junifer 0.0.6.dev194__tar.gz → 0.0.6.dev205__tar.gz

junifer-0.0.6.dev205/.github/workflows/ci.yml

@@ -0,0 +1,72 @@
+name: Run Tests
+
+on:
+  push:
+    paths:
+      - 'junifer/**'
+      - '.github/workflows/**'
+  pull_request:
+    paths:
+      - 'junifer/**'
+      - '.github/workflows/**'
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    # Use custom docs CI image
+    container: ghcr.io/juaml/junifer-ci:main
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+
+    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
+      run: |
+        # actions/checkout fails to identify Git as it's not in the CI image
+        apt-get -qq update && \
+        apt-get -qq install -y \
+        git \
+        git-annex \
+        make \
+        jq
+        # 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
+      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
+      run: |
+        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
+        git config --system --add safe.directory $(pwd)
+        tox
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true
+        flags: junifer
+      if: success() && matrix.python-version == 3.12

{junifer-0.0.6.dev194 → junifer-0.0.6.dev205}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev194
+Version: 0.0.6.dev205
 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.dev205/docs/changes/newsfragments/383.misc

@@ -0,0 +1 @@
+Adopt usage of custom CI image for testing junifer action by `Synchon Mandal`_

junifer-0.0.6.dev205/docs/changes/newsfragments/386.bugfix

@@ -0,0 +1 @@
+Use the :class:`junifer.pipeline.WorkDirManager` for temporary directories in the :class:`.DataladDataGrabber` by `Fede Raimondo`_

{junifer-0.0.6.dev194 → junifer-0.0.6.dev205}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev194'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev194')
+__version__ = version = '0.0.6.dev205'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev205')

{junifer-0.0.6.dev194 → junifer-0.0.6.dev205}/junifer/datagrabber/datalad_base.py

@@ -7,7 +7,6 @@
 
 import atexit
 import os
-import shutil
 import tempfile
 from pathlib import Path
 from typing import Dict, Optional, Tuple, Union
@@ -17,6 +16,7 @@ import datalad.api as dl
 from datalad.support.exceptions import IncompleteResultsError
 from datalad.support.gitrepo import GitRepo
 
+from ..pipeline import WorkDirManager
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseDataGrabber
 
@@ -78,7 +78,8 @@ class DataladDataGrabber(BaseDataGrabber):
         if datadir is None:
             logger.info("`datadir` is None, creating a temporary directory")
             # Create temporary directory
-            tmpdir = Path(tempfile.mkdtemp())
+            tmpdir = WorkDirManager().get_tempdir(prefix="datalad")
+            self._tmpdir = tmpdir
             datadir = tmpdir / "datadir"
             datadir.mkdir(parents=True, exist_ok=False)
             logger.info(f"`datadir` set to {datadir}")
@@ -104,7 +105,6 @@ class DataladDataGrabber(BaseDataGrabber):
                 "Datalad locks set to "
                 f"{datalad.cfg.get('datalad.locations.locks')}"
             )
-            self._tmpdir = tmpdir
             atexit.register(self._rmtmpdir)
         # TODO: uri can be converted to a positional argument
         if uri is None:
@@ -129,7 +129,7 @@ class DataladDataGrabber(BaseDataGrabber):
         """Remove temporary directory if it exists."""
         if self._tmpdir.exists():
             logger.debug("Removing temporary directory")
-            shutil.rmtree(self._tmpdir)
+            WorkDirManager().delete_tempdir(self._tmpdir)
 
     @property
     def datadir(self) -> Path:

{junifer-0.0.6.dev194 → junifer-0.0.6.dev205}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev194
+Version: 0.0.6.dev205
 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.dev194 → junifer-0.0.6.dev205}/junifer.egg-info/SOURCES.txt

@@ -82,7 +82,9 @@ docs/changes/newsfragments/373.misc
 docs/changes/newsfragments/374.misc
 docs/changes/newsfragments/380.misc
 docs/changes/newsfragments/382.misc
+docs/changes/newsfragments/383.misc
 docs/changes/newsfragments/384.misc
+docs/changes/newsfragments/386.bugfix
 docs/changes/newsfragments/387.change
 docs/changes/newsfragments/387.feature
 docs/extending/coordinates.rst

{junifer-0.0.6.dev194 → junifer-0.0.6.dev205}/tox.ini

@@ -12,9 +12,10 @@ python =
 
 [testenv]
 skip_install = false
-# Required for git-annex
 passenv =
     HOME
+    FSLDIR
+    FSLOUTPUTTYPE
 deps =
     pytest
 commands =

junifer-0.0.6.dev194/.github/workflows/ci.yml

@@ -1,119 +0,0 @@
-name: Run Tests
-
-on:
-  push:
-    paths:
-      - 'junifer/**'
-      - '.github/workflows/**'
-  pull_request:
-    paths:
-      - 'junifer/**'
-      - '.github/workflows/**'
-
-jobs:
-  run-tests:
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
-
-    steps:
-    - name: Set up system
-      run: |
-        bash -c "$(curl -fsSL http://neuro.debian.net/_files/neurodebian-travis.sh)"
-        sudo apt-get -qq update
-        sudo apt-get -qq install git-annex-standalone
-    - name: Configure git for datalad
-      run: |
-        git config --global user.email "runner@github.com"
-        git config --global user.name "GitHub Runner"
-    - 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: Install AFNI
-      run: |
-        echo "++ Distro information"
-        lsb_release -a
-
-        echo "++ Add universe repo"
-        sudo add-apt-repository -y universe
-
-        echo "++ Add PPAs for R programs"
-        sudo add-apt-repository -y "ppa:marutter/rrutter4.0"
-        sudo add-apt-repository -y "ppa:c2d4u.team/c2d4u4.0+"
-
-        echo "++ Update package manager info"
-        sudo apt-get -qq update
-
-        echo "++ Get main dependencies"
-        sudo apt-get -qq install -y tcsh libssl-dev gsl-bin libjpeg62 vim curl \
-        build-essential libcurl4-openssl-dev libxml2-dev libgfortran-11-dev \
-        libgomp1 r-base cmake rsync libxm4
-
-        sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19
-
-        curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
-        sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni
-        echo "/afni" >> $GITHUB_PATH
-      if: matrix.python-version == 3.12
-      # Bypass AFNI installation failure
-      continue-on-error: true
-    - name: Check AFNI
-      run: |
-        echo "Using AFNI : $(afni --version)"
-      if: matrix.python-version == 3.12
-      # Bypass AFNI installation failure
-      continue-on-error: true
-    - name: Install ANTs
-      run: |
-        sudo apt-get install -y -qq unzip
-        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.2/ants-2.5.2-ubuntu-22.04-X64-gcc.zip
-        unzip ants.zip -d /opt
-        mv /opt/ants-2.5.2/bin/* /opt/ants-2.5.2
-        rm ants.zip
-        echo "/opt/ants-2.5.2" >> $GITHUB_PATH
-      if: matrix.python-version == 3.12
-      # Bypass ANTs installation failure
-      continue-on-error: true
-    - name: Check ANTs
-      run: |
-        echo "Using ANTs : $(antsRegistration --version)"
-      if: matrix.python-version == 3.12
-      # Bypass ANTs installation failure
-      continue-on-error: true
-    - name: Install FSL
-      run: |
-        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/ --skip_registration
-        echo "FSLDIR=/opt/fsl" >> $GITHUB_ENV
-        echo "FSLOUTPUTTYPE=NIFTI_GZ" >> $GITHUB_ENV
-        echo "FSLMULTIFILEQUIT=TRUE" >> $GITHUB_ENV
-        echo "/opt/fsl/bin" >> $GITHUB_PATH
-      if: matrix.python-version == 3.12
-      # Bypass FSL installation failure
-      continue-on-error: true
-    - name: Check FSL
-      run: |
-        echo "Using FSL : $(flirt -version)"
-      if: matrix.python-version == 3.12
-      # Bypass FSL installation failure
-      continue-on-error: true
-    - name: Test with tox
-      run: |
-        tox
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: true
-        flags: junifer
-      if: success() && matrix.python-version == 3.12