Merge branch 'master' into enh/estimated-trt

Author: effigies

.github/workflows/build-test-publish.yml

@@ -122,7 +122,7 @@ jobs:
         git config --global user.name 'NiPreps Bot'
         git config --global user.email '[email protected]'
     - name: Install the latest version of uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v6
     - name: Set up Python ${{ matrix.python-version }}
       uses: conda-incubator/setup-miniconda@v3
       with:
@@ -147,7 +147,7 @@ jobs:
     - name: Install fsl and ANTs
       run: |
         # libitk 5.4.1+ segfaults with ants 2.5.4
-        conda install fsl-fugue fsl-topup ants 'libitk!=5.4.1,!=5.4.2'
+        conda install fsl-fugue fsl-topup ants 'libitk=5.4.0'
     - uses: actions/cache@v4
       with:
         path: ~/.cache/templateflow

.maint/update_requirements.py

@@ -1,3 +1,19 @@
+2.12.0 (March 21, 2025)
+=======================
+Feature release in the 2.12.x series.
+
+This release migrates from the deprecated ``niworkflows.reporting``
+module to the ``nireports`` package.
+
+* FIX: AttributeError for _ApplyCoeffsFieldInputSpec (#481)
+* ENH: Allow running SyN SDC without using prior (#480)
+* ENH: Allow estimated and fallback TotalReadoutTime (#477)
+* RF: Transition from niworkflows reporting interfaces (#473)
+* DOC: Fix broken link [skip ci] (#482)
+* MNT: Add `defaults` to `conda` channels in `build-test-publish` GHA (#474)
+* MNT: Update `niworkflows` version to 1.11.0 (#478)
+
+
 2.11.0 (December 18, 2024)
 ==========================
 Feature release in the 2.11.x series.

CHANGES.rst

@@ -76,7 +76,7 @@ Direct B0 mapping sequences
 Some MR schemes such as :abbr:`SEI (spiral-echo imaging)` can directly
 reconstruct an estimate of *the fieldmap in Hz*, :math:`V(i,j,k)`.
 These *fieldmaps* are described with more detail `here
-<https://cni.stanford.edu/wiki/GE_Processing#Fieldmaps>`__.
+<https://cni.su.domains/wiki/index.php?title=GE_Processing#Fieldmaps>`__.
 
 .. _sdc_phasediff :
 

docs/methods.rst

@@ -2,24 +2,28 @@ name: sdcflows
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated April 2023
+# Update this ~yearly; last updated Mar 2025
 dependencies:
-  - python=3.10
+  - python=3.12
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
-  - mkl-service=2.4
+  - mkl=2024.2.2
+  - mkl-service=2.4.2
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
-  - scipy=1.11
-  - matplotlib=3.8
-  - pandas=2.1
-  - h5py=3.8
+  - scipy=1.15
+  - matplotlib=3.9
+  - pandas=2.2
+  - h5py=3.13
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.22
+  - scikit-image=0.25
   # Utilities
-  - graphviz=6.0
+  - graphviz=11.0
   # Workflow dependencies: ANTs
-  - ants=2.4.4
-  # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
-  - fsl-fugue=2201.2
-  - fsl-topup=2203.1
+  - ants=2.5
+  # 5.4.1 and 5.4.2 cause segfaults with ants
+  # Try to remove this ASAP
+  # https://github.com/conda-forge/ants-feedstock/issues/19
+  - libitk=5.4.0
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
+  - fsl-fugue=2201.5
+  - fsl-topup=2203.5

env.yml

@@ -27,10 +27,10 @@ dependencies = [
     "nibabel >= 3.0",
     "nipype >= 1.8.5",
     "migas >= 0.4.0",
-    "nireports >= 24.1.0",
+    "nireports >= 25.0.1",
     "niworkflows >= 1.11.0",
     "nitransforms >= 24.1.0",
-    "numpy >= 1.22",
+    "numpy >= 1.23",
     "pybids >= 0.16.4",
     "scikit-image >= 0.18",
     "scipy >= 1.8.1",