Merge pull request #468 from effigies/chore/environment

chore(deps): Update pinned environment, use conda-forge connectome-workbench

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

requirements.txt

@@ -1,56 +1,73 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --strip-extras pyproject.toml -o requirements.txt -p 3.11 -c -
-astor==0.8.1
-    # via formulaic
-attrs==23.2.0
-    # via niworkflows
-bids-validator==1.14.6
+#    uv pip compile --strip-extras pyproject.toml -o requirements.txt -p 3.12 -c-
+acres==0.3.0
+    # via
+    #   smriprep (pyproject.toml)
+    #   nipype
+    #   niworkflows
+attrs==25.1.0
+    # via
+    #   jsonschema
+    #   niworkflows
+    #   referencing
+bids-validator==1.14.7.post0
     # via pybids
-certifi==2024.7.4
+bidsschematools==1.0.3
+    # via bids-validator
+certifi==2025.1.31
     # via requests
-charset-normalizer==3.3.2
+charset-normalizer==3.4.1
     # via requests
 ci-info==0.3.0
     # via etelemetry
-click==8.1.7
+click==8.1.8
     # via
+    #   bidsschematools
     #   nipype
     #   pybids
-contourpy==1.2.1
+contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
 docopt==0.6.2
     # via num2words
 etelemetry==0.3.1
     # via nipype
-filelock==3.15.4
+filelock==3.17.0
     # via nipype
-fonttools==4.53.1
+fonttools==4.56.0
     # via matplotlib
-formulaic==0.5.2
+formulaic==1.1.1
+    # via pybids
+frozendict==2.4.6
     # via pybids
-greenlet==3.0.3
+fsspec==2025.2.0
+    # via universal-pathlib
+greenlet==3.1.1
     # via sqlalchemy
-h5py==3.11.0
+h5py==3.13.0
     # via nitransforms
-idna==3.7
+idna==3.10
     # via requests
-imageio==2.34.2
+imageio==2.37.0
     # via scikit-image
-indexed-gzip==1.8.7
+indexed-gzip==1.9.4
     # via smriprep (pyproject.toml)
 interface-meta==1.3.0
     # via formulaic
 isodate==0.6.1
     # via rdflib
-jinja2==3.1.4
+jinja2==3.1.6
     # via niworkflows
 joblib==1.4.2
     # via
     #   nilearn
     #   scikit-learn
-kiwisolver==1.4.5
+jsonschema==4.23.0
+    # via bidsschematools
+jsonschema-specifications==2024.10.1
+    # via jsonschema
+kiwisolver==1.4.8
     # via matplotlib
 lazy-loader==0.4
     # via scikit-image
@@ -61,42 +78,42 @@ looseversion==1.3.0
     #   smriprep (pyproject.toml)
     #   nipype
     #   niworkflows
-lxml==5.2.2
+lxml==5.3.1
     # via
     #   nilearn
     #   prov
     #   svgutils
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via jinja2
-matplotlib==3.9.1
+matplotlib==3.9.4
     # via
     #   smriprep (pyproject.toml)
     #   niworkflows
     #   seaborn
-networkx==3.3
+networkx==3.4.2
     # via
     #   nipype
     #   prov
     #   scikit-image
-nibabel==5.2.1
+nibabel==5.3.2
     # via
     #   smriprep (pyproject.toml)
     #   nilearn
     #   nipype
     #   nitransforms
     #   niworkflows
     #   pybids
-nilearn==0.10.4
+nilearn==0.11.1
     # via niworkflows
-nipype==1.8.6
+nipype==1.9.2
     # via
     #   smriprep (pyproject.toml)
     #   niworkflows
-nitransforms==23.0.1
+nitransforms==24.1.1
     # via niworkflows
-niworkflows==1.10.2
+niworkflows==1.12.2
     # via smriprep (pyproject.toml)
-num2words==0.5.13
+num2words==0.5.14
     # via pybids
 numpy==1.26.4
     # via
@@ -119,7 +136,7 @@ numpy==1.26.4
     #   seaborn
     #   tifffile
     #   transforms3d
-packaging==24.1
+packaging==24.2
     # via
     #   smriprep (pyproject.toml)
     #   etelemetry
@@ -130,28 +147,30 @@ packaging==24.1
     #   nipype
     #   niworkflows
     #   scikit-image
-pandas==2.2.2
+pandas==2.2.3
     # via
     #   formulaic
     #   nilearn
     #   niworkflows
     #   pybids
     #   seaborn
-pillow==10.4.0
+pillow==11.1.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
 prov==2.0.1
     # via nipype
-pybids==0.16.5
+puremagic==1.28
+    # via nipype
+pybids==0.19.0
     # via
     #   smriprep (pyproject.toml)
     #   niworkflows
     #   templateflow
-pydot==3.0.1
+pydot==3.0.4
     # via nipype
-pyparsing==3.1.2
+pyparsing==3.2.1
     # via
     #   matplotlib
     #   pydot
@@ -162,26 +181,35 @@ python-dateutil==2.9.0.post0
     #   nipype
     #   pandas
     #   prov
-pytz==2024.1
+pytz==2025.1
     # via pandas
-pyyaml==6.0.1
+pyyaml==6.0.2
     # via
     #   smriprep (pyproject.toml)
+    #   bidsschematools
     #   niworkflows
 rdflib==6.3.2
     # via
     #   nipype
     #   prov
+referencing==0.36.2
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
 requests==2.32.3
     # via
     #   etelemetry
     #   nilearn
     #   templateflow
-scikit-image==0.23.2
+rpds-py==0.23.1
+    # via
+    #   jsonschema
+    #   referencing
+scikit-image==0.25.2
     # via niworkflows
-scikit-learn==1.4.2
+scikit-learn==1.6.1
     # via nilearn
-scipy==1.13.1
+scipy==1.15.2
     # via
     #   formulaic
     #   nilearn
@@ -193,39 +221,41 @@ scipy==1.13.1
     #   scikit-learn
 seaborn==0.13.2
     # via niworkflows
-simplejson==3.19.2
+simplejson==3.20.1
     # via nipype
-six==1.16.0
+six==1.17.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.31
+sqlalchemy==2.0.38
     # via pybids
 svgutils==0.3.4
     # via niworkflows
-templateflow==24.2.0
+templateflow==24.2.2
     # via
     #   smriprep (pyproject.toml)
     #   niworkflows
 threadpoolctl==3.5.0
     # via scikit-learn
-tifffile==2024.7.2
+tifffile==2025.2.18
     # via scikit-image
-tqdm==4.66.4
+tqdm==4.67.1
     # via templateflow
-traits==6.3.2
-    # via
-    #   nipype
-    #   niworkflows
+traits==7.0.2
+    # via nipype
 transforms3d==0.4.2
     # via niworkflows
 typing-extensions==4.12.2
     # via
     #   formulaic
+    #   nibabel
+    #   referencing
     #   sqlalchemy
-tzdata==2024.1
+tzdata==2025.1
     # via pandas
-urllib3==2.2.2
+universal-pathlib==0.2.6
+    # via pybids
+urllib3==2.3.0
     # via requests
-wrapt==1.16.0
+wrapt==1.17.2
     # via formulaic