chore(deps): Update pinned environment (#3440)

Author: effigies

env.yml

@@ -2,31 +2,35 @@ name: fmriprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated Jan 2024
+# Update this ~yearly; last updated Mar 2025
 dependencies:
-  - python=3.11
+  - python=3.12
   # Needed for svgo and bids-validator; consider moving to deno
   - nodejs=20
   # Intel Math Kernel Library for numpy
-  - mkl=2023.2.0
-  - mkl-service=2.4.0
+  - mkl=2024.2.2
+  - mkl-service=2.4.2
   # git-annex for templateflow users with DataLad superdatasets
   - git-annex=*=alldep*
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
-  - scipy=1.13
+  - scipy=1.15
   - matplotlib=3.9
   - pandas=2.2
-  - h5py=3.11
+  - h5py=3.13
   # Dependencies compiled against numpy, best to stick with conda
-  - nitime=0.10
-  - scikit-image=0.24
-  - scikit-learn=1.4
+  - nitime=0.11
+  - scikit-image=0.25
+  - scikit-learn=1.6
   # Utilities
-  - graphviz=9.0
-  - pandoc=3.1
+  - graphviz=11.0
+  - pandoc=3.6
   # Workflow dependencies: ANTs
   - 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: Convert3d
   - convert3d=1.4
   # Workflow dependencies: Connectome Workbench
@@ -35,7 +39,7 @@ dependencies:
   - fsl-bet2=2111.8
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3
-  - fsl-fugue=2201.4
+  - fsl-fugue=2201.5
   - fsl-mcflirt=2111.0
   - fsl-miscmaths=2203.2
   - fsl-topup=2203.5