diff --git a/env.yml b/env.yml index 0fa0a1a2461..389ebfbb95c 100644 --- a/env.yml +++ b/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 diff --git a/requirements.txt b/requirements.txt index c988b83492e..c2d3c2574a0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,30 +1,30 @@ # 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 @@ -32,29 +32,29 @@ 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 @@ -64,7 +64,7 @@ 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 @@ -72,14 +72,14 @@ 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 @@ -205,13 +205,13 @@ 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) @@ -219,11 +219,11 @@ 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) @@ -231,12 +231,13 @@ 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