chore(env): Bring env.yml into line with fmriprep

Author: effigies

env.yml

@@ -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