Merge pull request #933 from effigies/chore/environment

chore(deps): Update pinned environment

Author: effigies

env.yml

@@ -2,27 +2,31 @@ name: niworkflows
 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=3.11
+  - python=3.12
   # 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=1.14
+  - scipy=1.15
   - matplotlib=3.9
   - pandas=2.2
-  - h5py=3.12
+  - h5py=3.13
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.24
-  - scikit-learn=1.5
+  - scikit-image=0.25
+  - scikit-learn=1.6
   # Utilities
-  - graphviz=9.0
+  - graphviz=11.0
   # Workflow dependencies: ANTs
   - ants=2.5
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.4)
-  - 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: FSL (versions pinned in 6.0.7.13)
+  - fsl-bet2=2111.8
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3
   - fsl-mcflirt=2111.0

requirements.txt

@@ -1,60 +1,60 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile pyproject.toml -p 3.11 -o requirements.txt
-acres==0.1.0
-    # via niworkflows (pyproject.toml)
-astor==0.8.1
-    # via formulaic
-attrs==24.2.0
+#    uv pip compile --strip-extras pyproject.toml -o requirements.txt -p 3.12 -c-
+acres==0.3.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   nipype
+attrs==25.1.0
     # via
     #   niworkflows (pyproject.toml)
     #   jsonschema
     #   referencing
 bids-validator==1.14.7.post0
     # via pybids
-bidsschematools==0.11.3
+bidsschematools==1.0.3
     # via bids-validator
-certifi==2024.8.30
+certifi==2025.1.31
     # via requests
-charset-normalizer==3.4.0
+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==1.3.0
+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==3.16.1
+filelock==3.17.0
     # via nipype
-fonttools==4.54.1
+fonttools==4.56.0
     # via matplotlib
-formulaic==0.5.2
+formulaic==1.1.1
+    # via pybids
+frozendict==2.4.6
     # via pybids
-fsspec==2024.10.0
+fsspec==2025.2.0
     # via universal-pathlib
 greenlet==3.1.1
     # via sqlalchemy
-h5py==3.12.1
+h5py==3.13.0
     # via nitransforms
 idna==3.10
     # via requests
-imageio==2.36.0
+imageio==2.37.0
     # via scikit-image
-importlib-resources==6.4.5
-    # via nibabel
 interface-meta==1.3.0
     # via formulaic
 isodate==0.6.1
     # via rdflib
-jinja2==3.1.5
+jinja2==3.1.6
     # via niworkflows (pyproject.toml)
 joblib==1.4.2
     # via
@@ -64,22 +64,22 @@ jsonschema==4.23.0
     # via bidsschematools
 jsonschema-specifications==2024.10.1
     # via jsonschema
-kiwisolver==1.4.7
+kiwisolver==1.4.8
     # via matplotlib
 lazy-loader==0.4
     # via scikit-image
 looseversion==1.3.0
     # via
     #   niworkflows (pyproject.toml)
     #   nipype
-lxml==5.3.0
+lxml==5.3.1
     # via
     #   nilearn
     #   prov
     #   svgutils
 markupsafe==3.0.2
     # via jinja2
-matplotlib==3.9.2
+matplotlib==3.9.4
     # via
     #   niworkflows (pyproject.toml)
     #   seaborn
@@ -95,13 +95,13 @@ nibabel==5.3.2
     #   nipype
     #   nitransforms
     #   pybids
-nilearn==0.10.4
+nilearn==0.11.1
     # via niworkflows (pyproject.toml)
-nipype==1.9.0
+nipype==1.9.2
     # via niworkflows (pyproject.toml)
-nitransforms==24.0.2
+nitransforms==24.1.1
     # via niworkflows (pyproject.toml)
-num2words==0.5.13
+num2words==0.5.14
     # via pybids
 numpy==1.26.4
     # via
@@ -123,7 +123,7 @@ numpy==1.26.4
     #   seaborn
     #   tifffile
     #   transforms3d
-packaging==24.1
+packaging==24.2
     # via
     #   niworkflows (pyproject.toml)
     #   etelemetry
@@ -140,7 +140,7 @@ pandas==2.2.3
     #   nilearn
     #   pybids
     #   seaborn
-pillow==11.0.0
+pillow==11.1.0
     # via
     #   imageio
     #   matplotlib
@@ -149,13 +149,13 @@ prov==2.0.1
     # via nipype
 puremagic==1.28
     # via nipype
-pybids==0.17.2
+pybids==0.19.0
     # via
     #   niworkflows (pyproject.toml)
     #   templateflow
-pydot==3.0.2
+pydot==3.0.4
     # via nipype
-pyparsing==3.2.0
+pyparsing==3.2.1
     # via
     #   matplotlib
     #   pydot
@@ -166,7 +166,7 @@ python-dateutil==2.9.0.post0
     #   nipype
     #   pandas
     #   prov
-pytz==2024.2
+pytz==2025.1
     # via pandas
 pyyaml==6.0.2
     # via
@@ -176,7 +176,7 @@ rdflib==6.3.2
     # via
     #   nipype
     #   prov
-referencing==0.35.1
+referencing==0.36.2
     # via
     #   jsonschema
     #   jsonschema-specifications
@@ -185,15 +185,15 @@ requests==2.32.3
     #   etelemetry
     #   nilearn
     #   templateflow
-rpds-py==0.20.1
+rpds-py==0.23.1
     # via
     #   jsonschema
     #   referencing
-scikit-image==0.24.0
+scikit-image==0.25.2
     # via niworkflows (pyproject.toml)
-scikit-learn==1.5.2
+scikit-learn==1.6.1
     # via nilearn
-scipy==1.14.1
+scipy==1.15.2
     # via
     #   niworkflows (pyproject.toml)
     #   formulaic
@@ -205,38 +205,39 @@ scipy==1.14.1
     #   scikit-learn
 seaborn==0.13.2
     # via niworkflows (pyproject.toml)
-simplejson==3.19.3
+simplejson==3.20.1
     # via nipype
-six==1.16.0
+six==1.17.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.36
+sqlalchemy==2.0.38
     # via pybids
 svgutils==0.3.4
     # via niworkflows (pyproject.toml)
 templateflow==24.2.2
     # via niworkflows (pyproject.toml)
 threadpoolctl==3.5.0
     # via scikit-learn
-tifffile==2024.9.20
+tifffile==2025.2.18
     # via scikit-image
-tqdm==4.66.6
+tqdm==4.67.1
     # via templateflow
-traits==6.4.3
+traits==7.0.2
     # via nipype
 transforms3d==0.4.2
     # via niworkflows (pyproject.toml)
 typing-extensions==4.12.2
     # via
     #   formulaic
     #   nibabel
+    #   referencing
     #   sqlalchemy
-tzdata==2024.2
+tzdata==2025.1
     # via pandas
-universal-pathlib==0.2.5
+universal-pathlib==0.2.6
     # via pybids
-urllib3==2.2.3
+urllib3==2.3.0
     # via requests
-wrapt==1.16.0
+wrapt==1.17.2
     # via formulaic