chore: Update conda environment definition

Author: effigies

Dockerfile

@@ -56,15 +56,6 @@ COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exc
 RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
      | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt
 
-# Connectome Workbench 1.5.0
-FROM downloader as workbench
-RUN mkdir /opt/workbench && \
-    curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
-    unzip workbench-linux64-v1.5.0.zip -d /opt && \
-    rm workbench-linux64-v1.5.0.zip && \
-    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
-    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
-
 # Micromamba
 FROM downloader as micromamba
 
@@ -122,7 +113,6 @@ RUN apt-get update && \
 
 # Install files from stages
 COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
-COPY --from=workbench /opt/workbench /opt/workbench
 
 # Simulate SetUpFreeSurfer.sh
 ENV OS="Linux" \
@@ -141,10 +131,6 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
 
-# Workbench config
-ENV PATH="/opt/workbench/bin_linux64:$PATH" \
-    LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
-
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users smriprep
 WORKDIR /home/smriprep

env.yml

@@ -2,30 +2,36 @@ name: smriprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated March 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
-  - 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=1.13
-  - matplotlib=3.8
+  - scipy=1.15
+  - matplotlib=3.9
   - pandas=2.2
-  - h5py=3.11
+  - h5py=3.13
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.23
-  - scikit-learn=1.4
+  - 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
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
-  - fsl-bet2=2111.4
+  # 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: Connectome Workbench
+  - connectome-workbench-cli=2.0
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
+  - fsl-bet2=2111.8
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3
   - fsl-miscmaths=2203.2