Merge branch 'master' into fix/dup_bids-id_force-syn

Author: oesteban

.github/workflows/build-test-publish.yml

@@ -2,9 +2,20 @@ name: CI
 
 on:
   push:
+    branches:
+      - master
+      - main
+      - maint/*
+    tags:
+      - '*'
   pull_request:
+    branches:
+      - master
+      - main
+      - maint/*
   schedule:
-    - cron: 0 0 * * 0
+    # 9am EST / 10am EDT Mondays
+    - cron: 0 14 * * 0
   # Allow job to be triggered manually from GitHub interface
   workflow_dispatch:
 
@@ -49,18 +60,32 @@ jobs:
       AFNI_IMSAVE_WARNINGS: NO
       AFNI_TTATLAS_DATASET: /opt/afni/atlases
       AFNI_PLUGINPATH: /opt/afni/plugins
+      MARKS: ${{ matrix.marks }}
+      DEPENDS: ${{ matrix.dependencies }}
     strategy:
-      max-parallel: 6
+      fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        marks: ["not slow"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        dependencies:  ["latest", "pre"]
+        marks: ["fast"]
         include:
           - python-version: "3.9"
-            marks: "slow and not veryslow"
+            dependencies: "min"
+            marks: "fast"
+          - python-version: "3.9"
+            dependencies: "latest"
+            marks: "slow"
           - python-version: "3.12"
+            dependencies: "latest"
             marks: "veryslow"
+        exclude:
+          - python-version: "3.9"
+            dependencies: "pre"
+          - python-version: "3.10"
+            dependencies: "pre"
 
     steps:
+    - uses: actions/checkout@v4
     - uses: actions/cache@v4
       with:
         path: /var/lib/apt
@@ -89,18 +114,22 @@ jobs:
           curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \
           tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
         fi
+        ls -l ${AFNI_HOME}
+        echo "PATH=${AFNI_HOME}:$PATH" | tee -a $GITHUB_ENV
 
     - name: Git settings (pacify DataLad)
       run: |
         git config --global user.name 'NiPreps Bot'
         git config --global user.email '[email protected]'
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v5
     - name: Set up Python ${{ matrix.python-version }}
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         auto-activate-base: true
         python-version: ${{ matrix.python-version }}
-        channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
+        channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge,defaults
     - uses: actions/cache@v4
       id: conda
       env:
@@ -110,22 +139,15 @@ jobs:
           ~/conda_pkgs_dir
           /home/runner/.cache/pip
         key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
-        restore-keys: |
-          python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
     - name: Install DataLad
       run: |
-        conda install git-annex=*=alldep* pip
-        pip install datalad datalad-osf
+        conda install git-annex=*=alldep*
+        uv tool install datalad --with=datalad-next --with=datalad-osf
+        uv tool install datalad-osf --with=datalad-next
     - name: Install fsl and ANTs
       run: |
-        conda install fsl-fugue fsl-topup ants
-    - uses: actions/checkout@v4
-    - name: Install dependencies
-      timeout-minutes: 5
-      run: |
-        pip install .[tests]
-
-
+        # libitk 5.4.1+ segfaults with ants 2.5.4
+        conda install fsl-fugue fsl-topup ants 'libitk=5.4.0'
     - uses: actions/cache@v4
       with:
         path: ~/.cache/templateflow
@@ -134,7 +156,7 @@ jobs:
           tf-cache-
     - name: Get TemplateFlow's required objects
       run: |
-        python tools/cache_templateflow.py
+        uv run tools/cache_templateflow.py
 
     - uses: actions/cache@v4
       with:
@@ -198,25 +220,23 @@ jobs:
         mkdir -p $( dirname $FS_LICENSE )
         echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE
 
-    - name: Run pytest with coverage
+    - name: Install tox
       run: |
-        export PATH=${AFNI_HOME}:$PATH
-        export FSLDIR=${CONDA_PREFIX}
-        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
-          --durations=20 --durations-min=10 -m "$MARKS"
-      env:
-        MARKS: ${{ matrix.marks }}
+        uv tool install tox --with=tox-uv --with=tox-gh-actions
+    - name: Show tox config
+      run: tox c
+    - name: Run tox
+      run: tox -v --exit-and-dump-after 1200
 
-    - uses: codecov/codecov-action@v4
+    - uses: codecov/codecov-action@v5
       with:
-        file: cov.xml
         token: ${{ secrets.CODECOV_TOKEN }}
       if: ${{ always() }}
 
   publish:
     name: Publish released package to pypi.org
     environment: release-pypi
-    if: github.event.action == 'published'
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
     needs: [build-package, test]
     permissions:

.maint/update_requirements.py

@@ -1,3 +1,34 @@
+2.12.0 (March 21, 2025)
+=======================
+Feature release in the 2.12.x series.
+
+This release migrates from the deprecated ``niworkflows.reporting``
+module to the ``nireports`` package.
+
+* FIX: AttributeError for _ApplyCoeffsFieldInputSpec (#481)
+* ENH: Allow running SyN SDC without using prior (#480)
+* ENH: Allow estimated and fallback TotalReadoutTime (#477)
+* RF: Transition from niworkflows reporting interfaces (#473)
+* DOC: Fix broken link [skip ci] (#482)
+* MNT: Add `defaults` to `conda` channels in `build-test-publish` GHA (#474)
+* MNT: Update `niworkflows` version to 1.11.0 (#478)
+
+
+2.11.0 (December 18, 2024)
+==========================
+Feature release in the 2.11.x series.
+
+This release supports numpy 2 and Python 3.13.
+
+* FIX: Normalize BIDS-URIs to subject-relative (#458)
+* FIX: Only fit high-frequency spline for SyN-SDC (#457)
+* ENH: Allow Jacobian correction to be toggled on/off (#462)
+* ENH: Dilate fmap and bold masks during coregistration (#463)
+* TEST: Clear registry consistently to avoid order dependency (#464)
+* DOC: Plot correct workflow in init_syn_preprocessing_wf docstring (#460)
+* CI: Drop CircleCI, using GHA only (#459)
+
+
 2.10.0 (July 04, 2024)
 ======================
 Feature release in the 2.10.x series.

CHANGES.rst

@@ -48,6 +48,7 @@
     "nilearn",
     "nipy",
     "nitime",
+    "nireports",
     "pandas",
     "seaborn",
     "skimage",

docs/conf.py

@@ -76,7 +76,7 @@ Direct B0 mapping sequences
 Some MR schemes such as :abbr:`SEI (spiral-echo imaging)` can directly
 reconstruct an estimate of *the fieldmap in Hz*, :math:`V(i,j,k)`.
 These *fieldmaps* are described with more detail `here
-<https://cni.stanford.edu/wiki/GE_Processing#Fieldmaps>`__.
+<https://cni.su.domains/wiki/index.php?title=GE_Processing#Fieldmaps>`__.
 
 .. _sdc_phasediff :
 

docs/methods.rst

@@ -18,4 +18,3 @@ sphinx >= 7.2.2
 sphinx-argparse
 sphinxcontrib-apidoc
 templateflow
-traits < 6.4

docs/requirements.txt

@@ -2,24 +2,28 @@ name: sdcflows
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated April 2023
+# Update this ~yearly; last updated Mar 2025
 dependencies:
-  - python=3.10
+  - python=3.12
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
-  - mkl-service=2.4
+  - mkl=2024.2.2
+  - mkl-service=2.4.2
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
-  - scipy=1.11
-  - matplotlib=3.8
-  - pandas=2.1
-  - h5py=3.8
+  - scipy=1.15
+  - matplotlib=3.9
+  - pandas=2.2
+  - h5py=3.13
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.22
+  - scikit-image=0.25
   # Utilities
-  - graphviz=6.0
+  - graphviz=11.0
   # Workflow dependencies: ANTs
-  - ants=2.4.4
-  # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
-  - fsl-fugue=2201.2
-  - fsl-topup=2203.1
+  - ants=2.5
+  # 5.4.1 and 5.4.2 cause segfaults with ants
+  # Try to remove this ASAP
+  # https://github.com/conda-forge/ants-feedstock/issues/19
+  - libitk=5.4.0
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
+  - fsl-fugue=2201.5
+  - fsl-topup=2203.5