Merge remote-tracking branch 'upstream/master' into origin/fix/dcm2niix_crop

Author: effigies

.codespellrc

@@ -9,4 +9,5 @@ skip = .git,*.pdf,*.svg,external
 # Reson - short journal name
 # ALS, FWE - neuroimaging specific abbrevs
 # Comision - foreign word used
-ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile
+# expad - AFNI flag
+ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile,expad

.git-blame-ignore-revs

@@ -1,3 +1,13 @@
+# Tue Feb 27 14:28:18 2024 -0500 - effigies@gmail.com - STY: black 2024.2 [ignore-rev]
+f1cbc1c941f8d02659f8ef245aac0862efb80ccf
+# Mon Sep 11 13:36:40 2023 +0200 - 37933899+servoz@users.noreply.github.com - run black for nipype/interfaces/spm/preprocess.py
+b9cac5e993143febb01ade42e56b41009427a4b6
+# Wed Jul 5 16:31:45 2023 -0400 - effigies@gmail.com - STY: Run black and fix typo
+34a4ac6eeff8d4924b40875c45df5d84a97da90b
+# Wed Jul 5 11:30:42 2023 -0400 - effigies@gmail.com - STY: black
+3b89ca85faf2428ecf7844de9c0db4aa7c329c93
+# Wed Jul 5 09:49:31 2023 -0400 - effigies@gmail.com - STY: black
+4a6a7d9d25d5d1e1f0eb55828dede58f8b9c9f80
 # Wed Apr 5 14:01:05 2023 -0400 - effigies@gmail.com - STY: black [ignore-rev]
 a9ce9b78a402ebacf7726ad6454bb75b1447f52f
 # Wed Sep 14 14:12:07 2022 -0400 - mathiasg@stanford.edu - STY: Black

.github/dependabot.yml

@@ -5,3 +5,7 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"

.github/workflows/contrib.yml

@@ -50,7 +50,7 @@ jobs:
           submodules: recursive
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -71,12 +71,13 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
           path: test-results.xml

.github/workflows/tests.yml

@@ -40,14 +40,14 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - run: pip install --upgrade build twine
       - name: Build sdist and wheel
         run: python -m build
       - run: twine check dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/
@@ -59,11 +59,11 @@ jobs:
       matrix:
         package: ['wheel', 'sdist']
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Display Python version
@@ -124,7 +124,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -145,14 +145,15 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.deb-depends }}
           path: test-results.xml
         if: ${{ always() && matrix.check == 'test' }}
 
@@ -162,7 +163,7 @@ jobs:
     needs: [stable, test-package]
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/

.pre-commit-config.yaml

@@ -2,17 +2,17 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.2.0
     hooks:
       - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
     - id: codespell

.zenodo.json

@@ -911,6 +911,11 @@
       "name": "Wu, Jianxiao",
       "orcid": "0000-0002-4866-272X",
     },
+    {
+      "affiliation": "Lund University",
+      "name": "Anijärv, Toomas Erik",
+      "orcid": "0000-0002-3650-4230",
+    },
   ],
   "keywords": [
     "neuroimaging",

nipype/algorithms/modelgen.py

@@ -417,9 +417,9 @@ def _generate_standard_design(
                                 sessinfo[i]["cond"][cid]["pmod"][j]["poly"] = info.pmod[
                                     cid
                                 ].poly[j]
-                                sessinfo[i]["cond"][cid]["pmod"][j][
-                                    "param"
-                                ] = info.pmod[cid].param[j]
+                                sessinfo[i]["cond"][cid]["pmod"][j]["param"] = (
+                                    info.pmod[cid].param[j]
+                                )
 
             sessinfo[i]["regress"] = []
             if hasattr(info, "regressors") and info.regressors is not None:

nipype/algorithms/rapidart.py

@@ -584,9 +584,9 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
             if displacement is not None:
                 dmap = np.zeros((x, y, z, timepoints), dtype=np.float64)
                 for i in range(timepoints):
-                    dmap[
-                        voxel_coords[0], voxel_coords[1], voxel_coords[2], i
-                    ] = displacement[i, :]
+                    dmap[voxel_coords[0], voxel_coords[1], voxel_coords[2], i] = (
+                        displacement[i, :]
+                    )
                 dimg = Nifti1Image(dmap, affine)
                 dimg.to_filename(displacementfile)
         else:

nipype/caching/memory.py

@@ -2,6 +2,7 @@
 Using nipype with persistence and lazy recomputation but without explicit
 name-steps pipeline: getting back scope in command-line based programming.
 """
+
 import os
 import hashlib
 import pickle

nipype/interfaces/afni/preprocess.py

@@ -180,7 +180,7 @@ class AlignEpiAnatPy(AFNIPythonCommand):
     >>> al_ea.cmdline # doctest: +ELLIPSIS
     'python2 ...align_epi_anat.py -anat structural.nii -epi_base 0 -epi_strip 3dAutomask -epi \
 functional.nii -save_skullstrip -suffix _al -tshift off -volreg off'
-    >>> res = allineate.run()  # doctest: +SKIP
+    >>> res = al_ea.run()  # doctest: +SKIP
 
     See Also
     --------

nipype/interfaces/ants/legacy.py

@@ -4,7 +4,6 @@
 are preserved for backwards compatibility.
 """
 
-
 import os
 from glob import glob
 

nipype/interfaces/ants/registration.py

@@ -1,6 +1,7 @@
 """The ants module provides basic functions for interfacing with ants
    functions.
 """
+
 import os
 
 from ...utils.filemanip import ensure_list

nipype/interfaces/ants/resampling.py

@@ -1,5 +1,6 @@
 """ANTS Apply Transforms interface
 """
+
 import os
 
 from .base import ANTSCommand, ANTSCommandInputSpec
@@ -349,6 +350,7 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         "MultiLabel",
         "Gaussian",
         "BSpline",
+        "GenericLabel",
         argstr="%s",
         usedefault=True,
     )
@@ -357,6 +359,7 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         traits.Tuple(
             traits.Float(), traits.Float()  # Gaussian/MultiLabel (sigma, alpha)
         ),
+        traits.Tuple(traits.Str()),  # GenericLabel
     )
     transforms = InputMultiObject(
         traits.Either(File(exists=True), "identity"),
@@ -497,6 +500,7 @@ def _format_arg(self, opt, spec, val):
                 "BSpline",
                 "MultiLabel",
                 "Gaussian",
+                "GenericLabel",
             ] and isdefined(self.inputs.interpolation_parameters):
                 return "--interpolation {}[ {} ]".format(
                     self.inputs.interpolation,

nipype/interfaces/ants/segmentation.py

@@ -1,4 +1,5 @@
 """Wrappers for segmentation utilities within ANTs."""
+
 import os
 from glob import glob
 from ...external.due import BibTeX

nipype/interfaces/ants/utils.py

@@ -1,4 +1,5 @@
 """ANTs' utilities."""
+
 import os
 from warnings import warn
 from ..base import traits, isdefined, TraitedSpec, File, Str, InputMultiObject

nipype/interfaces/base/core.py

@@ -380,9 +380,11 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         """
         rtc = RuntimeContext(
             resource_monitor=config.resource_monitor and self.resource_monitor,
-            ignore_exception=ignore_exception
-            if ignore_exception is not None
-            else self.ignore_exception,
+            ignore_exception=(
+                ignore_exception
+                if ignore_exception is not None
+                else self.ignore_exception
+            ),
         )
 
         with indirectory(cwd or os.getcwd()):

nipype/interfaces/c3.py

@@ -1,4 +1,5 @@
 """Convert3D is a command-line tool for converting 3D images between common file formats."""
+
 import os
 from glob import glob
 

nipype/interfaces/cmtk/__init__.py

@@ -1,4 +1,5 @@
 """CMP implements a full processing pipeline for creating connectomes with dMRI data."""
+
 from .cmtk import ROIGen, CreateMatrix, CreateNodes
 from .nx import NetworkXMetrics, AverageNetworks
 from .parcellation import Parcellate

nipype/interfaces/dcm2nii.py

@@ -1,4 +1,5 @@
 """dcm2nii converts images from the proprietary scanner DICOM format to NIfTI."""
+
 import os
 import re
 from copy import deepcopy

nipype/interfaces/diffusion_toolkit/__init__.py

@@ -1,4 +1,5 @@
 """Diffusion Toolkit performs data reconstruction and fiber tracking on diffusion MR images."""
+
 from .base import Info
 from .postproc import SplineFilter, TrackMerge
 from .dti import DTIRecon, DTITracker

nipype/interfaces/dipy/__init__.py

@@ -1,4 +1,5 @@
 """DIPY is a computational neuroimaging tool for diffusion MRI."""
+
 from .tracks import StreamlineTractography, TrackDensityMap
 from .tensors import TensorMode, DTI
 from .preprocess import Resample, Denoise

nipype/interfaces/dipy/reconstruction.py

@@ -2,6 +2,7 @@
 Interfaces to the reconstruction algorithms in dipy
 
 """
+
 import os.path as op
 
 import numpy as np

nipype/interfaces/dtitk/__init__.py

@@ -5,6 +5,7 @@
 <http://dti-tk.sourceforge.net/pmwiki/pmwiki.php>`_ command line tools.
 
 """
+
 from .registration import (
     Rigid,
     Affine,

nipype/interfaces/fsl/epi.py

@@ -1059,9 +1059,9 @@ def _list_outputs(self):
         if os.path.exists(out_shell_alignment_parameters):
             outputs["out_shell_alignment_parameters"] = out_shell_alignment_parameters
         if os.path.exists(out_shell_pe_translation_parameters):
-            outputs[
-                "out_shell_pe_translation_parameters"
-            ] = out_shell_pe_translation_parameters
+            outputs["out_shell_pe_translation_parameters"] = (
+                out_shell_pe_translation_parameters
+            )
         if os.path.exists(out_outlier_map):
             outputs["out_outlier_map"] = out_outlier_map
         if os.path.exists(out_outlier_n_stdev_map):

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -70,7 +70,7 @@ def func():
         "center": ("-c 54 75 80", [54, 75, 80]),
         "threshold": ("-t", True),
         "mesh": ("-e", True),
-        "surfaces": ("-A", True)
+        "surfaces": ("-A", True),
         # 'verbose': ('-v', True),
         # 'flags': ('--i-made-this-up', '--i-made-this-up'),
     }

nipype/interfaces/mipav/__init__.py

@@ -1,4 +1,5 @@
 """MIPAV enables quantitative analysis and visualization of multimodal medical images."""
+
 from .developer import (
     JistLaminarVolumetricLayering,
     JistBrainMgdmSegmentation,

nipype/interfaces/mne/__init__.py

@@ -1,2 +1,3 @@
 """MNE is a software for exploring, visualizing, and analyzing human neurophysiological data."""
+
 from .base import WatershedBEM