[CI]: Upgrade Docker images and workflows

.github/workflows/ci-docs.yml

@@ -11,7 +11,7 @@ on:
       - '.github/workflows/**'
 jobs:
   run-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ on:
 
 jobs:
   run-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     # Use custom docs CI image
     container: ghcr.io/juaml/junifer-ci:main
     strategy:
@@ -31,16 +31,16 @@ jobs:
       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: |
-        # actions/checkout fails to identify Git as it's not in the CI image
-        apt-get -qq update && \
-        apt-get -qq install -y \
+        sudo apt-get update
+        sudo apt-get install -y \
         git \
         git-annex \
         make \
         jq
-        # Copy xfms directory
-        mkdir -p $HOME/junifer/data/xfms && \
+    - name: Copy xfms directory
+        mkdir -p $HOME/junifer/data/xfms
         cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -59,8 +59,8 @@ jobs:
         git config --global user.email "[email protected]"
         git config --global user.name "GitHub Runner"
     - name: Test with tox
+      # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
       run: |
-        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
         git config --system --add safe.directory $(pwd)
         tox
     - name: Upload coverage to Codecov

.github/workflows/docker-ci-publish.yml

@@ -26,7 +26,7 @@ env:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     permissions:
       contents: read
       packages: write

.github/workflows/docker-docs-publish.yml

@@ -26,7 +26,7 @@ env:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     permissions:
       contents: read
       packages: write

.github/workflows/docs-preview.yml

@@ -17,7 +17,7 @@ concurrency: preview-${{ github.ref }}
 
 jobs:
   build-docs:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     # Use custom docs CI image
     container: ghcr.io/juaml/junifer-docs:main
     steps:

.github/workflows/docs.yml

@@ -12,26 +12,26 @@ on:
 
 jobs:
   build-docs:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     # 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: |
-        # actions/checkout fails to identify Git as it's not in the CI image
-        apt-get -qq update && \
-        apt-get -qq install -y \
+        sudo apt-get update
+        sudo apt-get install -y \
         git \
         git-annex \
         make \
         jq
-        # Copy xfms directory
-        mkdir -p $HOME/junifer/data/xfms && \
+    - name: Copy xfms directory
+        mkdir -p $HOME/junifer/data/xfms
         cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
-    - name: Checkout source
+    - name: Checkout repository
       uses: actions/checkout@v4
       with:
         # require all of history to see all tagged versions' docs
@@ -59,8 +59,8 @@ 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: |
-        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
         git config --system --add safe.directory $(pwd)
         make -C docs/ html
         touch docs/_build/.nojekyll

.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

.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:

Dockerfile-ci

@@ -41,7 +41,8 @@ RUN apt-get update && \
     file \
     dc \
     libquadmath0 \
-    libgomp1
+    libgomp1 \
+    && rm -rf /var/lib/apt/lists/*
 
 # Add xfms
 COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms

Dockerfile-docs

@@ -10,7 +10,8 @@ RUN apt-get update && \
     apt-get install -y \
     # ANTs runtime stuff
     libhdf5-dev \
-    bc
+    bc \
+    && rm -rf /var/lib/apt/lists/*
 
 # Add xfms
 COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms

docs/changes/newsfragments/396.misc

@@ -0,0 +1 @@
+Update Docker image recipes and GitHub Actions workflows by `Synchon Mandal`_

ignore_words.txt

@@ -6,3 +6,5 @@ arange
 sinc
 whit
 amin
+lets
+lIns

junifer/markers/complexity/tests/test_complexity_base.py

@@ -8,7 +8,7 @@
 
 pytest.importorskip("neurokit2")
 
-from junifer.markers.complexity.complexity_base import (  # noqa: E402
+from junifer.markers.complexity.complexity_base import (
     ComplexityBase,
 )
 

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -12,11 +12,11 @@
 pytest.importorskip("neurokit2")
 
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import HurstExponent  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import HurstExponent
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -11,11 +11,11 @@
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import MultiscaleEntropyAUC  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import MultiscaleEntropyAUC
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -11,11 +11,11 @@
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import PermEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import PermEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_range_entropy.py

@@ -12,11 +12,11 @@
 pytest.importorskip("neurokit2")
 
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import RangeEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import RangeEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -12,11 +12,11 @@
 pytest.importorskip("neurokit2")
 
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import RangeEntropyAUC  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import RangeEntropyAUC
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -11,11 +11,11 @@
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import SampleEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import SampleEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )