PY
+rm -rf /tmp/nilearn-venv
+du -sh "$HOME/nilearn_data"
+EOF
+
+ENTRYPOINT ["/start.sh"]

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev211
+Version: 0.0.8.dev249
 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>
@@ -42,9 +42,9 @@ Requires-Dist: tqdm<4.68.0,>=4.66.1
 Requires-Dist: templateflow<25.0.0,>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
 Requires-Dist: lazy_loader==0.4
-Requires-Dist: importlib_metadata; python_version < "3.9"
+Requires-Dist: importlib_metadata; python_version < "3.11"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
-Requires-Dist: junifer_data==1.3.0
+Requires-Dist: junifer-data>=1.4.0
 Requires-Dist: structlog<26.0.0,>=25.0.0
 Requires-Dist: pydantic>=2.11.4
 Requires-Dist: aenum<3.2.0,>=3.1.0
@@ -69,7 +69,7 @@ Requires-Dist: sphinx<8.4.0,>=7.3.0; extra == "docs"
 Requires-Dist: sphinx-gallery<0.20.0,>=0.17.0; extra == "docs"
 Requires-Dist: furo<2025.10.0,>=2024.4.27; extra == "docs"
 Requires-Dist: numpydoc<=1.9.0,>=1.6.0; extra == "docs"
-Requires-Dist: julearn==0.3.3; extra == "docs"
+Requires-Dist: julearn==0.3.5; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
 Requires-Dist: towncrier<=25.8.0,>=24.7.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<=1.0.0,>=0.8.1; extra == "docs"

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/codecov.yml

@@ -1,5 +1,7 @@
 codecov:
-  notify: {}
+  notify:
+    # Wait for the coverage of both test jobs (external and the rest)
+    after_n_builds: 2
   require_ci_to_pass: false
 
 comment:                  # this is a top-level key
@@ -7,6 +9,7 @@ comment:                  # this is a top-level key
   behavior: default
   require_changes: false  # if true: only post the comment if coverage changes
   require_base: no        # [yes :: must have a base report to post]
+  after_n_builds: 2       # wait for both test jobs before commenting
 
 coverage:
   status:
@@ -27,13 +30,3 @@ flag_management:
         - type: patch
           target: 95%
           threshold: 1%
-    - name: docs
-      paths:
-        - docs/
-      statuses:
-        - type: project
-          target: 100%
-          threshold: 1%
-        - type: patch
-          target: 95%
-          threshold: 1%

{junifer-0.0.8.dev211 → junifer-0.0.8.dev249}/docs/changes/newsfragments/502.bugfix

@@ -1 +1 @@
-Fix type issues and update model configs for :class:`.BaseDataGrabber`, :class:`.BasePreprocessor`, :class:`.BaseMarker` and :class:`.BaseStorage` by `Synchon Mandal`_
+Fix type issues and update model configs for :class:`.BaseDataGrabber`, :class:`.BasePreprocessor`, :class:`.BaseMarker` and :class:`.BaseFeatureStorage` by `Synchon Mandal`_

junifer-0.0.8.dev249/docs/changes/newsfragments/511.bugfix

@@ -0,0 +1 @@
+Fix ``get_versions`` (used by ``junifer wtf``) missing packages without ``top_level.txt`` (e.g. ``looseversion``, ``typing_extensions``) on Python 3.10 by using ``importlib_metadata`` for Python < 3.11 by `Fede Raimondo`_

junifer-0.0.8.dev249/docs/changes/newsfragments/511.bugfix.1

@@ -0,0 +1 @@
+Fix :meth:`.PatternDataGrabber.get_elements` returning elements that miss some of the data types when several types use all the replacements by `Fede Raimondo`_

junifer-0.0.8.dev249/docs/changes/newsfragments/511.change

@@ -0,0 +1 @@
+Sanitise the VOI names of built-in coordinates by replacing spaces with ``_`` and adding a ``-{i}`` suffix to duplicated names, which changes the feature names of e.g. ``Dosenbach`` and ``Seitzman2018`` by `Fede Raimondo`_

junifer-0.0.8.dev249/docs/changes/newsfragments/511.enh

@@ -0,0 +1 @@
+Drop the files fetched by :class:`.DataladDataGrabber` in a single call and without checking their availability on the remote, making cleanup much faster by `Fede Raimondo`_