chore: Bump pins, update RTD config (#3425)

Finally realized that the `requirements.txt` + not bumping the minimum
sdcflows means that the unstable image is still using 2.10.0, which has
the SyN problems that I have been thinking have been dealt with.

Now they should be.

Fixing RTD build failures in passing.

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -51,8 +51,7 @@ sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_desc-preproc_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_desc-preproc_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_desc-preproc_probseg.nii.gz
 sub-01/fmap
-sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz

.circleci/ds005_partial_outputs.txt

@@ -73,8 +73,7 @@ sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 sub-01/fmap
-sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz

.circleci/ds210_fasttrack_outputs.txt

@@ -17,8 +17,7 @@ sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_desc-preproc_probseg.nii.
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_desc-preproc_probseg.nii.gz
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_desc-preproc_probseg.nii.gz
 sub-02/fmap
-sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz

.circleci/ds210_outputs.txt

@@ -27,8 +27,7 @@ sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
 sub-02/fmap
-sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
+sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz

.readthedocs.yml

@@ -17,3 +17,6 @@ python:
       extra_requirements:
         - doc
     - path: wrapper/
+
+sphinx:
+  configuration: docs/conf.py

pyproject.toml

@@ -24,18 +24,18 @@ dependencies = [
     "looseversion >= 1.3",
     "nibabel >= 4.0.1",
     "nipype >= 1.8.5",
-    "nireports >= 24.0.3",
+    "nireports >= 24.1.0",
     "nitime >= 0.9",
-    "nitransforms >= 24.1.0",
-    "niworkflows >= 1.12.1",
+    "nitransforms >= 24.1.1",
+    "niworkflows >= 1.12.2",
     "numpy >= 1.24",
     "packaging >= 24",
     "pandas >= 1.2",
     "psutil >= 5.4",
     "pybids >= 0.16",
     "requests >= 2.27",
-    "sdcflows >= 2.10.0",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git",
+    "sdcflows >= 2.11.0",
+    "smriprep >= 0.17.0",
     "tedana >= 23.0.2",
     "templateflow >= 24.2.2",
     "transforms3d >= 0.4",

requirements.txt

@@ -1,11 +1,13 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -p 3.11
-acres==0.1.0
+acres==0.2.0
     # via
     #   fmriprep (pyproject.toml)
+    #   nireports
     #   niworkflows
+    #   sdcflows
     #   smriprep
-annexremote==1.6.5
+annexremote==1.6.6
     # via
     #   datalad
     #   datalad-next
@@ -30,17 +32,17 @@ bidsschematools==0.11.0
     # via bids-validator
 bokeh==3.4.1
     # via tedana
-boto3==1.35.4
+boto3==1.36.9
     # via datalad
-botocore==1.35.4
+botocore==1.36.9
     # via
     #   boto3
     #   s3transfer
 certifi==2024.7.4
     # via
     #   requests
     #   sentry-sdk
-cffi==1.17.0
+cffi==1.17.1
     # via cryptography
 chardet==5.2.0
     # via datalad
@@ -63,11 +65,11 @@ contourpy==1.2.1
     # via
     #   bokeh
     #   matplotlib
-cryptography==43.0.0
+cryptography==44.0.0
     # via secretstorage
 cycler==0.12.1
     # via matplotlib
-datalad==1.1.3
+datalad==1.1.5
     # via
     #   fmriprep (pyproject.toml)
     #   datalad-next
@@ -96,15 +98,15 @@ greenlet==3.0.3
     # via sqlalchemy
 h5py==3.11.0
     # via nitransforms
-humanize==4.10.0
+humanize==4.11.0
     # via
     #   datalad
     #   datalad-next
 idna==3.7
     # via requests
 imageio==2.35.1
     # via scikit-image
-importlib-metadata==8.4.0
+importlib-metadata==8.6.1
     # via keyring
 importlib-resources==6.4.4
     # via nireports
@@ -124,7 +126,7 @@ jaraco-context==6.0.1
     # via
     #   keyring
     #   keyrings-alt
-jaraco-functools==4.0.2
+jaraco-functools==4.1.0
     # via keyring
 jeepney==0.8.0
     # via
@@ -146,7 +148,7 @@ jsonschema==4.23.0
     # via bidsschematools
 jsonschema-specifications==2023.12.1
     # via jsonschema
-keyring==25.3.0
+keyring==25.6.0
     # via datalad
 keyrings-alt==5.0.2
     # via datalad
@@ -190,12 +192,12 @@ migas==0.4.0
     # via
     #   fmriprep (pyproject.toml)
     #   sdcflows
-more-itertools==10.4.0
+more-itertools==10.6.0
     # via
     #   datalad-next
     #   jaraco-classes
     #   jaraco-functools
-msgpack==1.0.8
+msgpack==1.1.0
     # via datalad
 networkx==3.3
     # via
@@ -228,16 +230,16 @@ nipype==1.8.6
     #   niworkflows
     #   sdcflows
     #   smriprep
-nireports==23.2.2
+nireports==24.1.0
     # via fmriprep (pyproject.toml)
 nitime==0.10.2
     # via fmriprep (pyproject.toml)
-nitransforms==24.0.2
+nitransforms==24.1.1
     # via
     #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.11.0
+niworkflows==1.12.2
     # via
     #   fmriprep (pyproject.toml)
     #   sdcflows
@@ -300,15 +302,15 @@ pandas==2.2.2
     #   pybids
     #   seaborn
     #   tedana
-patool==2.4.0
+patool==3.1.0
     # via datalad
 pillow==10.4.0
     # via
     #   bokeh
     #   imageio
     #   matplotlib
     #   scikit-image
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via datalad
 prometheus-client==0.20.0
     # via codecarbon
@@ -355,7 +357,7 @@ python-dateutil==2.9.0.post0
     #   nipype
     #   pandas
     #   prov
-python-gitlab==4.9.0
+python-gitlab==5.6.0
     # via datalad
 pytz==2024.1
     # via
@@ -402,7 +404,7 @@ rpds-py==0.20.0
     # via
     #   jsonschema
     #   referencing
-s3transfer==0.10.2
+s3transfer==0.11.2
     # via boto3
 scikit-image==0.24.0
     # via
@@ -427,15 +429,15 @@ scipy==1.13.0
     #   scikit-learn
     #   sdcflows
     #   tedana
-sdcflows==2.10.0
+sdcflows==2.11.0
     # via fmriprep (pyproject.toml)
 seaborn==0.13.2
     # via
     #   nireports
     #   niworkflows
 secretstorage==3.3.3
     # via keyring
-sentry-sdk==2.13.0
+sentry-sdk==2.20.0
     # via fmriprep (pyproject.toml)
 shellingham==1.5.4
     # via typer
@@ -448,7 +450,7 @@ six==1.16.0
     #   osfclient
     #   pybtex
     #   python-dateutil
-smriprep==0.16.0
+smriprep==0.17.0
     # via fmriprep (pyproject.toml)
 sqlalchemy==2.0.32
     # via pybids
@@ -458,7 +460,7 @@ svgutils==0.3.4
     #   niworkflows
 tedana==24.0.1
     # via fmriprep (pyproject.toml)
-templateflow==24.2.0
+templateflow==24.2.2
     # via
     #   fmriprep (pyproject.toml)
     #   nireports
@@ -484,10 +486,7 @@ tqdm==4.66.5
     #   tedana
     #   templateflow
 traits==6.3.2
-    # via
-    #   nipype
-    #   niworkflows
-    #   sdcflows
+    # via nipype
 transforms3d==0.4.2
     # via
     #   fmriprep (pyproject.toml)
@@ -518,5 +517,5 @@ wrapt==1.16.0
     # via formulaic
 xyzservices==2024.6.0
     # via bokeh
-zipp==3.20.0
+zipp==3.21.0
     # via importlib-metadata