Merge branch 'master' into enh/fs_long

Author: effigies

.github/dependabot.yml

@@ -2,9 +2,12 @@
 
 version: 2
 updates:
-
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"

.github/workflows/pythonpackage.yml

@@ -35,6 +35,8 @@ jobs:
         run: |
           if [[ -z "$COMMIT_MSG" ]]; then
             COMMIT_MSG=$(git show -s --format=%s)
+          else
+            COMMIT_MSG=$(echo $COMMIT_MSG | head -n 1)
           fi
           echo $COMMIT_MSG
           echo "commit_message=$COMMIT_MSG" >> $GITHUB_OUTPUT
@@ -55,7 +57,7 @@ jobs:
       run: pipx run build
     - name: Check distributions
       run: pipx run twine check dist/*
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: dist
         path: dist/
@@ -77,12 +79,13 @@ jobs:
 
     env:
       INSTALL_TYPE: ${{ matrix.install }}
+      FSLOUTPUTTYPE: NIFTI_GZ
 
     steps:
     - uses: actions/checkout@v4
       if: matrix.install == 'repo' || matrix.install == 'editable'
     - name: Fetch packages
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: dist
         path: dist/

LICENSE

@@ -1,3 +1,4 @@
+
                                  Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "packaging",
     "pybids >= 0.11.1",
     "pyyaml",
-    "templateflow >= 0.6",
+    "templateflow >= 24.1",
 ]
 dynamic = ["version"]
 
@@ -115,8 +115,11 @@ per-file-ignores = [
 ]
 
 [tool.pytest.ini_options]
+minversion = "7"
+log_cli_level = "INFO"
+xfail_strict = true
 norecursedirs = [".git"]
-addopts = "-svx --doctest-modules"
+addopts = ["-svx", "--doctest-modules", "-ra", "--strict-config", "--strict-markers"]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
@@ -163,7 +166,7 @@ extend-select = [
   "PT",
   "Q",
 ]
-extend-ignore = [
+ignore = [
   "S311",  # We are not using random for cryptographic purposes
   "ISC001",
   "S603",

requirements.txt

@@ -188,7 +188,7 @@ sqlalchemy==2.0.28
     # via pybids
 svgutils==0.3.4
     # via niworkflows
-templateflow==24.0.0
+templateflow==24.2.0
     # via niworkflows
 threadpoolctl==3.3.0
     # via scikit-learn

smriprep/cli/run.py

@@ -420,7 +420,16 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None):
             from niworkflows.utils.misc import _copy_any
             from templateflow import api
 
-            dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
+            dseg_tsv = str(
+                api.get(
+                    'fsaverage',
+                    hemi=None,
+                    atlas=None,
+                    segmentation='aparc',
+                    suffix='dseg',
+                    extension=['.tsv'],
+                )
+            )
             _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aseg_dseg.tsv'))
             _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aparcaseg_dseg.tsv'))
         logger.log(25, 'sMRIPrep finished without errors')