Merge remote-tracking branch 'upstream/master' into enh/fs_long

Author: bpinsard

.circleci/config.yml

@@ -458,6 +458,9 @@ jobs:
           name: Run anatomical workflow on ds005
           no_output_timeout: 2h
           command: |
+            # Remove part of FreeSurfer output to ensure that at least
+            # some of recon-all is attempted
+            rm /tmp/ds005/freesurfer/sub-01/mri/ribbon.mgz
             bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph
       - run:
           name: Combine coverage

.git-blame-ignore-revs

@@ -0,0 +1,6 @@
+# 2023-11-21 - [email protected] - STY: ruff --fix smriprep [git-blame-ignore-rev]
+3a586cf46cb1bb963b93d9546f20273194d15de5
+# 2023-11-20 - [email protected] - STY: ruff --fix smriprep [git-blame-ignore-rev]
+c5e8b6b8ddb69284a4cba58e2512b299f1e29464
+# 2023-11-20 - [email protected] - STY: ruff format smriprep [git-blame-ignore-rev]
+8d62c0f3f3c6a911b1dfe2e9a2016b8de7da051a

.github/workflows/pythonpackage.yml

@@ -88,7 +88,7 @@ jobs:
         path: dist/
       if: matrix.install == 'sdist' || matrix.install == 'wheel'
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Select archive
@@ -112,9 +112,10 @@ jobs:
     - uses: codecov/codecov-action@v3
       name: Submit to CodeCov
 
-  flake8:
+  style:
     if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - run: pipx run flake8 smriprep
+    - run: pipx run ruff smriprep
+    - run: pipx run ruff format --diff smriprep

.pre-commit-config.yaml

@@ -10,17 +10,8 @@ repos:
       - id: check-added-large-files
       - id: check-toml
       - id: check-json
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
     hooks:
-      - id: flake8
-  # - repo: https://github.com/psf/black
-  #   rev: 23.1.0
-  #   hooks:
-  #     - id: black
-  #       files: ^smriprep/|^wrapper/
-  # - repo: https://github.com/pycqa/isort
-  #   rev: 5.12.0
-  #   hooks:
-  #     - id: isort
-  #       files: ^smriprep/|^wrapper/
+      - id: ruff
+      - id: ruff-format

CHANGES.rst

@@ -1,3 +1,29 @@
+0.13.2 (December 08, 2023)
+==========================
+Bug fix release in the 0.13.x series.
+
+This release fixes a check for skull-stripping in auto mode, and adds
+missing fsLR atlases to the Python package resources.
+The Docker image has also been updated to ensure FreeSurfer can be run
+from the sMRIPrep container.
+
+With thanks to Patrick Sadil for reports and fixes.
+
+* ENH: Add 59k atlases (#405)
+* FIX: Repair FreeSurfer dependency in Dockerfile (tcsh) (#404)
+* FIX: Invert result of skull-strip check in auto mode (#402)
+
+
+0.13.1 (November 21, 2023)
+==========================
+Bug fix release in the 0.13.x series.
+
+This release fixes a bug with a workflow connection that was not properly
+named, and which would cause an error when T2-weighted images were provided.
+
+* FIX: T1w_preproc -> t1w_preproc (#399)
+
+
 0.13.0 (November 20, 2023)
 ==========================
 New feature release in the 0.13.x series.

Dockerfile

@@ -93,7 +93,7 @@ ENV DEBIAN_FRONTEND="noninteractive" \
     LC_ALL="en_US.UTF-8"
 
 # Some baseline tools
-# bc is needed for FreeSurfer
+# bc, tcsh are needed for FreeSurfer
 # libglu1-mesa is needed for Connectome Workbench
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -105,6 +105,7 @@ RUN apt-get update && \
                     libglu1-mesa \
                     lsb-release \
                     netbase \
+                    tcsh \
                     xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY: help docker
+.PHONY: help docker .git-blame-ignore-revs
 .DEFAULT: help
 
 tag="latest"
@@ -15,3 +15,9 @@ docker:
 	--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
 	--build-arg VCS_REF=`git rev-parse --short HEAD` \
 	--build-arg VERSION=`python setup.py --version` .
+
+
+.git-blame-ignore-revs:
+	git log --grep "\[git-blame-ignore-rev\]" --pretty=format:"# %ad - %ae - %s%n%H" --date short \
+		> .git-blame-ignore-revs
+	echo >> .git-blame-ignore-revs

pyproject.toml

@@ -99,7 +99,6 @@ version-file = "smriprep/_version.py"
 
 [tool.black]
 line-length = 99
-target-version = ['py39']
 skip-string-normalization = true
 
 [tool.isort]
@@ -136,3 +135,38 @@ source = [
     "smriprep/",
     "*/site-packages/smriprep",
 ]
+
+[tool.ruff]
+line-length = 99
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
+]
+
+[tool.ruff.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+
+[tool.ruff.format]
+quote-style = "single"

smriprep/__about__.py

@@ -27,17 +27,15 @@
 try:
     from ._version import __version__
 except ImportError:  # pragma: no cover
-    __version__ = "0+unknown"
+    __version__ = '0+unknown'
 
-__copyright__ = "Copyright 2019, Center for Reproducible Neuroscience, Stanford University"
+__copyright__ = 'Copyright 2019, Center for Reproducible Neuroscience, Stanford University'
 __credits__ = [
-    "Oscar Esteban",
-    "Chris Gorgolewski",
-    "Christopher J. Markiewicz",
-    "Russell A. Poldrack",
+    'Oscar Esteban',
+    'Chris Gorgolewski',
+    'Christopher J. Markiewicz',
+    'Russell A. Poldrack',
 ]
-__url__ = "https://github.com/nipreps/smriprep"
+__url__ = 'https://github.com/nipreps/smriprep'
 
-DOWNLOAD_URL = "https://github.com/nipreps/{name}/archive/{ver}.tar.gz".format(
-    name=__package__, ver=__version__
-)
+DOWNLOAD_URL = f'https://github.com/nipreps/{__package__}/archive/{__version__}.tar.gz'

smriprep/__init__.py

@@ -15,7 +15,7 @@
 )
 
 __all__ = [
-    "__copyright__",
-    "__credits__",
-    "__version__",
+    '__copyright__',
+    '__credits__',
+    '__version__',
 ]