MAINT: Bump requirements while at it [skip ci]

Author: mgxd

requirements.txt

@@ -4,9 +4,10 @@
 #
 #    pip-compile --extra=container --output-file=requirements.txt --strip-extras pyproject.toml
 #
-acres==0.1.0
+acres==0.2.0
     # via
     #   nibabies (pyproject.toml)
+    #   nipype
     #   niworkflows
     #   smriprep
 annexremote==1.6.6
@@ -26,21 +27,23 @@ backports-tarfile==1.2.0
     # via jaraco-context
 bids-validator==1.14.7.post0
     # via pybids
-bidsschematools==0.11.3
+bidsschematools==1.0.0
     # via bids-validator
 bokeh==3.5.2
     # via tedana
-boto3==1.35.32
+boto3==1.35.80
     # via datalad
-botocore==1.35.32
+botocore==1.35.80
     # via
     #   boto3
     #   s3transfer
 certifi==2024.8.30
     # via requests
+cffi==1.17.1
+    # via cryptography
 chardet==5.2.0
     # via datalad
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 ci-info==0.3.0
     # via
@@ -51,13 +54,15 @@ click==8.1.7
     #   bidsschematools
     #   nipype
     #   pybids
-contourpy==1.3.0
+contourpy==1.3.1
     # via
     #   bokeh
     #   matplotlib
+cryptography==44.0.0
+    # via secretstorage
 cycler==0.12.1
     # via matplotlib
-datalad==1.1.3
+datalad==1.1.4
     # via
     #   datalad-next
     #   datalad-osf
@@ -76,27 +81,31 @@ fasteners==0.19
     # via datalad
 filelock==3.16.1
     # via nipype
-fonttools==4.54.1
+fonttools==4.55.3
     # via matplotlib
 formulaic==0.5.2
     # via pybids
-fsspec==2024.9.0
+fsspec==2024.10.0
     # via universal-pathlib
+greenlet==3.1.1
+    # via sqlalchemy
 h5py==3.12.1
     # via nitransforms
-humanize==4.10.0
+humanize==4.11.0
     # via
     #   datalad
     #   datalad-next
 idna==3.10
     # via requests
-imageio==2.35.1
+imageio==2.36.1
     # via scikit-image
 importlib-metadata==8.5.0
     # via keyring
 importlib-resources==6.4.5
-    # via nireports
-indexed-gzip==1.8.7
+    # via
+    #   nibabel
+    #   nireports
+indexed-gzip==1.9.4
     # via smriprep
 interface-meta==1.3.0
     # via formulaic
@@ -114,6 +123,10 @@ jaraco-context==6.0.1
     #   keyrings-alt
 jaraco-functools==4.1.0
     # via keyring
+jeepney==0.8.0
+    # via
+    #   keyring
+    #   secretstorage
 jinja2==3.1.4
     # via
     #   bokeh
@@ -129,9 +142,9 @@ joblib==1.4.2
     #   scikit-learn
 jsonschema==4.23.0
     # via bidsschematools
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
-keyring==25.4.1
+keyring==25.5.0
     # via datalad
 keyrings-alt==5.0.2
     # via datalad
@@ -156,9 +169,9 @@ lxml==5.3.0
     #   svgutils
 mapca==0.0.5
     # via tedana
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via jinja2
-matplotlib==3.9.2
+matplotlib==3.9.3
     # via
     #   nireports
     #   nitime
@@ -177,7 +190,7 @@ more-itertools==10.5.0
     #   jaraco-functools
 msgpack==1.1.0
     # via datalad
-networkx==3.3
+networkx==3.4.2
     # via
     #   nipype
     #   prov
@@ -201,30 +214,30 @@ nilearn==0.10.4
     #   nireports
     #   niworkflows
     #   tedana
-nipype==1.8.6
+nipype==1.9.1
     # via
     #   nibabies (pyproject.toml)
     #   nireports
     #   niworkflows
     #   sdcflows
     #   smriprep
-nireports==24.0.2
+nireports==24.0.3
     # via nibabies (pyproject.toml)
 nitime==0.11
     # via nibabies (pyproject.toml)
-nitransforms==24.0.2
+nitransforms==24.1.0
     # via
     #   nibabies (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.11.0
+niworkflows==1.12.1
     # via
     #   nibabies (pyproject.toml)
     #   sdcflows
     #   smriprep
 num2words==0.5.13
     # via pybids
-numpy==1.26.4
+numpy==2.1.1
     # via
     #   bokeh
     #   contourpy
@@ -255,7 +268,7 @@ numpy==1.26.4
     #   transforms3d
 osfclient==0.0.5
     # via datalad-osf
-packaging==24.1
+packaging==24.2
     # via
     #   bokeh
     #   datalad
@@ -267,6 +280,7 @@ packaging==24.1
     #   nilearn
     #   nipype
     #   niworkflows
+    #   pooch
     #   scikit-image
     #   smriprep
 pandas==2.2.2
@@ -281,21 +295,27 @@ pandas==2.2.2
     #   robustica
     #   seaborn
     #   tedana
-patool==3.0.0
+patool==3.1.0
     # via datalad
-pillow==10.4.0
+pillow==11.0.0
     # via
     #   bokeh
     #   imageio
     #   matplotlib
     #   scikit-image
 platformdirs==4.3.6
-    # via datalad
+    # via
+    #   datalad
+    #   pooch
+pooch==1.8.2
+    # via nibabies (pyproject.toml)
 prov==2.0.1
     # via nipype
-psutil==6.0.0
+psutil==6.1.0
     # via nibabies (pyproject.toml)
-pybids==0.17.2
+puremagic==1.28
+    # via nipype
+pybids==0.18.1
     # via
     #   nibabies (pyproject.toml)
     #   nireports
@@ -307,9 +327,11 @@ pybtex==0.24.0
     # via tedana
 pybtex-apa-style==1.3
     # via tedana
-pydot==3.0.2
+pycparser==2.22
+    # via cffi
+pydot==3.0.3
     # via nipype
-pyparsing==3.1.4
+pyparsing==3.2.0
     # via
     #   matplotlib
     #   pydot
@@ -321,7 +343,7 @@ python-dateutil==2.9.0.post0
     #   nipype
     #   pandas
     #   prov
-python-gitlab==4.12.2
+python-gitlab==5.1.0
     # via datalad
 pytz==2024.2
     # via pandas
@@ -348,18 +370,19 @@ requests==2.32.3
     #   nibabies (pyproject.toml)
     #   nilearn
     #   osfclient
+    #   pooch
     #   python-gitlab
     #   requests-toolbelt
     #   templateflow
 requests-toolbelt==1.0.0
     # via python-gitlab
 robustica==0.1.4
     # via tedana
-rpds-py==0.20.0
+rpds-py==0.22.3
     # via
     #   jsonschema
     #   referencing
-s3transfer==0.10.2
+s3transfer==0.10.4
     # via boto3
 scikit-image==0.24.0
     # via
@@ -392,17 +415,19 @@ seaborn==0.13.2
     # via
     #   nireports
     #   niworkflows
+secretstorage==3.3.3
+    # via keyring
 simplejson==3.19.3
     # via nipype
-six==1.16.0
+six==1.17.0
     # via
     #   isodate
     #   osfclient
     #   pybtex
     #   python-dateutil
-smriprep==0.16.1
+smriprep @ git+https://github.com/nipreps/smriprep.git@dev-nibabies
     # via nibabies (pyproject.toml)
-sqlalchemy==2.0.35
+sqlalchemy==2.0.36
     # via pybids
 svgutils==0.3.4
     # via
@@ -421,15 +446,15 @@ threadpoolctl==3.5.0
     # via
     #   scikit-learn
     #   tedana
-tifffile==2024.9.20
+tifffile==2024.12.12
     # via scikit-image
 toml==0.10.2
     # via
     #   nibabies (pyproject.toml)
     #   sdcflows
-tornado==6.4.1
+tornado==6.4.2
     # via bokeh
-tqdm==4.66.5
+tqdm==4.67.1
     # via
     #   datalad
     #   osfclient
@@ -439,25 +464,25 @@ tqdm==4.66.5
 traits==6.3.2
     # via
     #   nipype
-    #   niworkflows
     #   sdcflows
 transforms3d==0.4.2
     # via niworkflows
 typing-extensions==4.12.2
     # via
     #   formulaic
+    #   nibabel
     #   sqlalchemy
 tzdata==2024.2
     # via pandas
-universal-pathlib==0.2.5
+universal-pathlib==0.2.6
     # via pybids
 urllib3==2.2.3
     # via
     #   botocore
     #   requests
-wrapt==1.16.0
+wrapt==1.17.0
     # via formulaic
 xyzservices==2024.9.0
     # via bokeh
-zipp==3.20.2
+zipp==3.21.0
     # via importlib-metadata