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

Author: bpinsard

.circleci/config.yml

@@ -442,6 +442,7 @@ jobs:
           keys:
             - ds005-anat-v0-{{ .Branch }}-{{ epoch }}
             - ds005-anat-v0-{{ .Branch }}
+            - ds005-anat-v0-master
             - ds005-anat-v0-next
       - restore_cache:
           keys:

.circleci/nipype.cfg

@@ -1,4 +1,4 @@
 [execution]
 stop_on_first_crash = true
 poll_sleep_duration = 0.01
-hash_method = content
+hash_method = content

.gitattributes

@@ -1 +1,2 @@
 smriprep/_version.py export-subst
+*.gii binary

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/pythonpackage.yml

@@ -27,7 +27,7 @@ jobs:
       commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
     steps:
       - name: Get repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
       - name: Print head git commit message
@@ -37,7 +37,7 @@ jobs:
             COMMIT_MSG=$(git show -s --format=%s)
           fi
           echo $COMMIT_MSG
-          echo "::set-output name=commit_message::$COMMIT_MSG"
+          echo "commit_message=$COMMIT_MSG" >> $GITHUB_OUTPUT
         env:
           COMMIT_MSG: ${{ github.event.head_commit.message }}
 
@@ -46,7 +46,7 @@ jobs:
     if: "!contains(needs.check_if_skip.outputs.commit_message, '[skip ci]')"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Display Python version
@@ -65,7 +65,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         install: [repo]
         include:
           - python-version: "3.11"
@@ -79,7 +79,7 @@ jobs:
       INSTALL_TYPE: ${{ matrix.install }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       if: matrix.install == 'repo' || matrix.install == 'editable'
     - name: Fetch packages
       uses: actions/download-artifact@v3
@@ -116,5 +116,5 @@ jobs:
     if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: pipx run flake8 smriprep

.gitignore

@@ -1,4 +1,4 @@
-# Auto-generated by .maint/make_gitignore on Fri May 19 03:22:33 PM EDT 2023
+# Auto-generated by .maint/make_gitignore on Wed Nov  8 04:05:04 PM EST 2023
 # setuptools_scm
 _version.py
 
@@ -311,4 +311,3 @@ Icon
 Network Trash Folder
 Temporary Items
 .apdisk
->>>>>>> upstream/master

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
-exclude: ".*/data/.*"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
       - id: trailing-whitespace
-        exclude: .gitignore
+        exclude: '.gitignore|.*\.gii$'
       - id: end-of-file-fixer
+        exclude: 'data/itkIdentityTransform.txt|\.svg$'
       - id: check-yaml
       - id: check-added-large-files
       - id: check-toml

.zenodo.json

@@ -52,6 +52,18 @@
       "name": "Feczko, Eric",
       "orcid": "0000-0003-1337-5517",
       "type": "Researcher"
+    },
+    {
+      "affiliation": "Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, MD, USA",
+      "name": "Sadil, Patrick",
+      "orcid": "0000-0003-4141-1343",
+      "type": "Researcher"
+    },
+    {
+      "affiliation": "Neurospin, CEA, Université Paris-Saclay, CNRS, 91191 Gif-sur-Yvette, France",
+      "name": "Papadopoulos Orfanos, Dimitri",
+      "orcid": "0000-0002-1242-8990",
+      "type": "Researcher"
     }
   ],
   "keywords": [

CHANGES.rst

@@ -1,3 +1,53 @@
+0.13.0 (November 20, 2023)
+==========================
+New feature release in the 0.13.x series.
+
+This release adds support for MSM-Sulc, improving the alignment of subject
+surfaces to the fsLR template. This process is enabled by default, but may
+be disabled with the ``--no-msm`` flag.
+
+The ``--fast-track`` flag has been deprecated in favor of a more flexible
+``--derivatives`` flag. This flag can be used to specify one or more
+directories to search for derivatives. Derivatives found in these
+directories can be used to skip corresponding workflows. For derivatives
+that can be deterministically generated from other derivatives, sMRIPrep
+will regenerate the derivatives to avoid inconsistencies.
+
+This supports the 23.2.x series of fMRIPrep, which introduces a ``--level``
+flag to control the level of processing. This feature is not currently
+available in sMRIPrep, but will be in a future release. To preview this
+functionality, use fMRIPrep's ``--anat-only`` flag to run only structural
+workflows.
+
+* FIX: Add missing fsLR reg sphere to io_spec (#382)
+* FIX: Invert sulcal depth metric before passing to MSM, use HCP atlas files (#383)
+* FIX: Update surfaces with fsnative2t1w_xfm (#384)
+* FIX: Add surface-modify-sphere call to catch potential sphere elongation (#375)
+* ENH: Add T2w/FLAIR usage to boilerplate (#392)
+* ENH: Annotate mris_expand with thread usage (#386)
+* ENH: Add sphere registration to fit workflow, check for precomputed (#370)
+* ENH: Save msm registration sphere as desc-msm_sphere.surf.gii (#365)
+* ENH: Add Multimodal Surface Matching (#358)
+* ENH: Run pytest on CircleCI (#364)
+* ENH: Separate surfaces and morphometrics into standalone outputs (#359)
+* RF: Split template and fsLR resampling and sinking into isolated workflows (#388)
+* RF: Replace most of anat_ribbon_wf with a Python function (#363)
+* RF: Break up surface workflows for easier mix-and-match in fMRIPrep (#360)
+* TEST: Add smoke tests for main anatomical workflows (#390)
+* TEST: Add sloppy MSM configuration for use in debugging/CI (#366)
+* DOC: http:// → https:// (#377)
+* DOC: Fix misspelling found by codespell (#378)
+* MNT: Remove AFNI from smriprep docker container (#387)
+* MNT: Use a set literal, not a list literal (#379)
+* MNT: Update installation environment (#361)
+* MNT: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image (#357)
+* MNT: Infrastructure updates (#351)
+* MNT: fix flake8 warning (#349)
+* MNT: apply pyupgrade suggestions (#348)
+* MNT: fix typos found by codespell (#346)
+* MNT: Python 3.11 should be supported (#347)
+
+
 0.12.2 (August 16, 2023)
 ========================
 Bug-fix release in the 0.12.x series.

CONTRIBUTING.md

@@ -223,7 +223,7 @@ You're awesome. :wave::smiley:
 
 [link_git]: https://git-scm.com/
 [link_handbook]: https://guides.github.com/introduction/git-handbook/
-[link_swc_intro]: http://swcarpentry.github.io/git-novice/
+[link_swc_intro]: https://swcarpentry.github.io/git-novice/
 
 [writing_formatting_github]: https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github
 [markdown]: https://daringfireball.net/projects/markdown