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