Merge branch 'main' into fmaps

.github/workflows/docker.yml

@@ -21,7 +21,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3.6.1
+        uses: docker/setup-buildx-action@v3.7.1
 
       - name: Log in to Docker Hub
         uses: docker/[email protected]
@@ -31,7 +31,7 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v5.5.1
+        uses: docker/metadata-action@v5.6.1
         with:
           images: nipreps/fmripost-aroma
           # generate Docker tags based on the following events/attributes
@@ -40,7 +40,7 @@ jobs:
             type=semver,pattern={{version}}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v6.9.0
+        uses: docker/build-push-action@v6.10.0
         with:
           context: .
           push: true

.github/workflows/test.yml

@@ -64,7 +64,7 @@ jobs:
         run: tox c
       - name: Run tox
         run: tox -v --exit-and-dump-after 1200
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: ${{ always() }}
         with:
           files: cov.xml

.zenodo.json

@@ -18,6 +18,11 @@
     },
     {
       "name": "Caballero Gaudes, Cesar"
+    },
+    {
+      "affiliation": "Department of Psychology, University of Southern California",
+      "name": "Zimmerman, Jacob C.",
+      "orcid": "0000-0002-6010-8086"
     }
   ],
   "creators": [

src/fmripost_aroma/cli/run.py

@@ -223,7 +223,7 @@ def main():
 
         if sentry_sdk is not None and failed_reports:
             sentry_sdk.capture_message(
-                'Report generation failed for %d subjects' % failed_reports,
+                f'Report generation failed for {failed_reports} subjects',
                 level='error',
             )
         sys.exit(int((errno + len(failed_reports)) > 0))

src/fmripost_aroma/config.py

@@ -149,7 +149,7 @@
     # Just get so analytics track one hit
     from contextlib import suppress
 
-    from requests import ConnectionError, ReadTimeout
+    from requests import ConnectionError, ReadTimeout  # noqa: A004
     from requests import get as _get_url
 
     with suppress((ConnectionError, ReadTimeout)):

src/fmripost_aroma/data/io_spec.json

@@ -138,7 +138,6 @@
             },
             "anat2mni152nlin6asym": {
                 "datatype": "anat",
-                "run": null,
                 "from": ["anat", "T1w", "T2w"],
                 "to": "MNI152NLin6Asym",
                 "space": null,

src/fmripost_aroma/interfaces/confounds.py

@@ -91,7 +91,7 @@ def _get_ica_confounds(mixing, aroma_features, skip_vols, newpath=None):
 
     # Return dummy list of ones if no noise components were found
     if motion_ics.size == 0:
-        config.loggers.interfaces.warning('No noise components were classified')
+        config.loggers.interface.warning('No noise components were classified')
         return None, mixing_out
 
     # return dummy lists of zeros if no signal components were found