Merge tag '24.0.0'

24.0.0 (June 17, 2024) New feature release in the 24.0.x series. This release is an incremental improvement on 23.2.x, with some fixes for bugs discovered in the updated workflow. New features include separation of HTML reports by session for subjects with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability with less typical FreeSurfer directories, such as those generated by longitudinal FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow the recommendations of recent versions of BIDS. With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo and Wang Hao-Ting for their contributions! * FIX: Add "double" type to allowed DisplacementFieldTransform (#3287) * FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256) * FIX: Ensure proper templates are retrieved with sloppy (#3251) * FIX: Delete summary from functional report when separated by sessions (#3223) * FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215) * FIX: Re-enable anat fasttrack for dataset without t1w (#3202) * ENH: Use BIDSURI in init_ds_boldmask_wf (#3297) * ENH: Add templateflow to DatasetLinks (#3267) * ENH: Track proximal sources of functional GIFTIs (#3263) * ENH: Support named derivative paths (#3264) * ENH: Track Sources for standard-space outputs (#3262) * ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142) * ENH: Use BIDS URIs to track Sources in sidecars (#3255) * ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236) * ENH: Add metadata for motion parameters (#3245) * ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191) * ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208) * RF: Fix ITK warp conversion to nitransforms format (#3300) * RF: Load report assembler from nireports (#3177) * DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205) * TST: Update test to reflect new report generation behavior (#3210) * STY: Manual conversions to f-strings (#3241) * STY: Apply ruff/pyupgrade rule UP031 (#3280) * STY: Lint and style check full repository (#3221) * STY: Adopt ruff for linting and formatting (#3206) * MNT: Pin libitk 5.3 and note dependencies (#3298) * MNT: Upgrade ruff pre-commit, add fixing checks (#3283) * MNT: Complete transition from flake8/black to ruff (#3279) * MNT: Apply Repo-Review suggestions (#3194) * MNT: Verbatim copy of Apache license 2.0 (#3259) * MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234) * MNT: Drop copyright year, unused dunder fields (#3247) * MNT: Update environment pins (#3226) * MNT: Bump codecov/codecov-action from 3 to 4 (#3219) * DOCKER: Restore mincinfo binary (#3249) * CI: Move to new circle machine tags (#3248) * CI: Avoid ruff warning (#3244) * CI: Pass ruff tests (#3243)
nipreps · Jun 17, 2024 · a85821e · a85821e
2 parents 8748745 + 8731708
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diff --git a/.mailmap b/.mailmap
@@ -5,7 +5,7 @@ Alejandro de la Vega <aleph4@gmail.com> delavega4
 Anibal Sólon Heinsfeld <anibalsolon@gmail.com>
 Asier Erramuzpe <asier.erramuzpe@gmail.com>
 Basile Pinsard <basile.pinsard@umontreal.ca>
-Basile Pinsard <basile.pinsard@umontreal.ca> basile <basile.pinsard@gmail.com>
+Basile Pinsard <basile.pinsard@umontreal.ca> <basile.pinsard@gmail.com>
 Basile Pinsard <basile.pinsard@umontreal.ca> <bpinsard@imed.jussieu.fr>
 Blaise Frederick <blaise.frederick@gmail.com>
 Blaise Frederick <blaise.frederick@gmail.com> bbfrederick <blaise.frederick@gmail.com>
@@ -60,6 +60,7 @@ Pablo Velasco <pablo.velasco@nyu.edu>
 Rastko Ciric <rc042010@mymail.pomona.edu>
 Rastko Ciric <rc042010@mymail.pomona.edu> <rastko@stanford.edu>
 Rastko Ciric <rc042010@mymail.pomona.edu> <rciric@users.noreply.github.com>
+Rémi Gau <remi_gau@hotmail.com>
 Romain Valabregue <romain.valabregue@upmc.fr>
 Ross Blair <rblair2@stanford.edu>
 Ross Blair <rblair2@stanford.edu> <rosswilsonblair@gmail.com>

diff --git a/.maint/CONTRIBUTORS.md b/.maint/CONTRIBUTORS.md
@@ -20,6 +20,7 @@ Before every release, unlisted contributors will be invited again to add their n
 | Feingold          | Franklin     |  | 0000-0002-6533-2909 | Department of Psychology, Stanford University                                                                                                |
 | Finc              | Karolina     |  | 0000-0002-0157-030X | Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń                                                    |
 | Frederick         | Blaise B.    |  | 0000-0001-5832-5279 | McLean Hospital Brain Imaging Center, MA, USA                                                                                                |
+| Gau               | Rémi        |  | 0000-0002-1535-9767 | Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada             |
 | Groen             | Iris I. A.   |  | 0000-0002-5536-6128 | Department of Psychology, New York University, NY, USA                                                                                       |
 | Gomez             | Daniel E. P. |  | 0000-0001-8635-021X | Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen                                                            |
 | Ghosh             | Satrajit S.  |  | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA                                                                                          |

diff --git a/.zenodo.json b/.zenodo.json
@@ -14,12 +14,6 @@
       "orcid": "0000-0003-3030-6580",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Florey Institute of Neuroscience and Mental Health",
-      "name": "Smith, Robert E.",
-      "orcid": "0000-0003-3636-4642",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Neurospin, CEA",
       "name": "Papadopoulos, Dimitri",
@@ -32,6 +26,12 @@
       "orcid": "0000-0002-0157-030X",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Florey Institute of Neuroscience and Mental Health",
+      "name": "Smith, Robert E.",
+      "orcid": "0000-0003-3636-4642",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Feingold, Franklin",
@@ -44,22 +44,16 @@
       "orcid": "0000-0001-6377-3885",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Montreal Neurological Institute, McGill University",
-      "name": "Bhagwat, Nikhil",
-      "orcid": "0000-0001-6073-7141",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
       "orcid": "0000-0003-3456-2493",
       "type": "Researcher"
     },
     {
-      "affiliation": "Department of Psychology, New York University",
-      "name": "Benson, Noah C.",
-      "orcid": "0000-0002-2365-8265",
+      "affiliation": "Montreal Neurological Institute, McGill University",
+      "name": "Bhagwat, Nikhil",
+      "orcid": "0000-0001-6073-7141",
       "type": "Researcher"
     },
     {
@@ -80,16 +74,22 @@
       "orcid": "0000-0001-5504-8579",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Department of Psychology, New York University",
+      "name": "Benson, Noah C.",
+      "orcid": "0000-0002-2365-8265",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Machine Learning Team, National Institute of Mental Health, USA",
       "name": "Nielson, Dylan M.",
       "orcid": "0000-0003-4613-6643",
       "type": "Researcher"
     },
     {
-      "affiliation": "Child Mind Institute",
-      "name": "Heinsfeld, Anibal S.",
-      "orcid": "0000-0002-2050-0614",
+      "affiliation": "Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada",
+      "name": "Gau, Rémi",
+      "orcid": "0000-0002-1535-9767",
       "type": "Researcher"
     },
     {
@@ -105,15 +105,9 @@
       "type": "Researcher"
     },
     {
-      "affiliation": "Department of Psychology, University of California, Berkeley",
-      "name": "Lurie, Daniel J.",
-      "orcid": "0000-0001-8012-6399",
-      "type": "Researcher"
-    },
-    {
-      "affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
-      "name": "Erramuzpe, Asier",
-      "orcid": "0000-0002-9402-2184",
+      "affiliation": "Child Mind Institute",
+      "name": "Heinsfeld, Anibal S.",
+      "orcid": "0000-0002-2050-0614",
       "type": "Researcher"
     },
     {
@@ -123,9 +117,15 @@
       "type": "Researcher"
     },
     {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Wexler, Joseph B.",
-      "orcid": "0000-0001-6424-8740",
+      "affiliation": "Department of Psychology, University of California, Berkeley",
+      "name": "Lurie, Daniel J.",
+      "orcid": "0000-0001-8012-6399",
+      "type": "Researcher"
+    },
+    {
+      "affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
+      "name": "Erramuzpe, Asier",
+      "orcid": "0000-0002-9402-2184",
       "type": "Researcher"
     },
     {
@@ -140,6 +140,12 @@
       "orcid": "0000-0002-5740-9451",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Wexler, Joseph B.",
+      "orcid": "0000-0001-6424-8740",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Ma, Feilong",
@@ -298,16 +304,16 @@
     }
   ],
   "creators": [
-    {
-      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
-      "name": "Esteban, Oscar",
-      "orcid": "0000-0001-8435-6191"
-    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Markiewicz, Christopher J.",
       "orcid": "0000-0002-6533-164X"
     },
+    {
+      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
+      "name": "Esteban, Oscar",
+      "orcid": "0000-0001-8435-6191"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Goncalves, Mathias",

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,60 @@
+24.0.0 (June 17, 2024)
+======================
+
+New feature release in the 24.0.x series.
+
+This release is an incremental improvement on 23.2.x, with some
+fixes for bugs discovered in the updated workflow.
+
+New features include separation of HTML reports by session for subjects
+with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability
+with less typical FreeSurfer directories, such as those generated by longitudinal
+FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow
+the recommendations of recent versions of BIDS.
+
+With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo
+and Wang Hao-Ting for their contributions!
+
+* FIX: Add "double" type to allowed DisplacementFieldTransform (#3287)
+* FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256)
+* FIX: Ensure proper templates are retrieved with sloppy (#3251)
+* FIX: Delete summary from functional report when separated by sessions (#3223)
+* FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215)
+* FIX: Re-enable anat fasttrack for dataset without t1w (#3202)
+* ENH: Use BIDSURI in init_ds_boldmask_wf (#3297)
+* ENH: Add templateflow to DatasetLinks (#3267)
+* ENH: Track proximal sources of functional GIFTIs (#3263)
+* ENH: Support named derivative paths (#3264)
+* ENH: Track Sources for standard-space outputs (#3262)
+* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142)
+* ENH: Use BIDS URIs to track Sources in sidecars (#3255)
+* ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236)
+* ENH: Add metadata for motion parameters (#3245)
+* ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191)
+* ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208)
+* RF: Fix ITK warp conversion to nitransforms format (#3300)
+* RF: Load report assembler from nireports (#3177)
+* DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205)
+* TST: Update test to reflect new report generation behavior (#3210)
+* STY: Manual conversions to f-strings (#3241)
+* STY: Apply ruff/pyupgrade rule UP031 (#3280)
+* STY: Lint and style check full repository (#3221)
+* STY: Adopt ruff for linting and formatting (#3206)
+* MNT: Pin libitk 5.3 and note dependencies (#3298)
+* MNT: Upgrade ruff pre-commit, add fixing checks (#3283)
+* MNT: Complete transition from flake8/black to ruff (#3279)
+* MNT: Apply Repo-Review suggestions (#3194)
+* MNT: Verbatim copy of Apache license 2.0 (#3259)
+* MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234)
+* MNT: Drop copyright year, unused dunder fields (#3247)
+* MNT: Update environment pins (#3226)
+* MNT: Bump codecov/codecov-action from 3 to 4 (#3219)
+* DOCKER: Restore mincinfo binary (#3249)
+* CI: Move to new circle machine tags (#3248)
+* CI: Avoid ruff warning (#3244)
+* CI: Pass ruff tests (#3243)
+
+
 23.2.3 (May 20, 2024)
 =====================
 Bug fix release in the 23.2.x series.

diff --git a/env.yml b/env.yml
@@ -16,13 +16,13 @@ dependencies:
   - libitk=5.3
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
-  - scipy=1.11
+  - scipy=1.13
   - matplotlib=3.8
   - pandas=2.2
-  - h5py=3.10
+  - h5py=3.11
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.10
-  - scikit-image=0.22
+  - scikit-image=0.23
   - scikit-learn=1.4
   # Utilities
   - graphviz=9.0

diff --git a/pyproject.toml b/pyproject.toml
@@ -22,18 +22,18 @@ dependencies = [
     "looseversion",
     "nibabel >= 4.0.1",
     "nipype >= 1.8.5",
-    "nireports @ git+https://github.com/nipreps/nireports.git@main",
+    "nireports >= 23.2.1",
     "nitime",
     "nitransforms >= 21.0.0",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+    "niworkflows >= 1.10.1",
     "numpy >= 1.22",
     "packaging",
     "pandas",
     "psutil >= 5.4",
     "pybids >= 0.15.2",
     "requests",
-    "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
+    "sdcflows >= 2.8.1",
+    "smriprep >= 0.15.0",
     "tedana >= 23.0.2",
     "templateflow >= 24.1.0",
     "transforms3d",