Merge pull request #389 from nipreps/rel/0.13.0

REL: 0.13.0

.github/workflows/pythonpackage.yml

@@ -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"

.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.

Dockerfile

@@ -74,16 +74,14 @@ RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bi
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
+COPY requirements.txt /tmp/requirements.txt
 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@^2.8 bids-validator@1.11.0 && \
+RUN /opt/conda/envs/smriprep/bin/npm install -g svgo@^3.0 bids-validator@^1.13 && \
     rm -r ~/.npm
 
-COPY requirements.txt /tmp/requirements.txt
-RUN /opt/conda/envs/smriprep/bin/pip install --no-cache-dir -r /tmp/requirements.txt
-
 #
 # Main stage
 #

README.rst

@@ -39,7 +39,7 @@ a combination of tools from well-known software packages, including
 `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`__,
 `ANTs <https://stnava.github.io/ANTs/>`__,
 `FreeSurfer <https://surfer.nmr.mgh.harvard.edu/>`__,
-and `AFNI <https://afni.nimh.nih.gov/>`__.
+and `Connectome Workbench <https://humanconnectome.org/software/connectome-workbench>`__.
 
 More information and documentation can be found at
 https://www.nipreps.org/smriprep/.

env.yml

@@ -4,28 +4,31 @@ channels:
   - conda-forge
 # Update this ~yearly; last updated April 2023
 dependencies:
-  - python >=3.10,<3.11
+  - python=3.10
   # Needed for svgo and bids-validator; consider moving to deno
-  - nodejs=16
+  - nodejs=18
   # Intel Math Kernel Library for numpy
   - mkl=2022.1
   - mkl-service=2.4
   # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.25
+  - numpy=1.26
   - scipy=1.11
-  - matplotlib=3.7,!=3.7.2
-  - pandas=2.0
-  - h5py=3.8
+  - matplotlib=3.8
+  - pandas=2.1
+  - h5py=3.10
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.21
+  - scikit-image=0.22
   - scikit-learn=1.3
   # Utilities
   - graphviz=6.0
   - pandoc=3.1
   # Workflow dependencies: ANTs
-  - ants=2.4.4
+  - ants=2.5.0
   # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
-  - fsl-bet2=2111.0
-  - fsl-flirt=2111.0
-  - fsl-fast4=2111.0
+  - fsl-bet2=2111.4
+  - fsl-flirt=2111.2
+  - fsl-fast4=2111.3
   - fsl-miscmaths=2203.2
+  - pip
+  - pip:
+    - -r requirements.txt

pyproject.toml

@@ -12,14 +12,13 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Image Recognition",
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 license = {file = "LICENSE"}
 requires-python = ">=3.10"
 dependencies = [
-    "importlib_resources >= 1.3; python_version < '3.9'",
     "indexed_gzip >= 0.8.8",
     "lockfile",
     "looseversion",

requirements.txt

@@ -1,48 +1,48 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
-#    pip-compile --resolver=backtracking
+#    pip-compile --strip-extras
 #
 astor==0.8.1
     # via formulaic
 attrs==23.1.0
     # via niworkflows
-bids-validator==1.12.0
+bids-validator==1.13.1
     # via pybids
-certifi==2023.7.22
+certifi==2023.11.17
     # via requests
-charset-normalizer==3.2.0
+charset-normalizer==3.3.2
     # via requests
 ci-info==0.3.0
     # via etelemetry
 click==8.1.7
     # via
     #   nipype
     #   pybids
-contourpy==1.1.0
+contourpy==1.2.0
     # via matplotlib
-cycler==0.11.0
+cycler==0.12.1
     # via matplotlib
 docopt==0.6.2
     # via num2words
-etelemetry==0.3.0
+etelemetry==0.3.1
     # via nipype
-filelock==3.12.2
+filelock==3.13.1
     # via nipype
-fonttools==4.42.1
+fonttools==4.44.3
     # via matplotlib
 formulaic==0.5.2
     # via pybids
-greenlet==2.0.2
+greenlet==3.0.1
     # via sqlalchemy
-h5py==3.9.0
+h5py==3.10.0
     # via nitransforms
 idna==3.4
     # via requests
-imageio==2.31.2
+imageio==2.32.0
     # via scikit-image
-indexed-gzip==1.8.3
+indexed-gzip==1.8.7
     # via smriprep (pyproject.toml)
 interface-meta==1.3.0
     # via formulaic
@@ -72,12 +72,12 @@ lxml==4.9.3
     #   svgutils
 markupsafe==2.1.3
     # via jinja2
-matplotlib==3.7.1
+matplotlib==3.8.2
     # via
     #   niworkflows
     #   seaborn
     #   smriprep (pyproject.toml)
-networkx==3.1
+networkx==3.2.1
     # via
     #   nipype
     #   prov
@@ -90,19 +90,19 @@ nibabel==5.1.0
     #   niworkflows
     #   pybids
     #   smriprep (pyproject.toml)
-nilearn==0.10.1
+nilearn==0.10.2
     # via niworkflows
 nipype==1.8.6
     # via
     #   niworkflows
     #   smriprep (pyproject.toml)
 nitransforms==23.0.1
     # via niworkflows
-niworkflows==1.8.1
+niworkflows==1.9.0
     # via smriprep (pyproject.toml)
-num2words==0.5.12
+num2words==0.5.13
     # via pybids
-numpy==1.25.2
+numpy==1.26.2
     # via
     #   contourpy
     #   formulaic
@@ -116,30 +116,30 @@ numpy==1.25.2
     #   niworkflows
     #   pandas
     #   pybids
-    #   pywavelets
     #   scikit-image
     #   scikit-learn
     #   scipy
     #   seaborn
     #   smriprep (pyproject.toml)
     #   tifffile
-packaging==23.1
+packaging==23.2
     # via
+    #   etelemetry
     #   matplotlib
     #   nibabel
     #   nilearn
     #   nipype
     #   niworkflows
     #   scikit-image
     #   smriprep (pyproject.toml)
-pandas==2.0.3
+pandas==2.1.3
     # via
     #   formulaic
     #   nilearn
     #   niworkflows
     #   pybids
     #   seaborn
-pillow==10.0.0
+pillow==10.0.1
     # via
     #   imageio
     #   matplotlib
@@ -153,7 +153,7 @@ pybids==0.16.3
     #   templateflow
 pydot==1.4.2
     # via nipype
-pyparsing==3.0.9
+pyparsing==3.1.1
     # via
     #   matplotlib
     #   pydot
@@ -164,10 +164,8 @@ python-dateutil==2.8.2
     #   nipype
     #   pandas
     #   prov
-pytz==2023.3
+pytz==2023.3.post1
     # via pandas
-pywavelets==1.4.1
-    # via scikit-image
 pyyaml==6.0.1
     # via
     #   niworkflows
@@ -181,11 +179,11 @@ requests==2.31.0
     #   etelemetry
     #   nilearn
     #   templateflow
-scikit-image==0.21.0
+scikit-image==0.22.0
     # via niworkflows
-scikit-learn==1.3.0
+scikit-learn==1.3.2
     # via nilearn
-scipy==1.11.2
+scipy==1.11.4
     # via
     #   formulaic
     #   nilearn
@@ -195,25 +193,25 @@ scipy==1.11.2
     #   pybids
     #   scikit-image
     #   scikit-learn
-seaborn==0.12.2
+seaborn==0.13.0
     # via niworkflows
-simplejson==3.19.1
+simplejson==3.19.2
     # via nipype
 six==1.16.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.20
+sqlalchemy==2.0.23
     # via pybids
 svgutils==0.3.4
     # via niworkflows
-templateflow==23.0.0
+templateflow==23.1.0
     # via
     #   niworkflows
     #   smriprep (pyproject.toml)
 threadpoolctl==3.2.0
     # via scikit-learn
-tifffile==2023.8.25
+tifffile==2023.9.26
     # via scikit-image
 tqdm==4.66.1
     # via templateflow
@@ -223,13 +221,13 @@ traits==6.3.2
     #   niworkflows
 transforms3d==0.4.1
     # via niworkflows
-typing-extensions==4.7.1
+typing-extensions==4.8.0
     # via
     #   formulaic
     #   sqlalchemy
 tzdata==2023.3
     # via pandas
-urllib3==2.0.4
+urllib3==2.1.0
     # via requests
-wrapt==1.15.0
+wrapt==1.16.0
     # via formulaic