junifer 0.0.7.dev334__tar.gz → 0.0.8__tar.gz

junifer-0.0.8/.dockerignore

@@ -0,0 +1,22 @@
+# .git/
+
+build
+dist
+tools
+*.egg-info
+*.egg/
+*.pyc
+*.swp
+
+.tox
+.pytest_cache
+.ruff_cache
+.coverage
+html/*
+__pycache__
+
+# Compiled Documentation
+docs/_build
+
+# Local environments
+.venv

junifer-0.0.8/.github/workflows/check-stale.yml

@@ -0,0 +1,16 @@
+name: Close stale issues
+
+on:
+  schedule:
+    - cron: '30 1 * * *'
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v11
+        with:
+          stale-issue-message: 'This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          days-before-stale: 30
+          days-before-close: 7
+          any-of-issue-labels: question

junifer-0.0.8/.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+# Cancel superseded runs of the same branch / PR, except on main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@v4
+        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-v8]
+    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@v10.3.0
+      - 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: ['3.11', '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@v10.3.0
+      - 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/.github/workflows/docker-publish.yml

@@ -0,0 +1,81 @@
+name: Docker
+
+on:
+  # Publish an image for every release
+  push:
+    tags:
+      - v*
+  # Only test that the image builds
+  pull_request:
+    branches: [ "main" ]
+    paths: [ "Dockerfile", ".github/workflows/docker-publish.yml" ]
+  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@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
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4.4.1
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v4.6.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        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@v7.4.0
+        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-0.0.8/.github/workflows/docs-preview.yml

@@ -0,0 +1,63 @@
+name: Build and preview docs
+
+on:
+  # Docs for main and tags are built by docs.yml
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+concurrency:
+  group: preview-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-docs:
+    runs-on: [self-hosted, linux, x64, data-v8]
+    permissions:
+      # Needed for preview deploy
+      pull-requests: write
+      contents: write
+    steps:
+    - name: Check ANTs
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      run: |
+        echo "Using ANTs : $(antsRegistration --version)"
+    - name: Check tooling
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      run: |
+        which make git-annex jq
+        ls -d "$HOME"/junifer_data/* && cat "$HOME/junifer-data-version"
+    - name: Checkout repository
+      uses: actions/checkout@v7
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      uses: actions/setup-python@v7
+      with:
+        python-version: "3.12"
+    - name: Set up uv
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      uses: astral-sh/setup-uv@v10.3.0
+    - name: Install Python dependencies
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      run: |
+        uv sync --locked --extra docs
+    - name: Configure Git for DataLad
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      run: |
+        git config --global user.email "junifer-runner@github.com"
+        git config --global user.name "GitHub Runner"
+    - name: Test build docs
+      if: github.event.action != 'closed' # The build is not needed when the preview is removed
+      run: |
+        BUILDDIR=_build/main uv run 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-0.0.8/.github/workflows/docs.yml

@@ -0,0 +1,63 @@
+name: Build and publish docs
+
+on:
+  push:
+    # Sequence of patterns matched against refs/heads
+    branches:
+      - main
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - v*
+  workflow_dispatch: {}
+
+jobs:
+  build-docs:
+    runs-on: [self-hosted, linux, x64, data-v8]
+    steps:
+    - name: Check ANTs
+      run: |
+        echo "Using ANTs : $(antsRegistration --version)"
+    - name: Check tooling
+      run: |
+        which make git-annex jq
+        ls -d "$HOME"/junifer_data/* && cat "$HOME/junifer-data-version"
+    - name: Checkout repository
+      uses: actions/checkout@v7
+      with:
+        # require all of history to see all tagged versions' docs
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: "3.12"
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.3.0
+    - name: Install Python dependencies
+      run: |
+        uv sync --locked --extra docs
+    - name: Configure Git for DataLad
+      run: |
+        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
+      uses: actions/checkout@v7
+      with:
+          ref: gh-pages
+          path: docs/_build
+    - name: Build docs
+      # Build all the versions with sphinx-polyversion; the versions already
+      # in gh-pages are kept and only the missing ones are built
+      # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
+      run: |
+        git config --global --add safe.directory $(pwd)
+        uv run make -C docs/ html
+        touch docs/_build/.nojekyll
+    - name: Publish docs to gh-pages
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/_build
+        keep_files: true

junifer-0.0.8/.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@v10.3.0
+      - 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/.github/workflows/publish.yml

@@ -0,0 +1,44 @@
+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@v7
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: "3.x"
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.3.0
+    - name: Build package
+      run:
+        uv build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+    - name: Make release on GitHub
+      uses: softprops/action-gh-release@v3
+      if: startsWith(github.ref, 'refs/tags/')
+      with:
+        files: |
+          dist/*.tar.gz
+          dist/*.whl
+        generate_release_notes: true
+        make_latest: true

junifer-0.0.8/.gitignore

@@ -0,0 +1,138 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/auto_examples
+docs/sg_execution_times.rst
+docs/generated
+docs/make.bat
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+ENV/
+env.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# vscode
+.vscode
+
+# OS Stuff
+.DS_store
+
+junifer/_version.py
+scratch/
+junifer_jobs/

junifer-0.0.8/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "junifer/external/BrainPrint"]
+	path = junifer/external/BrainPrint
+	url = https://github.com/juaml/BrainPrint.git

junifer-0.0.8/.python-version

@@ -0,0 +1 @@
+3.13