Merge tag '25.1.4'

25.1.4 (July 31, 2025)

Patch release in the 25.1.x series.

This includes additional fixes for non-unicode ``B0FieldIdentifier`` keys.

  * FIX: Allow warning kwargs (nipreps#3483)
  * FIX: Remove non-alphanumeric characters from fmapid in fmapreg transform (nipreps#3490)

Author: mgxd

CHANGES.rst

@@ -1,3 +1,13 @@
+25.1.4 (July 31, 2025)
+======================
+Patch release in the 25.1.x series.
+
+This includes additional fixes for non-unicode ``B0FieldIdentifier`` keys.
+
+  * FIX: Allow warning kwargs (#3483)
+  * FIX: Remove non-alphanumeric characters from fmapid in fmapreg transform (#3490)
+
+
 25.1.3 (June 19, 2025)
 ======================
 Patch release in the 25.1.x series.

constraints.txt

@@ -0,0 +1,7 @@
+# 25.1.x
+nireports ~= 25.0.1
+nitransforms ~= 24.1.2
+niworkflows ~= 1.13.5
+sdcflows ~= 2.13.2
+smriprep ~= 0.18.0
+templateflow ~= 24.2.2

fmriprep/utils/bids.py

@@ -26,6 +26,7 @@
 
 import json
 import os
+import re
 import sys
 from collections import defaultdict
 from functools import cache
@@ -85,8 +86,8 @@ def collect_derivatives(
         #   whereas relevant src file will be "bold".
         query = {**entities, **q}
         if xfm == 'boldref2fmap' and fieldmap_id:
-            # fieldmaps have ids like auto_00000
-            query['to'] = fieldmap_id.replace('_', '')
+            # fieldmaps have non-alphanumeric characters removed from their IDs in filenames
+            query['to'] = re.sub(r'[^a-zA-Z0-9]', '', fieldmap_id)
         item = layout.get(return_type='filename', **query)
         if not item:
             continue

fmriprep/workflows/bold/fit.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 import os
+import re
 import typing as ty
 
 import bids
@@ -514,7 +515,7 @@ def init_bold_fit_wf(
                 bids_root=layout.root,
                 output_dir=config.execution.fmriprep_dir,
                 source='boldref',
-                dest=fieldmap_id.replace('_', ''),
+                dest=re.sub(r'[^a-zA-Z0-9]', '', fieldmap_id),
                 name='ds_fmapreg_wf',
             )
             ds_fmapreg_wf.inputs.inputnode.source_files = [bold_file]

requirements.txt

@@ -1,6 +1,6 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -p 3.12
-acres==0.5.0
+#    uv pip compile --extra=container --strip-extras pyproject.toml -c constraints.txt -o requirements.txt -p 3.12
+acres==0.3.0
     # via
     #   fmriprep (pyproject.toml)
     #   bidsschematools
@@ -234,17 +234,20 @@ nipype==1.10.0
     #   smriprep
 nireports==25.2.0
     # via
+    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   sdcflows
 nitime==0.11
     # via fmriprep (pyproject.toml)
 nitransforms==24.1.2
     # via
+    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
 niworkflows==1.13.4
     # via
+    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   sdcflows
     #   smriprep
@@ -437,14 +440,16 @@ scipy==1.15.2
     #   scikit-learn
     #   sdcflows
     #   tedana
-sdcflows==2.13.1
-    # via fmriprep (pyproject.toml)
+sdcflows==2.13.2
+    # via
+    #   -c constraints.txt
+    #   fmriprep (pyproject.toml)
 seaborn==0.13.2
     # via
     #   nireports
     #   niworkflows
     #   tedana
-sentry-sdk==2.30.0
+sentry-sdk==2.28.0
     # via fmriprep (pyproject.toml)
 shellingham==1.5.4
     # via typer
@@ -456,7 +461,9 @@ six==1.17.0
     #   pybtex
     #   python-dateutil
 smriprep==0.18.0
-    # via fmriprep (pyproject.toml)
+    # via
+    #   -c constraints.txt
+    #   fmriprep (pyproject.toml)
 sniffio==1.3.1
     # via
     #   anyio
@@ -469,6 +476,7 @@ tedana==25.0.1
     # via fmriprep (pyproject.toml)
 templateflow==24.2.2
     # via
+    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   nireports
     #   niworkflows