Revert "Merge remote-tracking branch 'upstream/master' into fix-eddy-parallel-and-gpu"

This reverts commit 176bc81, reversing
changes made to 32bd190.

Author: mauriliogenovese

.github/workflows/prerelease.yml

@@ -30,14 +30,14 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v5
       - run: uv build
       - run: uvx twine check dist/*
-      - uses: actions/upload-artifact@v7
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/
@@ -49,32 +49,26 @@ jobs:
       matrix:
         package: ["wheel", "sdist"]
     steps:
-      - uses: actions/download-artifact@v8
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
-      - name: Verify artifacts are present
-        run: |
-          ls -l . dist/
-          wheel_file=$(find dist -name 'nipype-*.whl' | head -n 1)
-          tar_file=$(find dist -name 'nipype-*.tar.gz' | head -n 1)
-
-          echo "WHEEL=$wheel_file" >> $GITHUB_ENV
-          echo "SDIST=$tar_file" >> $GITHUB_ENV
-      - name: Install Python
-        uses: actions/setup-python@v6
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.13"
+          python-version: 3
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
+      - name: Update pip
+        run: pip install --upgrade pip
       - name: Install wheel
-        run: pip install $WHEEL[tests]
+        run: pip install dist/nipype-*.whl
         if: matrix.package == 'wheel'
       - name: Install sdist
-        run: pip install $SDIST[tests]
+        run: pip install dist/nipype-*.tar.gz
         if: matrix.package == 'sdist'
-      - name: Display nipype version
-        run: python -c 'import nipype; print(nipype.__version__)'
+      - run: python -c 'import nipype; print(nipype.__version__)'
+      - name: Install test extras
+        run: pip install nipype[tests]
       - name: Run tests
         run: pytest --doctest-modules -v --pyargs nipype
 
@@ -84,59 +78,62 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
-        dependencies: [none, full]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        dependencies: [none, full, pre]
         include:
           - os: ubuntu-latest
-            python-version: "3.10"
+            python-version: "3.9"
             dependencies: min
         exclude:
           # Skip some intermediate versions for full tests
-          - python-version: "3.11"
+          - python-version: "3.10"
             dependencies: full
-          - python-version: "3.12"
+          - python-version: "3.11"
             dependencies: full
+          # Do not test pre-releases for versions out of SPEC0
+          - python-version: "3.9"
+            dependencies: pre
+          - python-version: "3.10"
+            dependencies: pre
 
     env:
       DEPENDS: ${{ matrix.dependencies }}
 
     steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
+      - uses: actions/checkout@v4
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v5
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          uv tool install --with=tox-uv --with=tox-gh-actions tox
+          uv tool install tox --with=tox-uv --with=tox-gh-actions
       - name: Show tox config
         run: tox c
-      - name: Setup test suite
-        run: tox run -vv --notest
       - name: Run tox
-        run: tox -v --skip-pkg-install --exit-and-dump-after 1200
+        run: tox -v --exit-and-dump-after 1200
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v7
+        uses: actions/upload-artifact@v4
         with:
-          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.dependencies }}
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.deb-depends }}
           path: test-results.xml
-        if: always()
+        if: ${{ always() && matrix.check == 'test' }}
 
   publish:
     runs-on: ubuntu-latest
     environment: "Package deployment"
     needs: [test, test-package]
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v8
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -153,12 +150,12 @@ jobs:
         check: ['specs', 'style']
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v7
-      - name: Install tox
-        run: uv tool install --with=tox-uv tox
+        uses: astral-sh/setup-uv@v5
+      - name: Show tox config
+        run: uvx tox c
       - name: Show tox config (this call)
-        run: tox c -e ${{ matrix.check }}
+        run: uvx tox c -e ${{ matrix.check }}
       - name: Run check
-        run: tox -e ${{ matrix.check }}
+        run: uvx tox -e ${{ matrix.check }}

.github/workflows/tests.yml

@@ -21,7 +21,7 @@ nipype/testing/data/von-ray_errmap.nii.gz
 nipype/testing/data/von_errmap.nii.gz
 nipype/testing/data/.proc*
 crash*.pklz
-.coverage*
+.coverage
 htmlcov/
 __pycache__/
 *~
@@ -31,7 +31,3 @@ __pycache__/
 .pytest_cache
 .vscode/
 venv/
-_version.py
-uv.lock
-.venv/
-.tox/

.github/workflows/workflow_failure.md

@@ -1,53 +1,24 @@
-import importlib
 import os
 import shutil
-import tempfile
+from tempfile import mkdtemp
 import pytest
 import numpy as np
 import py.path as pp
 
 NIPYPE_DATADIR = os.path.realpath(
     os.path.join(os.path.dirname(__file__), "testing/data")
 )
-NIPYPE_TMPDIR = tempfile.mkdtemp()
-TMP_DATADIR = os.path.join(NIPYPE_TMPDIR, "data")
-
-
-def pytest_configure(config):
-    global TMP_DATADIR
-    # Pytest uses gettempdir() to construct its tmp_paths, but the logic to get
-    # `pytest-of-<user>/pytest-<n>` directories is contingent on not directly
-    # configuring the `config.option.base_temp` value.
-    # Instead of replicating that logic, inject a new directory into gettempdir()
-    #
-    # Use the discovered temp dir as a base, to respect user/system settings.
-    if ' ' not in (base_temp := tempfile.gettempdir()):
-        new_base = os.path.join(base_temp, "nipype tmp")
-        os.makedirs(new_base, exist_ok=True)
-        os.environ['TMPDIR'] = new_base
-        importlib.reload(tempfile)
-        assert tempfile.gettempdir() == new_base
-        TMP_DATADIR = os.path.join(new_base, "data")
-
-    # xdist will result in this being run multiple times
-    if not os.path.exists(TMP_DATADIR):
-        shutil.copytree(NIPYPE_DATADIR, TMP_DATADIR)
-
-
-def pytest_unconfigure(config):
-    shutil.rmtree(NIPYPE_TMPDIR)
-
-
-if "SUBJECTS_DIR" not in os.environ:
-    os.environ["SUBJECTS_DIR"] = NIPYPE_TMPDIR
+temp_folder = mkdtemp()
+data_dir = os.path.join(temp_folder, "data")
+shutil.copytree(NIPYPE_DATADIR, data_dir)
 
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
     doctest_namespace["np"] = np
     doctest_namespace["os"] = os
     doctest_namespace["pytest"] = pytest
-    doctest_namespace["datadir"] = TMP_DATADIR
+    doctest_namespace["datadir"] = data_dir
 
 
 @pytest.fixture(scope='session', autouse=True)
@@ -62,7 +33,7 @@ def _docdir(request):
     doctest_plugin = request.config.pluginmanager.getplugin("doctest")
     if isinstance(request.node, doctest_plugin.DoctestItem):
         # Get the fixture dynamically by its name.
-        tmpdir = pp.local(TMP_DATADIR)
+        tmpdir = pp.local(data_dir)
 
         # Chdir only for the duration of the test.
         with tmpdir.as_cwd():
@@ -71,3 +42,8 @@ def _docdir(request):
     else:
         # For normal tests, we have to yield, since this is a yield-fixture.
         yield
+
+
+def pytest_unconfigure(config):
+    # Delete temp folder after session is finished
+    shutil.rmtree(temp_folder)

.gitignore

@@ -2860,9 +2860,9 @@ class TNorm(AFNICommand):
     >>> tnorm = afni.TNorm()
     >>> tnorm.inputs.in_file = 'functional.nii'
     >>> tnorm.inputs.norm2 = True
-    >>> tnorm.inputs.out_file = 'errts+tlrc'
+    >>> tnorm.inputs.out_file = 'rm.errts.unit errts+tlrc'
     >>> tnorm.cmdline
-    '3dTnorm -norm2 -prefix errts+tlrc functional.nii'
+    '3dTnorm -norm2 -prefix rm.errts.unit errts+tlrc functional.nii'
     >>> res = tshift.run()  # doctest: +SKIP
 
     """

nipype/conftest.py

@@ -928,7 +928,7 @@ class LabelGeometry(ANTSCommand):
     >>> label_extract.inputs.dimension = 3
     >>> label_extract.inputs.label_image = 'atlas.nii.gz'
     >>> label_extract.cmdline
-    "LabelGeometryMeasures 3 atlas.nii.gz '[]' atlas.csv"
+    'LabelGeometryMeasures 3 atlas.nii.gz [] atlas.csv'
 
     >>> label_extract.inputs.intensity_image = 'ants_Warp.nii.gz'
     >>> label_extract.cmdline

nipype/interfaces/afni/preprocess.py

@@ -28,7 +28,7 @@ class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec):
     )
     mask_image = traits.Either(
         "none",
-        File(exists=True),
+        traits.File(exists=True),
         argstr="%s",
         desc="mask image",
         position=3,