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

.circleci/config.yml

@@ -4,14 +4,14 @@ _machine_defaults: &machine_defaults
     TZ: "/usr/share/zoneinfo/America/Los_Angeles"
     SCRATCH: "/scratch"
   machine:
-    image: ubuntu-2204:2023.04.2
+    image: default
     docker_layer_caching: true
   working_directory: /tmp/src/smriprep
   resource_class: large
 
 _python_defaults: &python_defaults
   docker:
-    - image: cimg/python:3.10.9
+    - image: cimg/python:3.12.2
       auth:
         username: $DOCKER_USER
         password: $DOCKER_PAT
@@ -115,8 +115,7 @@ jobs:
           name: Build Docker image
           no_output_timeout: 60m
           command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
+            pyenv local 3
             pip install hatch
             # Get version, update files.
             THISVERSION=$( hatch version )
@@ -139,8 +138,7 @@ jobs:
       - run:
           name: Check Docker image
           command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
+            pyenv local 3
             # Get version, update files.
             THISVERSION=$( hatch version )
             BUILT_VERSION=$( docker run --rm nipreps/smriprep:latest --version )
@@ -309,8 +307,7 @@ jobs:
       - run:
           name: Test smriprep-wrapper (Python 2)
           command: |
-            export PY2=$( pyenv versions | awk '/^\* 2/ { print $2 }' )
-            pyenv local $PY2
+            pyenv local 2.7
             echo -n "Python version: "
             python --version
             pip install --upgrade "pip<21"
@@ -322,8 +319,7 @@ jobs:
       - run:
           name: Test smriprep-wrapper (Python 3)
           command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
+            pyenv local 3
             echo -n "Python version: "
             python --version
             pip install --upgrade pip setuptools
@@ -440,10 +436,10 @@ jobs:
       - run: *pull_from_registry
       - restore_cache:
           keys:
-            - ds005-anat-v0-{{ .Branch }}-{{ epoch }}
-            - ds005-anat-v0-{{ .Branch }}
-            - ds005-anat-v0-master
-            - ds005-anat-v0-next
+            - ds005-anat-v1-{{ .Branch }}-{{ epoch }}
+            - ds005-anat-v1-{{ .Branch }}
+            - ds005-anat-v1-master
+            - ds005-anat-v1-next
       - restore_cache:
           keys:
             - testdata-v2-{{ .Branch }}-{{ epoch }}
@@ -500,7 +496,7 @@ jobs:
             rm -rf /tmp/ds005/work/reportlets
             rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
       - save_cache:
-          key: ds005-anat-v0-{{ .Branch }}-{{ epoch }}
+          key: ds005-anat-v1-{{ .Branch }}-{{ epoch }}
           paths:
             - /tmp/ds005/work
 
@@ -509,7 +505,8 @@ jobs:
           command: |
             mkdir -p /tmp/ds005/test
             find /tmp/ds005/derivatives -name "*" ! -path "*/figures*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
-            diff /tmp/src/smriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
+            sort /tmp/src/smriprep/.circleci/ds005_outputs.txt > /tmp/ds005/test/expected.out
+            diff /tmp/ds005/test/{expected,outputs}.out
             exit $?
       - store_artifacts:
           path: /tmp/ds005/derivatives
@@ -658,7 +655,8 @@ jobs:
           command: |
             mkdir -p /tmp/ds054/test
             find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
-            diff /tmp/src/smriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
+            sort /tmp/src/smriprep/.circleci/ds054_outputs.txt > /tmp/ds054/test/expected.out
+            diff /tmp/ds054/test/{expected,outputs}.out
             exit $?
       - run:
           name: Clean working directory

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
+# 2024-03-07 - mathiasg@stanford.edu - STY: ruff format smriprep [git-blame-ignore-rev]
+83a50d465145c6e8176c3f13d4673ed4e0bdb26f
 # 2023-11-21 - effigies@gmail.com - STY: ruff --fix smriprep [git-blame-ignore-rev]
 3a586cf46cb1bb963b93d9546f20273194d15de5
 # 2023-11-20 - effigies@gmail.com - STY: ruff --fix smriprep [git-blame-ignore-rev]

.github/workflows/pythonpackage.yml

@@ -109,13 +109,15 @@ jobs:
       run: python -m pip install "smriprep[tests]"
     - name: Run tests
       run: pytest -sv --doctest-modules --cov smriprep --pyargs smriprep
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       name: Submit to CodeCov
+      with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   style:
     if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - run: pipx run ruff smriprep
+    - run: pipx run ruff check smriprep
     - run: pipx run ruff format --diff smriprep

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       - id: check-toml
       - id: check-json
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.3.1
     hooks:
       - id: ruff
       - id: ruff-format

CHANGES.rst

@@ -1,3 +1,18 @@
+0.14.0 (March 11, 2024)
+=======================
+New feature release in the 0.14.x series.
+
+This release restores correct handling of cohort identifiers in templates.
+A feature release is warranted due to changes in the workflow structure.
+
+* FIX: Fetch templates during workflow construction (#418)
+* FIX: Re-add cohort identifier to template name (#416)
+* FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh) (#404)
+* FIX: Invert result of skull-strip check in auto mode (#402)
+* STY: Adopt ruff for linting and formatting (#397)
+* CHORE: Update ruff, ignore certain rules (#419)
+
+
 0.13.2 (December 08, 2023)
 ==========================
 Bug fix release in the 0.13.x series.

Dockerfile

@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2023 The NiPreps Developers
+# Copyright (c) The NiPreps Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,24 +23,26 @@
 # SOFTWARE.
 
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20230308
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
-# sMRIPrep wheel
+# Build wheel
 #
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/smriprep
-RUN python -m build /src/smriprep
+COPY . /src
+RUN python -m build /src
 
 #
 # Download stages
 #
 
 # Utilities for downloading packages
 FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2023.07.20"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     binutils \
@@ -67,19 +69,30 @@ RUN mkdir /opt/workbench && \
 
 # Micromamba
 FROM downloader as micromamba
+
+# Install a C compiler to build extensions when needed.
+# traits<6.4 wheels are not available for Python 3.11+, but build easily.
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2023.04.05"
+RUN echo "2024.03.08"
 RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
 COPY requirements.txt /tmp/requirements.txt
+WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
 
-ENV PATH="/opt/conda/envs/smriprep/bin:$PATH"
-RUN /opt/conda/envs/smriprep/bin/npm install -g svgo@^3.0 bids-validator@^1.13 && \
+# UV_USE_IO_URING for apparent race-condition (https://github.com/nodejs/node/issues/48444)
+# Check if this is still necessary when updating the base image.
+ENV PATH="/opt/conda/envs/smriprep/bin:$PATH" \
+    UV_USE_IO_URING=0
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
     rm -r ~/.npm
 
 #
@@ -179,7 +192,7 @@ ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
 # Installing SMRIPREP
-COPY --from=src /src/smriprep/dist/*.whl .
+COPY --from=src /src/dist/*.whl .
 RUN pip install --no-cache-dir $( ls *.whl )[telemetry,test]
 
 RUN find $HOME -type d -exec chmod go=u {} + && \

env.yml

@@ -2,29 +2,29 @@ name: smriprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated April 2023
+# Update this ~yearly; last updated March 2024
 dependencies:
-  - python=3.10
+  - python=3.11
   # Needed for svgo and bids-validator; consider moving to deno
-  - nodejs=18
+  - nodejs=20
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
+  - mkl=2023.2
   - mkl-service=2.4
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
   - scipy=1.11
   - matplotlib=3.8
-  - pandas=2.1
+  - pandas=2.2
   - h5py=3.10
   # Dependencies compiled against numpy, best to stick with conda
   - scikit-image=0.22
-  - scikit-learn=1.3
+  - scikit-learn=1.4
   # Utilities
-  - graphviz=6.0
+  - graphviz=9.0
   - pandoc=3.1
   # Workflow dependencies: ANTs
-  - ants=2.5.0
-  # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
+  - ants=2.5
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
   - fsl-bet2=2111.4
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib >= 2.2.0",
     "nibabel >= 4.0.1",
     "nipype >= 1.7.0",
-    "niworkflows >= 1.8.0",
+    "niworkflows >= 1.10.1",
     "numpy",
     "packaging",
     "pybids >= 0.11.1",
@@ -138,6 +138,8 @@ source = [
 
 [tool.ruff]
 line-length = 99
+
+[tool.ruff.lint]
 extend-select = [
   "F",
   "E",
@@ -161,11 +163,16 @@ extend-select = [
   "PT",
   "Q",
 ]
+extend-ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
+]
 
-[tool.ruff.flake8-quotes]
+[tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"
 
-[tool.ruff.extend-per-file-ignores]
+[tool.ruff.lint.extend-per-file-ignores]
 "*/test_*.py" = ["S101"]
 
 [tool.ruff.format]