Merge branch 'main' into pet3d

Author: Murat Bilgel

.coverage

@@ -27,7 +27,7 @@ dependencies = [
     "nireports >= 24.1.0",
     "nitime >= 0.9",
     "nitransforms >= 24.1.1",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@dev_petprep",
+    "niworkflows >= 1.14.0",
     "numpy >= 1.24",
     "packaging >= 24",
     "pandas >= 1.2",

pyproject.toml

@@ -1,8 +1,8 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -p 3.12 --constraint -
+#    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -p 3.12
 acres==0.3.0
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   nipype
     #   nireports
     #   niworkflows
@@ -15,7 +15,7 @@ annexremote==1.6.6
 anyio==4.8.0
     # via httpx
 apscheduler==3.11.0
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 arrow==1.3.0
     # via codecarbon
 attrs==25.1.0
@@ -59,7 +59,7 @@ click==8.1.8
     #   pybids
     #   typer
 codecarbon==2.8.3
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 contourpy==1.3.1
     # via
     #   bokeh
@@ -72,13 +72,13 @@ cycler==0.12.1
     # via matplotlib
 datalad==1.1.5
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   datalad-next
     #   datalad-osf
 datalad-next==1.5.0
     # via datalad-osf
 datalad-osf==0.3.0
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 distro==1.9.0
     # via datalad
 docopt==0.6.2
@@ -172,7 +172,7 @@ lockfile==0.12.2
     # via smriprep
 looseversion==1.3.0
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   datalad
     #   nipype
     #   niworkflows
@@ -199,8 +199,7 @@ matplotlib==3.9.4
 mdurl==0.1.2
     # via markdown-it-py
 migas==0.4.0
-    # via
-    #   fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 more-itertools==10.6.0
     # via
     #   datalad-next
@@ -215,7 +214,7 @@ networkx==3.4.2
     #   scikit-image
 nibabel==5.3.2
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   mapca
     #   nilearn
     #   nipype
@@ -233,27 +232,27 @@ nilearn==0.11.1
     #   tedana
 nipype==1.9.2
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   nireports
     #   niworkflows
     #   smriprep
 nireports==24.1.0
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 nitime==0.11
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 nitransforms==24.1.1
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   niworkflows
-niworkflows==1.13.4
+niworkflows==1.14.0
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   smriprep
 num2words==0.5.14
     # via pybids
 numpy==1.26.4
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   bokeh
     #   contourpy
     #   formulaic
@@ -284,7 +283,7 @@ osfclient==0.0.5
     # via datalad-osf
 packaging==24.2
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   bokeh
     #   datalad
     #   etelemetry
@@ -298,7 +297,7 @@ packaging==24.2
     #   smriprep
 pandas==2.2.3
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   bokeh
     #   codecarbon
     #   formulaic
@@ -326,15 +325,15 @@ prov==2.0.1
     # via nipype
 psutil==7.0.0
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   codecarbon
 puremagic==1.28
     # via nipype
 py-cpuinfo==9.0.0
     # via codecarbon
 pybids==0.19.0
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   nireports
     #   niworkflows
     #   smriprep
@@ -385,7 +384,7 @@ referencing==0.36.2
     #   jsonschema-specifications
 requests==2.32.3
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   codecarbon
     #   datalad
     #   etelemetry
@@ -407,8 +406,7 @@ rpds-py==0.23.1
 s3transfer==0.11.4
     # via boto3
 scikit-image==0.25.2
-    # via
-    #   niworkflows
+    # via niworkflows
 scikit-learn==1.6.1
     # via
     #   mapca
@@ -434,7 +432,7 @@ seaborn==0.13.2
 secretstorage==3.3.3
     # via keyring
 sentry-sdk==2.22.0
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 shellingham==1.5.4
     # via typer
 simplejson==3.20.1
@@ -445,7 +443,7 @@ six==1.17.0
     #   osfclient
     #   python-dateutil
 smriprep==0.17.0
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 sniffio==1.3.1
     # via
     #   anyio
@@ -457,10 +455,10 @@ svgutils==0.3.4
     #   nireports
     #   niworkflows
 tedana==23.0.2
-    # via fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 templateflow==24.2.2
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   nireports
     #   niworkflows
     #   smriprep
@@ -473,8 +471,7 @@ threadpoolctl==3.5.0
 tifffile==2025.2.18
     # via scikit-image
 toml==0.10.2
-    # via
-    #   fmriprep (pyproject.toml)
+    # via petprep (pyproject.toml)
 tornado==6.4.2
     # via bokeh
 tqdm==4.67.1
@@ -486,7 +483,7 @@ traits==7.0.2
     # via nipype
 transforms3d==0.4.2
     # via
-    #   fmriprep (pyproject.toml)
+    #   petprep (pyproject.toml)
     #   niworkflows
 typer==0.15.2
     # via codecarbon