diff --git a/env.yml b/env.yml index 58d1eddc0..a36a8a16b 100644 --- a/env.yml +++ b/env.yml @@ -4,7 +4,7 @@ channels: - conda-forge # Update this ~yearly; last updated April 2023 dependencies: - - python >=3.10,<3.11 + - python=3.10 # Needed for svgo and bids-validator; consider moving to deno - nodejs=16 # Intel Math Kernel Library for numpy @@ -13,14 +13,14 @@ dependencies: # git-annex for templateflow users with DataLad superdatasets - git-annex=*=alldep* # Base scientific python stack; required by FSL, so pinned here - - numpy=1.25 + - numpy=1.26 - scipy=1.11 - - matplotlib=3.7,!=3.7.2 - - pandas=2.0 + - matplotlib=3.8 + - pandas=2.1 - h5py=3.8 # Dependencies compiled against numpy, best to stick with conda - nitime=0.10 - - scikit-image=0.21 + - scikit-image=0.22 - scikit-learn=1.3 # Utilities - graphviz=6.0 diff --git a/requirements.txt b/requirements.txt index 2b2bd35fd..e7a880961 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ # This file is autogenerated by pip-compile with Python 3.10 # by the following command: # -# pip-compile --extra=container --resolver=backtracking +# pip-compile --extra=container # annexremote==1.6.0 # via @@ -13,7 +13,7 @@ apscheduler==3.10.4 # via # fmriprep # fmriprep (pyproject.toml) -arrow==1.2.3 +arrow==1.3.0 # via codecarbon astor==0.8.1 # via formulaic @@ -21,7 +21,7 @@ attrs==23.1.0 # via # niworkflows # sdcflows -bids-validator==1.12.0 +bids-validator==1.13.1 # via pybids bokeh==2.2.3 # via tedana @@ -31,11 +31,11 @@ certifi==2023.7.22 # via # requests # sentry-sdk -cffi==1.15.1 +cffi==1.16.0 # via cryptography chardet==5.2.0 # via datalad -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 # via requests ci-info==0.3.0 # via @@ -50,20 +50,20 @@ codecarbon==2.3.1 # via # fmriprep # fmriprep (pyproject.toml) -contourpy==1.1.0 +contourpy==1.1.1 # via matplotlib -cryptography==41.0.3 +cryptography==41.0.4 # via secretstorage -cycler==0.11.0 +cycler==0.12.1 # via matplotlib -cython==3.0.0 +cython==3.0.3 # via nitime datalad==0.19.3 # via # datalad-next # datalad-osf # fmriprep (pyproject.toml) -datalad-next==1.0.0b3 +datalad-next==1.0.0 # via datalad-osf datalad-osf==0.3.0 # via fmriprep (pyproject.toml) @@ -73,17 +73,17 @@ docopt==0.6.2 # via num2words etelemetry==0.3.0 # via nipype -fasteners==0.18 +fasteners==0.19 # via datalad -filelock==3.12.2 +filelock==3.12.4 # via nipype -fonttools==4.42.1 +fonttools==4.43.1 # via matplotlib formulaic==0.5.2 # via pybids fuzzywuzzy==0.18.0 # via codecarbon -greenlet==2.0.2 +greenlet==3.0.0 # via sqlalchemy h5py==3.8.0 # via nitransforms @@ -93,15 +93,19 @@ humanize==4.8.0 # datalad-next idna==3.4 # via requests -imageio==2.31.1 +imageio==2.31.5 # via scikit-image importlib-metadata==6.8.0 # via keyring -indexed-gzip==1.8.3 +importlib-resources==6.1.0 + # via + # niworkflows + # sdcflows +indexed-gzip==1.8.5 # via smriprep interface-meta==1.3.0 # via formulaic -iso8601==2.0.0 +iso8601==2.1.0 # via datalad isodate==0.6.1 # via rdflib @@ -126,7 +130,7 @@ keyring==24.2.0 # via datalad keyrings-alt==5.0.0 # via datalad -kiwisolver==1.4.4 +kiwisolver==1.4.5 # via matplotlib lazy-loader==0.3 # via scikit-image @@ -149,7 +153,7 @@ mapca==0.0.3 # via tedana markupsafe==2.1.3 # via jinja2 -matplotlib==3.7.2 +matplotlib==3.8.0 # via # nireports # nitime @@ -161,7 +165,7 @@ migas==0.3.0 # via fmriprep more-itertools==10.1.0 # via jaraco-classes -msgpack==1.0.5 +msgpack==1.0.7 # via datalad networkx==3.1 # via @@ -184,7 +188,7 @@ nibabel==5.1.0 # sdcflows # smriprep # tedana -nilearn==0.10.1 +nilearn==0.10.2 # via # mapca # nireports @@ -220,7 +224,7 @@ niworkflows==1.8.1 # smriprep num2words==0.5.12 # via pybids -numpy==1.25.2 +numpy==1.26.0 # via # bokeh # contourpy @@ -240,7 +244,6 @@ numpy==1.25.2 # niworkflows # pandas # pybids - # pywavelets # scikit-image # scikit-learn # scipy @@ -251,7 +254,7 @@ numpy==1.25.2 # tifffile osfclient==0.0.5 # via datalad-osf -packaging==23.1 +packaging==23.2 # via # bokeh # datalad @@ -264,7 +267,7 @@ packaging==23.1 # niworkflows # scikit-image # smriprep -pandas==2.0.3 +pandas==2.1.1 # via # codecarbon # fmriprep @@ -278,13 +281,13 @@ pandas==2.0.3 # tedana patool==1.12 # via datalad -pillow==10.0.0 +pillow==10.0.1 # via # bokeh # imageio # matplotlib # scikit-image -platformdirs==3.10.0 +platformdirs==3.11.0 # via datalad prometheus-client==0.17.1 # via codecarbon @@ -312,7 +315,7 @@ pydot==1.4.2 # via nipype pynvml==11.5.0 # via codecarbon -pyparsing==3.0.9 +pyparsing==3.1.1 # via # matplotlib # pydot @@ -327,12 +330,10 @@ python-dateutil==2.8.2 # prov python-gitlab==3.15.0 # via datalad -pytz==2023.3 +pytz==2023.3.post1 # via # apscheduler # pandas -pywavelets==1.4.1 - # via scikit-image pyyaml==6.0.1 # via # bokeh @@ -357,16 +358,16 @@ requests==2.31.0 # templateflow requests-toolbelt==1.0.0 # via python-gitlab -scikit-image==0.21.0 +scikit-image==0.22.0 # via # niworkflows # sdcflows -scikit-learn==1.3.0 +scikit-learn==1.3.1 # via # mapca # nilearn # tedana -scipy==1.11.2 +scipy==1.11.3 # via # formulaic # mapca @@ -384,15 +385,15 @@ sdcflows==2.5.1 # via # fmriprep # fmriprep (pyproject.toml) -seaborn==0.12.2 +seaborn==0.13.0 # via # nireports # niworkflows secretstorage==3.3.3 # via keyring -sentry-sdk==1.29.2 +sentry-sdk==1.32.0 # via fmriprep -simplejson==3.19.1 +simplejson==3.19.2 # via nipype six==1.16.0 # via @@ -404,7 +405,7 @@ smriprep==0.12.2 # via # fmriprep # fmriprep (pyproject.toml) -sqlalchemy==2.0.20 +sqlalchemy==2.0.21 # via pybids svgutils==0.3.4 # via @@ -426,7 +427,7 @@ threadpoolctl==3.2.0 # via # scikit-learn # tedana -tifffile==2023.8.12 +tifffile==2023.9.26 # via scikit-image toml==0.10.2 # via @@ -446,7 +447,9 @@ traits==6.3.2 # sdcflows transforms3d==0.4.1 # via niworkflows -typing-extensions==4.7.1 +types-python-dateutil==2.8.19.14 + # via arrow +typing-extensions==4.8.0 # via # bokeh # datalad @@ -454,9 +457,9 @@ typing-extensions==4.7.1 # sqlalchemy tzdata==2023.3 # via pandas -tzlocal==5.0.1 +tzlocal==5.1 # via apscheduler -urllib3==2.0.4 +urllib3==2.0.6 # via # requests # sentry-sdk @@ -464,5 +467,5 @@ wrapt==1.15.0 # via formulaic www-authenticate==0.9.2 # via datalad-next -zipp==3.16.2 +zipp==3.17.0 # via importlib-metadata