junifer 0.0.6.dev389__tar.gz → 0.0.6.dev407__tar.gz

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/.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:

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/.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 "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: |
-        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
         git config --system --add safe.directory $(pwd)
         tox
     - name: Upload coverage to Codecov

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/.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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/.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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/.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:

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/.github/workflows/docs.yml

@@ -12,7 +12,7 @@ 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:
@@ -20,18 +20,18 @@ jobs:
       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

junifer-0.0.6.dev407/.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-0.0.6.dev389 → junifer-0.0.6.dev407}/.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:

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: junifer
-Version: 0.0.6.dev389
+Version: 0.0.6.dev407
 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.dev407/docs/changes/newsfragments/396.misc

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

junifer-0.0.6.dev407/docs/changes/newsfragments/420.bugfix

@@ -0,0 +1 @@
+Fix ``t_r`` tampering by :func:`nilearn.image.clean_img` in :class:`.fMRIPrepConfoundRemover` by `Fede Raimondo`_ and `Synchon Mandal`_

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/ignore_words.txt

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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev389'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev389')
+__version__ = version = '0.0.6.dev407'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev407')

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_complexity_base.py

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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -12,11 +12,11 @@ import pytest
 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-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -11,11 +11,11 @@ import pytest
 
 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-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_perm_entropy.py

@@ -11,11 +11,11 @@ import pytest
 
 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-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_range_entropy.py

@@ -12,11 +12,11 @@ import pytest
 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-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -12,11 +12,11 @@ import pytest
 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-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_sample_entropy.py

@@ -11,11 +11,11 @@ import pytest
 
 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,
 )
 

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/markers/complexity/tests/test_weighted_perm_entropy.py

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

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -596,6 +596,8 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
             t_r=t_r,
             mask_img=mask_img,
         )
+        # Fix t_r as nilearn messes it up
+        cleaned_img.header["pixdim"][4] = t_r
         # Save deconfounded data
         deconfounded_img_path = element_tempdir / "deconfounded_data.nii.gz"
         nib.save(cleaned_img, deconfounded_img_path)

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -460,22 +460,32 @@ def test_fMRIPrepConfoundRemover_fit_transform() -> None:
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        # Get original data
+        input_img = element_data["BOLD"]["data"]
+        input_bold = input_img.get_fdata().copy()
+        input_tr = input_img.header.get_zooms()[3]
+        # Fit-transform
         output = confound_remover.fit_transform(element_data)
-        trans_bold = output["BOLD"]["data"].get_fdata()
+        output_img = output["BOLD"]["data"]
+        output_bold = output_img.get_fdata()
+        output_tr = output_img.header.get_zooms()[3]
+
         # Transformation is in place
         assert_array_equal(
-            trans_bold, element_data["BOLD"]["data"].get_fdata()
+            output_bold, element_data["BOLD"]["data"].get_fdata()
         )
 
         # Data should have the same shape
-        assert orig_bold.shape == trans_bold.shape
+        assert input_bold.shape == output_bold.shape
 
         # but be different
         assert_raises(
-            AssertionError, assert_array_equal, orig_bold, trans_bold
+            AssertionError, assert_array_equal, input_bold, output_bold
         )
 
+        # Check t_r
+        assert input_tr == output_tr
+
         assert "meta" in output["BOLD"]
         assert "preprocess" in output["BOLD"]["meta"]
         t_meta = output["BOLD"]["meta"]["preprocess"]
@@ -506,22 +516,32 @@ def test_fMRIPrepConfoundRemover_fit_transform_masks() -> None:
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        # Get original data
+        input_img = element_data["BOLD"]["data"]
+        input_bold = input_img.get_fdata().copy()
+        input_tr = input_img.header.get_zooms()[3]
+        # Fit-transform
         output = confound_remover.fit_transform(element_data)
-        trans_bold = output["BOLD"]["data"].get_fdata()
+        output_img = output["BOLD"]["data"]
+        output_bold = output_img.get_fdata()
+        output_tr = output_img.header.get_zooms()[3]
+
         # Transformation is in place
         assert_array_equal(
-            trans_bold, element_data["BOLD"]["data"].get_fdata()
+            output_bold, element_data["BOLD"]["data"].get_fdata()
         )
 
         # Data should have the same shape
-        assert orig_bold.shape == trans_bold.shape
+        assert input_bold.shape == output_bold.shape
 
         # but be different
         assert_raises(
-            AssertionError, assert_array_equal, orig_bold, trans_bold
+            AssertionError, assert_array_equal, input_bold, output_bold
         )
 
+        # Check t_r
+        assert input_tr == output_tr
+
         assert "meta" in output["BOLD"]
         assert "preprocess" in output["BOLD"]["meta"]
         t_meta = output["BOLD"]["meta"]["preprocess"]

{junifer-0.0.6.dev389 → junifer-0.0.6.dev407}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: junifer
-Version: 0.0.6.dev389
+Version: 0.0.6.dev407
 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.dev389 → junifer-0.0.6.dev407}/junifer.egg-info/SOURCES.txt

@@ -28,7 +28,7 @@ tox.ini
 .github/workflows/docs-preview.yml
 .github/workflows/docs.yml
 .github/workflows/lint.yml
-.github/workflows/pypi.yml
+.github/workflows/publish.yml
 docs/Makefile
 docs/builtin.rst
 docs/conf.py
@@ -97,6 +97,7 @@ docs/changes/newsfragments/391.misc
 docs/changes/newsfragments/392.feature
 docs/changes/newsfragments/393.misc
 docs/changes/newsfragments/395.enh
+docs/changes/newsfragments/396.misc
 docs/changes/newsfragments/398.bugfix
 docs/changes/newsfragments/401.feature
 docs/changes/newsfragments/402.change
@@ -119,6 +120,7 @@ docs/changes/newsfragments/413.change
 docs/changes/newsfragments/414.misc
 docs/changes/newsfragments/415.change
 docs/changes/newsfragments/416.enh
+docs/changes/newsfragments/420.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

junifer-0.0.6.dev389/.github/workflows/pypi.yml

@@ -1,31 +0,0 @@
-name: Build and publish to PyPI
-on:
-  push:
-    branches:
-      - main
-    tags:
-      - 'v*'
-jobs:
-  build-n-publish:
-    name: Build and publish to PyPI
-    runs-on: ubuntu-latest
-    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:
-        pip install build
-    - name: Build a binary wheel and a source tarball
-      run:
-        python -m build --sdist --wheel --outdir dist/ .
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.pypi_token }}