diff --git a/env.yml b/env.yml index fcf88e4bbaf..0fa0a1a2461 100644 --- a/env.yml +++ b/env.yml @@ -10,13 +10,13 @@ dependencies: - mkl-service=2.4 # Base scientific python stack; required by FSL, so pinned here - numpy=1.26 - - scipy=1.11 - - matplotlib=3.8 + - scipy=1.14 + - matplotlib=3.9 - pandas=2.2 - - h5py=3.10 + - h5py=3.12 # Dependencies compiled against numpy, best to stick with conda - - scikit-image=0.22 - - scikit-learn=1.4 + - scikit-image=0.24 + - scikit-learn=1.5 # Utilities - graphviz=9.0 # Workflow dependencies: ANTs diff --git a/requirements.txt b/requirements.txt index 11947b4d3c6..72938a987f6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,21 +1,30 @@ # This file was autogenerated by uv via the following command: -# uv pip compile pyproject.toml -c - -p 3.11 -o requirements.txt +# 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==23.2.0 -bids-validator==1.14.1 +attrs==24.2.0 + # via + # niworkflows (pyproject.toml) + # jsonschema + # referencing +bids-validator==1.14.7.post0 # via pybids -certifi==2024.7.4 +bidsschematools==0.11.3 + # via bids-validator +certifi==2024.8.30 # via requests -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 # via requests ci-info==0.3.0 # via etelemetry click==8.1.7 # via + # bidsschematools # nipype # pybids -contourpy==1.2.0 +contourpy==1.3.0 # via matplotlib cycler==0.12.1 # via matplotlib @@ -23,62 +32,80 @@ docopt==0.6.2 # via num2words etelemetry==0.3.1 # via nipype -filelock==3.13.1 +filelock==3.16.1 # via nipype -fonttools==4.49.0 +fonttools==4.54.1 # via matplotlib formulaic==0.5.2 # via pybids -greenlet==3.0.3 +fsspec==2024.10.0 + # via universal-pathlib +greenlet==3.1.1 # via sqlalchemy -h5py==3.10.0 +h5py==3.12.1 # via nitransforms -idna==3.6 +idna==3.10 # via requests -imageio==2.34.0 +imageio==2.36.0 # via scikit-image +importlib-resources==6.4.5 + # via nibabel interface-meta==1.3.0 # via formulaic isodate==0.6.1 # via rdflib -jinja2==3.1.3 -joblib==1.3.2 +jinja2==3.1.4 + # via niworkflows (pyproject.toml) +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==1.4.7 # via matplotlib -lazy-loader==0.3 +lazy-loader==0.4 # via scikit-image looseversion==1.3.0 - # via nipype -lxml==5.1.0 + # via + # niworkflows (pyproject.toml) + # nipype +lxml==5.3.0 # via # nilearn # prov # svgutils -markupsafe==2.1.5 +markupsafe==3.0.2 # via jinja2 -matplotlib==3.8.3 - # via seaborn -networkx==3.2.1 +matplotlib==3.9.2 + # via + # niworkflows (pyproject.toml) + # seaborn +networkx==3.4.2 # via # nipype # prov # scikit-image -nibabel==5.2.1 +nibabel==5.3.2 # via + # niworkflows (pyproject.toml) # nilearn # nipype # nitransforms # pybids -nilearn==0.10.3 -nipype==1.8.6 -nitransforms==23.0.1 +nilearn==0.10.4 + # via niworkflows (pyproject.toml) +nipype==1.9.0 + # via niworkflows (pyproject.toml) +nitransforms==24.0.2 + # via niworkflows (pyproject.toml) num2words==0.5.13 # via pybids numpy==1.26.4 # via + # niworkflows (pyproject.toml) # contourpy # formulaic # h5py @@ -95,32 +122,40 @@ numpy==1.26.4 # scipy # seaborn # tifffile -packaging==23.2 + # transforms3d +packaging==24.1 # via + # niworkflows (pyproject.toml) # etelemetry + # lazy-loader # matplotlib # nibabel # nilearn # nipype # scikit-image -pandas==2.2.1 +pandas==2.2.3 # via + # niworkflows (pyproject.toml) # formulaic # nilearn # pybids # seaborn -pillow==10.2.0 +pillow==11.0.0 # via # imageio # matplotlib # scikit-image -prov==2.0.0 +prov==2.0.1 # via nipype -pybids==0.16.4 - # via templateflow -pydot==2.0.0 +puremagic==1.28 # via nipype -pyparsing==3.1.2 +pybids==0.17.2 + # via + # niworkflows (pyproject.toml) + # templateflow +pydot==3.0.2 + # via nipype +pyparsing==3.2.0 # via # matplotlib # pydot @@ -131,23 +166,36 @@ python-dateutil==2.9.0.post0 # nipype # pandas # prov -pytz==2024.1 +pytz==2024.2 # via pandas -pyyaml==6.0.1 -rdflib==7.0.0 +pyyaml==6.0.2 + # via + # niworkflows (pyproject.toml) + # bidsschematools +rdflib==6.3.2 # via # nipype # prov -requests==2.31.0 +referencing==0.35.1 + # via + # jsonschema + # jsonschema-specifications +requests==2.32.3 # via # etelemetry # nilearn # templateflow -scikit-image==0.22.0 -scikit-learn==1.4.1.post1 +rpds-py==0.20.1 + # via + # jsonschema + # referencing +scikit-image==0.24.0 + # via niworkflows (pyproject.toml) +scikit-learn==1.5.2 # via nilearn -scipy==1.11.4 +scipy==1.14.1 # via + # niworkflows (pyproject.toml) # formulaic # nilearn # nipype @@ -156,32 +204,39 @@ scipy==1.11.4 # scikit-image # scikit-learn seaborn==0.13.2 -simplejson==3.19.2 + # via niworkflows (pyproject.toml) +simplejson==3.19.3 # via nipype six==1.16.0 # via # isodate # python-dateutil -sqlalchemy==2.0.28 +sqlalchemy==2.0.36 # via pybids svgutils==0.3.4 -templateflow==24.0.0 -threadpoolctl==3.3.0 + # via niworkflows (pyproject.toml) +templateflow==24.2.2 + # via niworkflows (pyproject.toml) +threadpoolctl==3.5.0 # via scikit-learn -tifffile==2024.2.12 +tifffile==2024.9.20 # via scikit-image -tqdm==4.66.2 +tqdm==4.66.6 # via templateflow -traits==6.3.2 +traits==6.4.3 # via nipype -transforms3d==0.4.1 -typing-extensions==4.10.0 +transforms3d==0.4.2 + # via niworkflows (pyproject.toml) +typing-extensions==4.12.2 # via # formulaic + # nibabel # sqlalchemy -tzdata==2024.1 +tzdata==2024.2 # via pandas -urllib3==2.2.1 +universal-pathlib==0.2.5 + # via pybids +urllib3==2.2.3 # via requests wrapt==1.16.0 # via formulaic