Merge pull request #324 from nipreps/rel/23.1.0

REL: 23.1.0

.github/workflows/pytest.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/style.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
 
     steps:
     - uses: actions/checkout@v3

CHANGES.md

@@ -1,4 +1,4 @@
-23.1.0 (TBD)
+23.1.0 (November 22, 2023)
 ============
 The next minor release of *NiBabies*, this release includes a number of new goodies, including:
 
@@ -17,6 +17,9 @@ An option to determine and exclude high-variance voxels from being projected to
 ### Single anatomical processing
 Running *NiBabies* is now less restrictive, and will still process data missing either a T1w / T2w image. However, for best results, it is recommended to collect and include both for processing.
 
+### Anat-specific derivatives inputs
+Previous, *NiBabies* expected input from the `--derivatives` flag to be in T1w space, using the entity `space-orig`. This has now been changed to support derivatives in either T1w or T2w space. For more information, please see https://nibabies.readthedocs.io/en/23.1.0/faqs.html#leveraging-precomputed-results
+
 
 ## Full Changelog
   * CI: Purge codecov python package (#282)
@@ -35,6 +38,7 @@ Running *NiBabies* is now less restrictive, and will still process data missing
   * FIX: Ensure age is extracted from sessions file (#291)
   * FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (#298)
   * FIX: Recify "goodvoxels" surface projection (#301)
+  * FIX: Connect derivatives mask to mcribs recon (#323)
   * MAINT: Drop TemplateFlowSelect patches (#290)
 
 23.0.0 (January 23, 2023)

pyproject.toml

@@ -12,31 +12,31 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Image Recognition",
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
 ]
 license = {file = "LICENSE"}
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     'importlib_resources; python_version < "3.9"',
     "nibabel >= 5.0.0",
     "nipype >= 1.8.5",
     "nitime",
-    "nitransforms >= 21.0.0",
-    "niworkflows >= 1.8.1",
+    "nitransforms >= 23.0.1",
+    "niworkflows >= 1.9.0",
 #    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy >= 1.21.0",
     "packaging",
     "pandas",
     "psutil >= 5.4",
     "pybids >= 0.15.0",
     "requests",
-    "sdcflows >= 2.5.1",
+    "sdcflows ~= 2.5.2",
 #    "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-    "smriprep >= 0.12.1",
+    "smriprep ~= 0.12.1",
 #    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
-    "tedana ~= 0.0.12",
+    "tedana >= 0.0.12",
     "templateflow >= 0.6",
     "toml",
 ]
@@ -100,7 +100,6 @@ version-file = "nibabies/_version.py"
 
 [tool.black]
 line-length = 99
-target-version = ['py39']
 skip-string-normalization = true
 
 [tool.isort]

requirements.txt

@@ -50,6 +50,8 @@ idna==3.4
     # via requests
 imageio==2.31.1
     # via scikit-image
+importlib-resources==6.1.1
+    # via niworkflows
 indexed-gzip==1.7.1
     # via smriprep
 interface-meta==1.3.0
@@ -126,12 +128,12 @@ nipype==1.8.6
     #   smriprep
 nitime==0.10.1
     # via nibabies (pyproject.toml)
-nitransforms==23.0.0
+nitransforms==23.0.1
     # via
     #   nibabies (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.8.1
+niworkflows==1.9.0
     # via
     #   nibabies (pyproject.toml)
     #   sdcflows
@@ -258,7 +260,7 @@ scipy==1.11.1
     #   scikit-learn
     #   sdcflows
     #   tedana
-sdcflows==2.5.1
+sdcflows==2.5.2
     # via nibabies (pyproject.toml)
 seaborn==0.12.2
     # via niworkflows
@@ -268,7 +270,7 @@ six==1.16.0
     # via
     #   isodate
     #   python-dateutil
-smriprep==0.12.1
+smriprep==0.12.2
     # via nibabies (pyproject.toml)
 sqlalchemy==2.0.17
     # via pybids