junifer 0.0.5.dev240__tar.gz → 0.0.6__tar.gz

junifer-0.0.6/.dockerignore

@@ -0,0 +1,19 @@
+# .git/
+
+build
+dist
+tools
+*.egg-info
+*.egg/
+*.pyc
+*.swp
+
+.tox
+.pytest_cache
+.ruff_cache
+.coverage
+html/*
+__pycache__
+
+# Compiled Documentation
+docs/_build

{junifer-0.0.5.dev240 → junifer-0.0.6}/.github/dependabot.yml

@@ -1,10 +1,14 @@
 # Set update schedule for GitHub Actions
-
 version: 2
 updates:
-
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+    # Group updates to avoid extra PRs
+    groups:
+      # Group name
+      actions:
+        patterns:
+          - "*"

{junifer-0.0.5.dev240 → junifer-0.0.6}/.github/workflows/ci-docs.yml

@@ -4,18 +4,24 @@ on:
   push:
     paths-ignore:
       - 'junifer/**'
+      - 'docs/changes/newsfragments/**'
       - '.github/workflows/**'
+      - 'tox.ini'
+      - 'pyproject.toml'
   pull_request:
     paths-ignore:
       - 'junifer/**'
+      - 'docs/changes/newsfragments/**'
       - '.github/workflows/**'
+      - 'tox.ini'
+      - 'pyproject.toml'
 jobs:
   run-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - run: 'echo "No build required"'
       - name: Create mock coverage.xml file
@@ -40,12 +46,12 @@ jobs:
           echo '</package>' >> coverage.xml
           echo '</packages>' >> coverage.xml
           echo '</coverage>' >> coverage.xml
-        if: matrix.python-version == 3.11
+        if: matrix.python-version == 3.12
       - name: Upload mock coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           # Allow coverage upload failure
           fail_ci_if_error: false
           flags: docs
-        if: success() && matrix.python-version == 3.11
+        if: success() && matrix.python-version == 3.12

junifer-0.0.6/.github/workflows/ci.yml

@@ -0,0 +1,78 @@
+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:
+    - 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/v2
+        cp -ar /root/junifer_data/v2/. $HOME/junifer_data/v2/
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      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-0.0.6/.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-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@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@d7d6bc7722e3daa8354c50bcb52f4837da5e9b6a #v3.8.1
+        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@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2 # v3.10.0
+
+      # 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@9780b0c442fbb1117ed29e0efdff1e18412f7567 # v3.3.0
+        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@902fa8ec7d6ecbf8d84d538b9b233a880e428804 # v5.7.0
+        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@471d1dc4e07e5cdedd4c2171150001c434f0b7a4 # v6.15.0
+        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/.github/workflows/docker-docs-publish.yml

@@ -0,0 +1,100 @@
+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@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@d7d6bc7722e3daa8354c50bcb52f4837da5e9b6a #v3.8.1
+        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@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2 # v3.10.0
+
+      # 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@9780b0c442fbb1117ed29e0efdff1e18412f7567 # v3.3.0
+        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@902fa8ec7d6ecbf8d84d538b9b233a880e428804 # v5.7.0
+        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@471d1dc4e07e5cdedd4c2171150001c434f0b7a4 # v6.15.0
+        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-0.0.6/.github/workflows/docs-preview.yml

@@ -0,0 +1,68 @@
+name: Build and preview docs
+
+on:
+  push:
+    branches-ignore:
+      - 'main'
+    tags-ignore:
+      - v*
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+concurrency: preview-${{ github.ref }}
+
+jobs:
+  build-docs:
+    # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
+    runs-on: ubuntu-22.04
+    permissions:
+      # Needed for preview deploy
+      pull-requests: 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
+      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/v2
+        cp -ar /root/junifer_data/v2/. $HOME/junifer_data/v2/
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install -e ".[docs,neurokit2]"
+    - name: Configure Git for DataLad
+      run: |
+        git config --global user.email "junifer-runner@github.com"
+        git config --global user.name "GitHub Runner"
+    - name: Test build docs
+      run: |
+        BUILDDIR=_build/main make -C docs/ local
+    - name: Deploy preview
+      if: github.event_name == 'pull_request'
+      uses: rossjrw/pr-preview-action@v1
+      with:
+        source-dir: docs/_build/main

{junifer-0.0.5.dev240 → junifer-0.0.6}/.github/workflows/docs.yml

@@ -8,52 +8,50 @@ on:
     # Sequence of patterns matched against refs/tags
     tags:
       - v*
+  workflow_dispatch: {}
 
 jobs:
   build-docs:
-    runs-on: ubuntu-latest
+    # 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
     steps:
-    - name: Checkout source
+    - 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
+      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/v2
+        cp -ar /root/junifer_data/v2/. $HOME/junifer_data/v2/
+    - name: Checkout repository
       uses: actions/checkout@v4
       with:
         # require all of history to see all tagged versions' docs
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.11
+    - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
-    - name: Check for sudo
-      shell: bash
-      run: |
-        if type sudo >/dev/null 2>&1; then SUDO="sudo"; else SUDO=""; fi
-        echo "SUDO=$SUDO" >> $GITHUB_ENV
-    - name: Install dependencies
+        python-version: "3.12"
+    - name: Install Python dependencies
       run: |
-        $SUDO bash -c "$(curl -fsSL http://neuro.debian.net/_files/neurodebian-travis.sh)"
-        $SUDO apt-get update -qq
-        $SUDO apt-get install git-annex-standalone
         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
-    - name: Configure git for datalad
+    - name: Configure Git for DataLad
       run: |
-        git config --global user.email "runner@github.com"
-        git config --global user.name "GITHUB CI Runner"
-    - name: Install ANTs
-      run: |
-        echo "++ Add universe repo"
-        sudo add-apt-repository -y universe
-
-        echo "++ Update package manager info"
-        sudo apt-get update -qq
-
-        echo "++ Downloading ANTs"
-        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
-        unzip ants.zip -d /opt
-        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
-        rm ants.zip
-        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
+        git config --global user.email "junifer-runner@github.com"
+        git config --global user.name "GitHub Runner"
     - name: Checkout gh-pages
       # As we already did a deploy of gh-pages above, it is guaranteed to be there
       # so check it out so we can selectively build docs below
@@ -63,7 +61,9 @@ 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: |
+        git config --system --add safe.directory $(pwd)
         make -C docs/ html
         touch docs/_build/.nojekyll
         cp docs/redirect.html docs/_build/index.html

{junifer-0.0.5.dev240 → junifer-0.0.6}/.github/workflows/lint.yml

@@ -12,7 +12,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

junifer-0.0.6/.github/workflows/publish.yml

@@ -0,0 +1,46 @@
+name: Build and publish
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+
+jobs:
+  build-and-publish:
+    name: Build and publish
+    runs-on: ubuntu-latest
+    permissions:
+      # Needed for PyPI publishing
+      id-token: write
+      # Needed for GitHub releases
+      contents: write
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install build
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build
+    - name: Build package
+      run:
+        python -m build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+    - name: Make release on GitHub
+      uses: softprops/action-gh-release@v2
+      if: startsWith(github.ref, 'refs/tags/')
+      with:
+        files: |
+          dist/*.tar.gz
+          dist/*.whl
+        generate_release_notes: true
+        make_latest: true

{junifer-0.0.5.dev240 → junifer-0.0.6}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-docstring-first
@@ -17,24 +17,24 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.16
+    rev: v0.23
     hooks:
       - id: validate-pyproject
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 24.10.0
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.2
+    rev: v0.9.3
     hooks:
       - id: ruff
         types_or: [python, jupyter]
         exclude: ^(__init__.py)
         args: [--output-format, grouped, --show-fixes]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.0
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
@@ -48,7 +48,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
+    rev: "1.19.1"
     hooks:
       - id: blacken-docs
         additional_dependencies: