Merge branch 'master' into ruff

Author: effigies

.maint/CONTRIBUTORS.md

@@ -13,6 +13,7 @@ Before every release, unlisted contributors will be invited again to add their n
 | Bellec            | Pierre       |  | 0000-0002-9111-0699 | SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada                                                                                 |
 | Benson            | Noah C.      |  | 0000-0002-2365-8265 | Department of Psychology, New York University                                                                                                |
 | Bhagwat           | Nikhil       |  | 0000-0001-6073-7141 | Montreal Neurological Institute, McGill University                                                                                           |
+| Camacho           | Milton       |  | 0000-0002-5379-5076 | Department of Pediadrics, University of Calgary                                                                                           |
 | Callenberg        | Keith        |  | 0000-0001-7786-9300 | Department of Psychiatry, University of Pittsburgh                                                                                           |
 | Cieslak           | Matthew      |  | 0000-0002-1931-4734 | Perelman School of Medicine, University of Pennsylvania, PA, USA                                                                             |
 | de la Vega        | Alejandro    |  | 0000-0001-9062-3778 | University of Texas at Austin                                                                                                                |

.pre-commit-config.yaml

@@ -12,10 +12,8 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.1
+    rev: v0.12.2
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [ --fix ]
       - id: ruff-format
-      - id: ruff
-        args: [ --select, ISC001, --fix ]

docs/usage.rst

@@ -35,8 +35,6 @@ Command-Line Arguments
 .. argparse::
    :ref: fmriprep.cli.parser._build_parser
    :prog: fmriprep
-   :nodefault:
-   :nodefaultconst:
 
 
 The command-line interface of the docker wrapper

fmriprep/_warnings.py

@@ -29,17 +29,20 @@
 _wlog.addHandler(logging.NullHandler())
 
 
-def _warn(message, category=None, stacklevel=1, source=None):
+def _warn(message, category=None, stacklevel=1, source=None, **kwargs):
     """Redefine the warning function."""
     if category is not None:
         category = type(category).__name__
         category = category.replace('type', 'WARNING')
 
+    if kwargs:
+        logging.getLogger('py.warnings').warning('Extra warning kwargs: %s', kwargs)
+
     logging.getLogger('py.warnings').warning('%s: %s', category or 'WARNING', message)
 
 
-def _showwarning(message, category, filename, lineno, file=None, line=None):
-    _warn(message, category=category)
+def _showwarning(message, category, filename, lineno, file=None, line=None, **kwargs):
+    _warn(message, category=category, **kwargs)
 
 
 warnings.warn = _warn

fmriprep/cli/parser.py

@@ -23,6 +23,7 @@
 """Parser."""
 
 import sys
+from pathlib import Path
 
 from .. import config
 
@@ -32,9 +33,13 @@ def _build_parser(**kwargs):
 
     ``kwargs`` are passed to ``argparse.ArgumentParser`` (mainly useful for debugging).
     """
-    from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
+    from argparse import (
+        Action,
+        ArgumentDefaultsHelpFormatter,
+        ArgumentParser,
+        BooleanOptionalAction,
+    )
     from functools import partial
-    from pathlib import Path
 
     from niworkflows.utils.spaces import OutputReferencesAction, Reference
     from packaging.version import Version
@@ -413,7 +418,7 @@ def _fallback_trt(value, parser):
         '--slice-time-ref',
         required=False,
         action='store',
-        default=None,
+        default=0.5,
         type=SliceTimeRef,
         help='The time of the reference slice to correct BOLD values to, as a fraction '
         'acquisition time. 0 indicates the start, 0.5 the midpoint, and 1 the end '
@@ -496,7 +501,6 @@ def _fallback_trt(value, parser):
     )
     g_conf.add_argument(
         '--project-goodvoxels',
-        required=False,
         action='store_true',
         default=False,
         help='Exclude voxels whose timeseries have locally high coefficient of variation '
@@ -521,10 +525,11 @@ def _fallback_trt(value, parser):
         '(default is 91k, which equates to 2mm resolution)',
     )
     g_outputs.add_argument(
-        '--no-msm',
-        action='store_false',
+        '--msm',
+        action=BooleanOptionalAction,
+        default=True,
         dest='run_msmsulc',
-        help='Disable Multimodal Surface Matching surface registration.',
+        help='Enable or disable Multimodal Surface Matching surface registration.',
     )
 
     g_confounds = parser.add_argument_group('Options relating to confounds')
@@ -634,10 +639,11 @@ def _fallback_trt(value, parser):
         '(default: OUTPUT_DIR/freesurfer)',
     )
     g_fs.add_argument(
-        '--no-submm-recon',
-        action='store_false',
+        '--submm-recon',
+        action=BooleanOptionalAction,
+        default=True,
         dest='hires',
-        help='Disable sub-millimeter (hires) reconstruction',
+        help='Enable or disable sub-millimeter (hi-res) reconstruction.',
     )
     g_fs.add_argument(
         '--fs-no-reconall',
@@ -656,6 +662,7 @@ def _fallback_trt(value, parser):
     g_carbon = parser.add_argument_group('Options for carbon usage tracking')
     g_carbon.add_argument(
         '--track-carbon',
+        default=False,
         action='store_true',
         help='Tracks power draws using CodeCarbon package',
     )
@@ -682,7 +689,6 @@ def _fallback_trt(value, parser):
         '--work-dir',
         action='store',
         type=Path,
-        default=Path('work').absolute(),
         help='Path where intermediate results should be stored',
     )
     g_other.add_argument(
@@ -776,6 +782,9 @@ def parse_args(args=None, namespace=None):
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts), init=['nipype'])
 
+    if config.execution.work_dir is None:
+        config.execution.work_dir = Path('work').absolute()
+
     # Consistency checks
     force_set = set(config.workflow.force)
     ignore_set = set(config.workflow.ignore)

fmriprep/cli/tests/test_parser.py

@@ -270,3 +270,19 @@ def test_derivatives(tmp_path):
         parser.parse_args(temp_args)
 
     _reset_config()
+
+
+@pytest.mark.parametrize(
+    ('supp_args', 'opt', 'expected'),
+    [
+        (['--no-submm-recon'], 'hires', False),
+        (['--submm-recon'], 'hires', True),
+        ([], 'hires', True),
+        (['--no-msm'], 'run_msmsulc', False),
+    ],
+)
+def test_optional_booleans(tmp_path, supp_args, opt, expected):
+    out_path = str(tmp_path / 'out')
+    args = [str(tmp_path), out_path, 'participant'] + supp_args
+    pargs = _build_parser().parse_args(args)
+    assert getattr(pargs, opt) == expected

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["hatchling", "hatch-vcs", "nipreps-versions"]
+requires = ["hatchling>=1.27", "hatch-vcs", "nipreps-versions"]
 build-backend = "hatchling.build"
 
 [project]
@@ -11,13 +11,13 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Image Recognition",
-    "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
-license = {file = "LICENSE"}
+license = "Apache-2.0"
+license-files = ["LICENSE"]
 requires-python = ">=3.10"
 dependencies = [
     "acres >= 0.2.0",

requirements.txt

@@ -312,7 +312,7 @@ pandas==2.2.3
     #   tedana
 patool==4.0.1
     # via datalad
-pillow==11.2.1
+pillow==11.3.0
     # via
     #   bokeh
     #   imageio