Merge remote-tracking branches 'tsalo/use-output-dir' and 'origin/mnt/pins'

Author: effigies

requirements.txt

@@ -1,12 +1,14 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -P 3.10
+#    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -p 3.11
 acres==0.1.0
+    # via fmriprep (pyproject.toml)
 annexremote==1.6.5
     # via
     #   datalad
     #   datalad-next
     #   datalad-osf
 apscheduler==3.10.4
+    # via fmriprep (pyproject.toml)
 arrow==1.3.0
     # via codecarbon
 astor==0.8.1
@@ -15,13 +17,15 @@ attrs==23.2.0
     # via
     #   niworkflows
     #   sdcflows
+backports-tarfile==1.2.0
+    # via jaraco-context
 bids-validator==1.14.6
     # via pybids
 bokeh==3.4.1
     # via tedana
-boto3==1.34.144
+boto3==1.34.149
     # via datalad
-botocore==1.34.144
+botocore==1.34.149
     # via
     #   boto3
     #   s3transfer
@@ -45,21 +49,24 @@ click==8.1.7
     #   nipype
     #   pybids
 codecarbon==2.5.0
+    # via fmriprep (pyproject.toml)
 contourpy==1.2.1
     # via
     #   bokeh
     #   matplotlib
-cryptography==42.0.8
+cryptography==43.0.0
     # via secretstorage
 cycler==0.12.1
     # via matplotlib
-datalad==1.1.1
+datalad==1.1.2
     # via
+    #   fmriprep (pyproject.toml)
     #   datalad-next
     #   datalad-osf
 datalad-next==1.5.0
     # via datalad-osf
 datalad-osf==0.3.0
+    # via fmriprep (pyproject.toml)
 distro==1.9.0
     # via datalad
 docopt==0.6.2
@@ -74,6 +81,8 @@ fonttools==4.53.1
     # via matplotlib
 formulaic==0.5.2
     # via pybids
+fsspec==2024.6.1
+    # via universal-pathlib
 greenlet==3.0.3
     # via sqlalchemy
 h5py==3.11.0
@@ -86,6 +95,10 @@ idna==3.7
     # via requests
 imageio==2.34.2
     # via scikit-image
+importlib-metadata==8.2.0
+    # via keyring
+importlib-resources==6.4.0
+    # via nireports
 indexed-gzip==1.8.7
     # via smriprep
 interface-meta==1.3.0
@@ -134,6 +147,7 @@ lockfile==0.12.2
     # via smriprep
 looseversion==1.3.0
     # via
+    #   fmriprep (pyproject.toml)
     #   datalad
     #   nipype
     #   niworkflows
@@ -156,7 +170,9 @@ matplotlib==3.9.1
     #   smriprep
     #   tedana
 migas==0.4.0
-    # via sdcflows
+    # via
+    #   fmriprep (pyproject.toml)
+    #   sdcflows
 more-itertools==10.3.0
     # via
     #   datalad-next
@@ -171,6 +187,7 @@ networkx==3.3
     #   scikit-image
 nibabel==5.2.1
     # via
+    #   fmriprep (pyproject.toml)
     #   mapca
     #   nilearn
     #   nipype
@@ -189,24 +206,29 @@ nilearn==0.10.4
     #   tedana
 nipype==1.8.6
     # via
+    #   fmriprep (pyproject.toml)
     #   nireports
     #   niworkflows
     #   sdcflows
     #   smriprep
 nireports==23.2.1
 nitime==0.11
+    # via fmriprep (pyproject.toml)
 nitransforms==23.0.1
     # via
+    #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
 niworkflows==1.10.2
     # via
+    #   fmriprep (pyproject.toml)
     #   sdcflows
     #   smriprep
 num2words==0.5.13
     # via pybids
 numpy==1.26.4
     # via
+    #   fmriprep (pyproject.toml)
     #   bokeh
     #   contourpy
     #   formulaic
@@ -236,6 +258,7 @@ osfclient==0.0.5
     # via datalad-osf
 packaging==24.1
     # via
+    #   fmriprep (pyproject.toml)
     #   bokeh
     #   datalad
     #   etelemetry
@@ -249,6 +272,7 @@ packaging==24.1
     #   smriprep
 pandas==2.2.2
     # via
+    #   fmriprep (pyproject.toml)
     #   bokeh
     #   codecarbon
     #   formulaic
@@ -273,11 +297,14 @@ prometheus-client==0.20.0
 prov==2.0.1
     # via nipype
 psutil==6.0.0
-    # via codecarbon
+    # via
+    #   fmriprep (pyproject.toml)
+    #   codecarbon
 py-cpuinfo==9.0.0
     # via codecarbon
-pybids==0.16.5
+pybids==0.17.0
     # via
+    #   fmriprep (pyproject.toml)
     #   nireports
     #   niworkflows
     #   sdcflows
@@ -319,14 +346,15 @@ pyyaml==6.0.1
     #   niworkflows
     #   pybtex
     #   smriprep
-rapidfuzz==3.9.4
+rapidfuzz==3.9.5
     # via codecarbon
 rdflib==6.3.2
     # via
     #   nipype
     #   prov
 requests==2.32.3
     # via
+    #   fmriprep (pyproject.toml)
     #   codecarbon
     #   datalad
     #   etelemetry
@@ -369,7 +397,8 @@ seaborn==0.13.2
     #   niworkflows
 secretstorage==3.3.3
     # via keyring
-sentry-sdk==2.10.0
+sentry-sdk==2.11.0
+    # via fmriprep (pyproject.toml)
 simplejson==3.19.2
     # via nipype
 six==1.16.0
@@ -387,8 +416,10 @@ svgutils==0.3.4
     #   nireports
     #   niworkflows
 tedana==24.0.1
+    # via fmriprep (pyproject.toml)
 templateflow==24.2.0
     # via
+    #   fmriprep (pyproject.toml)
     #   nireports
     #   niworkflows
     #   sdcflows
@@ -397,10 +428,12 @@ threadpoolctl==3.5.0
     # via
     #   scikit-learn
     #   tedana
-tifffile==2024.7.2
+tifffile==2024.7.24
     # via scikit-image
 toml==0.10.2
-    # via sdcflows
+    # via
+    #   fmriprep (pyproject.toml)
+    #   sdcflows
 tornado==6.4.1
     # via bokeh
 tqdm==4.66.4
@@ -415,7 +448,9 @@ traits==6.3.2
     #   niworkflows
     #   sdcflows
 transforms3d==0.4.2
-    # via niworkflows
+    # via
+    #   fmriprep (pyproject.toml)
+    #   niworkflows
 types-python-dateutil==2.9.0.20240316
     # via arrow
 typing-extensions==4.12.2
@@ -426,6 +461,8 @@ tzdata==2024.1
     # via pandas
 tzlocal==5.2
     # via apscheduler
+universal-pathlib==0.2.2
+    # via pybids
 urllib3==2.2.2
     # via
     #   botocore
@@ -435,3 +472,5 @@ wrapt==1.16.0
     # via formulaic
 xyzservices==2024.6.0
     # via bokeh
+zipp==3.19.2
+    # via importlib-metadata