FIX: Tests

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
 # isort addition
 6f809fa9950654cbb7f755922c45dffbc88dc45d
+# Ruff 0.9.2
+03e848c6f7c102cc9e0907a38c311afe5c357e77

.readthedocs.yml

@@ -1,19 +1,21 @@
 version: 2
 
+sphinx:
+  configuration: docs/conf.py
 build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
   jobs:
     post_checkout:
-      - git fetch --unshallow
+    - git fetch --unshallow
 
 python:
   install:
-    - requirements: docs/requirements.txt
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
-    - method: pip
-      path: wrapper/
+  - requirements: docs/requirements.txt
+  - method: pip
+    path: .
+    extra_requirements:
+    - doc
+  - method: pip
+    path: wrapper/

nibabies/__init__.py

@@ -1 +1,28 @@
-from .__about__ import __version__  # noqa: F401
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Top-module metadata."""
+
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ = '0+unknown'

nibabies/cli/parser.py

@@ -32,8 +32,8 @@ class DeprecatedAction(Action):
         def __call__(self, parser, namespace, values, option_string=None):
             new_opt, rem_vers = deprecations.get(self.dest, (None, None))
             msg = (
-                f"{self.option_strings} has been deprecated and will be removed in "
-                f"{rem_vers or 'a later version'}."
+                f'{self.option_strings} has been deprecated and will be removed in '
+                f'{rem_vers or "a later version"}.'
             )
             if new_opt:
                 msg += f' Please use `{new_opt}` instead.'
@@ -140,7 +140,7 @@ def _slice_time_ref(value, parser):
             value = float(value)
         except ValueError as e:
             raise parser.error(
-                "Slice time reference must be number, 'start', or 'middle'. " f'Received {value}.'
+                f"Slice time reference must be number, 'start', or 'middle'. Received {value}."
             ) from e
         if not 0 <= value <= 1:
             raise parser.error(f'Slice time reference must be in range 0-1. Received {value}.')
@@ -182,7 +182,7 @@ def _str_none(val):
         'output_dir',
         action='store',
         type=Path,
-        help='the output path for the outcomes of preprocessing and visual ' 'reports',
+        help='the output path for the outcomes of preprocessing and visual reports',
     )
     parser.add_argument(
         'analysis_level',
@@ -297,7 +297,7 @@ def _str_none(val):
     g_perfm.add_argument(
         '--low-mem',
         action='store_true',
-        help='attempt to reduce memory usage (will increase disk usage ' 'in working directory)',
+        help='attempt to reduce memory usage (will increase disk usage in working directory)',
     )
     g_perfm.add_argument(
         '--use-plugin',
@@ -497,8 +497,7 @@ def _str_none(val):
         action='store',
         default=0.5,
         type=float,
-        help='Threshold for flagging a frame as an outlier on the basis of framewise '
-        'displacement',
+        help='Threshold for flagging a frame as an outlier on the basis of framewise displacement',
     )
     g_confounds.add_argument(
         '--dvars-spike-threshold',
@@ -507,7 +506,7 @@ def _str_none(val):
         action='store',
         default=1.5,
         type=float,
-        help='Threshold for flagging a frame as an outlier on the basis of standardised ' 'DVARS',
+        help='Threshold for flagging a frame as an outlier on the basis of standardised DVARS',
     )
 
     #  ANTs options
@@ -657,7 +656,7 @@ def _str_none(val):
         '--stop-on-first-crash',
         action='store_true',
         default=False,
-        help='Force stopping on first crash, even if a work directory' ' was specified.',
+        help='Force stopping on first crash, even if a work directory was specified.',
     )
     g_other.add_argument(
         '--notrack',
@@ -875,8 +874,7 @@ def parse_args(args=None, namespace=None):
         from ..utils.bids import validate_input_dir
 
         build_log.info(
-            'Making sure the input data is BIDS compliant (warnings can be ignored in most '
-            'cases).'
+            'Making sure the input data is BIDS compliant (warnings can be ignored in most cases).'
         )
         validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
@@ -896,8 +894,8 @@ def parse_args(args=None, namespace=None):
     missing_subjects = participant_label - set(all_subjects)
     if missing_subjects:
         parser.error(
-            "One or more participant labels were not found in the BIDS directory: "
-            f"{', '.join(missing_subjects)}."
+            'One or more participant labels were not found in the BIDS directory: '
+            f'{", ".join(missing_subjects)}.'
         )
 
     config.execution.participant_label = sorted(participant_label)

nibabies/config.py

@@ -413,7 +413,7 @@ class execution(_Config):
     """Force usage of this anatomical scan as the structural reference."""
     reports_only = False
     """Only build the reports, based on the reportlets found in a cached working directory."""
-    run_uuid = f"{strftime('%Y%m%d-%H%M%S')}_{uuid4()}"
+    run_uuid = f'{strftime("%Y%m%d-%H%M%S")}_{uuid4()}'
     """Unique identifier of this particular run."""
     segmentation_atlases_dir = None
     """Directory with atlases to use for JLF segmentations"""
@@ -622,7 +622,7 @@ class workflow(_Config):
 class loggers:
     """Keep loggers easily accessible (see :py:func:`init`)."""
 
-    _fmt = '%(asctime)s,%(msecs)d %(name)-2s ' '%(levelname)-2s:\n\t %(message)s'
+    _fmt = '%(asctime)s,%(msecs)d %(name)-2s %(levelname)-2s:\n\t %(message)s'
     _datefmt = '%y%m%d-%H:%M:%S'
 
     default = logging.getLogger()

nibabies/interfaces/metric.py

@@ -78,8 +78,7 @@
         argstr='-exponent %f ',
         position=9,
         default=6.0,
-        desc='exponent n to use in (area / (distance ^ n)) as the '
-        'weighting function (default 6)',
+        desc='exponent n to use in (area / (distance ^ n)) as the weighting function (default 6)',
     )
 
     corrected_areas = File(
@@ -246,16 +245,14 @@
     def _format_arg(self, opt, spec, val):
         if opt in ['current_area', 'new_area']:
             if not self.inputs.area_surfs and not self.inputs.area_metrics:
-                raise ValueError(
-                    f'{opt} was set but neither area_surfs or' ' area_metrics were set'
-                )
+                raise ValueError(f'{opt} was set but neither area_surfs or area_metrics were set')
         if opt == 'method':
             if (
                 val == 'ADAP_BARY_AREA'
                 and not self.inputs.area_surfs
                 and not self.inputs.area_metrics
             ):
-                raise ValueError('Exactly one of area_surfs or area_metrics' ' must be specified')
+                raise ValueError('Exactly one of area_surfs or area_metrics must be specified')
         if opt == 'valid_roi_out' and val:
             # generate a filename and add it to argstr
             roi_out = self._gen_filename(self.inputs.in_file, suffix='_roi')

nibabies/utils/bids.py

@@ -41,7 +41,9 @@
 
 
 def write_derivative_description(bids_dir, deriv_dir, dataset_links=None):
-    from ..__about__ import DOWNLOAD_URL, __packagename__, __version__
+    from nibabies import __version__
+
+    DOWNLOAD_URL = f'https://github.com/nipreps/nibabies/archive/{__version__}.tar.gz'
 
     bids_dir = Path(bids_dir)
     deriv_dir = Path(deriv_dir)
@@ -51,7 +53,7 @@
         'DatasetType': 'derivative',
         'GeneratedBy': [
             {
-                'Name': __packagename__,
+                'Name': 'NiBabies',
                 'Version': __version__,
                 'CodeURL': DOWNLOAD_URL,
             }
@@ -63,7 +65,7 @@
     if 'NIBABIES_DOCKER_TAG' in os.environ:
         desc['GeneratedBy'][0]['Container'] = {
             'Type': 'docker',
-            'Tag': f"nipreps/nibabies:{os.environ['NIBABIES_DOCKER_TAG']}",
+            'Tag': f'nipreps/nibabies:{os.environ["NIBABIES_DOCKER_TAG"]}',
         }
     if 'NIBABIES_SINGULARITY_URL' in os.environ:
         desc['GeneratedBy'][0]['Container'] = {

nibabies/workflows/anatomical/fit.py

@@ -170,11 +170,11 @@ def init_infant_anat_fit_wf(
 
     # Stage 2 - Anatomicals
     t1w_buffer = pe.Node(
-        niu.IdentityInterface(fields=['t1w_preproc', 't1w_mask' 't1w_brain']),
+        niu.IdentityInterface(fields=['t1w_preproc', 't1w_maskt1w_brain']),
         name='t1w_buffer',
     )
     t2w_buffer = pe.Node(
-        niu.IdentityInterface(fields=['t2w_preproc', 't2w_mask' 't2w_brain', 't2w_probmap']),
+        niu.IdentityInterface(fields=['t2w_preproc', 't2w_maskt2w_brain', 't2w_probmap']),
         name='t2w_buffer',
     )
     anat_buffer = pe.Node(
@@ -453,7 +453,7 @@ def init_infant_anat_fit_wf(
     t2w_mask = precomputed.get('t2w_mask')
     anat_mask = precomputed.get(f'{anat}_mask')
     refine_mask = False
-    # T1w masking - define pre-emptively
+    # T1w masking - define preemptively
     apply_t1w_mask = pe.Node(ApplyMask(), name='apply_t1w_mask')
     apply_t2w_mask = apply_t1w_mask.clone(name='apply_t2w_mask')
 

nibabies/workflows/anatomical/registration.py

@@ -537,9 +537,11 @@ def _load_intermediate_xfms(intermediate, std):
 
 
 def _create_inverse_composite(in_file, out_file='inverse_composite.h5'):
-    """Build a composite transform with SimpleITK.
+    """
+    Build a composite transform with SimpleITK.
 
     This serves as a workaround for a bug in ANTs's CompositeTransformUtil
+    https://github.com/ANTsX/ANTs/issues/1827
     where composite transforms cannot be created with a displacement field placed first.
 
     Parameters
@@ -553,6 +555,8 @@ def _create_inverse_composite(in_file, out_file='inverse_composite.h5'):
     -------
     out_file : str
         Absolute path to the composite transform.
+    """
+
     from pathlib import Path
 
     import SimpleITK as sitk

nibabies/workflows/anatomical/segmentation.py

@@ -288,7 +288,7 @@
     import numpy as np
 
     img = nb.load(in_file)
-    out_file = Path(f"labels{''.join(Path(in_file).suffixes)}").absolute()
+    out_file = Path(f'labels{"".join(Path(in_file).suffixes)}').absolute()
 
     new_data = np.asanyarray(img.get_fdata(), dtype=dtype)
     img.set_data_dtype(dtype)

nibabies/workflows/base.py

@@ -118,7 +118,7 @@ def init_nibabies_wf(subworkflows_list: list[SubjectSession]):
                 freesurfer_home=os.getenv('FREESURFER_HOME'),
                 spaces=execution_spaces.get_fs_spaces(),
             ),
-            name=f"fsdir_run_{config.execution.run_uuid.replace('-', '_')}",
+            name=f'fsdir_run_{config.execution.run_uuid.replace("-", "_")}',
             run_without_submitting=True,
         )
         if config.execution.fs_subjects_dir is not None:
@@ -291,9 +291,9 @@ def init_single_subject_wf(
 
     if subject_data['roi']:
         warnings.warn(
-            f"Lesion mask {subject_data['roi']} found. "
-            "Future versions of NiBabies will use alternative conventions. "
-            "Please refer to the documentation before upgrading.",
+            f'Lesion mask {subject_data["roi"]} found. '
+            'Future versions of NiBabies will use alternative conventions. '
+            'Please refer to the documentation before upgrading.',
             FutureWarning,
             stacklevel=1,
         )
@@ -939,7 +939,7 @@ def map_fieldmap_estimation(
     for bold_file, estimator_key in all_estimators.items():
         if len(estimator_key) > 1:
             config.loggers.workflow.warning(
-                f"Several fieldmaps <{', '.join(estimator_key)}> are "
+                f'Several fieldmaps <{", ".join(estimator_key)}> are '
                 f"'IntendedFor' <{bold_file}>, using {estimator_key[0]}"
             )
             estimator_key[1:] = []

nibabies/workflows/bold/base.py

@@ -37,8 +37,8 @@
 from niworkflows.utils.connections import listify
 
 from nibabies import config
+from nibabies._types import Anatomical
 from nibabies.interfaces import DerivativesDataSink
-from nibabies.types import Anatomical
 from nibabies.utils.misc import estimate_bold_mem_usage
 
 # BOLD workflows

nibabies/workflows/bold/fit.py

@@ -34,13 +34,13 @@
 from sdcflows.workflows.apply.registration import init_coeff2epi_wf
 
 from nibabies import config
+from nibabies._types import Anatomical
 from nibabies.interfaces.reports import FunctionalSummary
 from nibabies.interfaces.resampling import (
     DistortionParameters,
     ReconstructFieldmap,
     ResampleSeries,
 )
-from nibabies.types import Anatomical
 from nibabies.utils.bids import extract_entities
 from nibabies.utils.misc import estimate_bold_mem_usage
 

nibabies/workflows/bold/outputs.py

@@ -31,10 +31,10 @@
 from niworkflows.utils.images import dseg_label
 
 from nibabies import config
+from nibabies._types import Anatomical
 from nibabies.config import DEFAULT_DISMISS_ENTITIES, DEFAULT_MEMORY_MIN_GB, dismiss_echo
 from nibabies.interfaces import DerivativesDataSink
 from nibabies.interfaces.bids import BIDSURI
-from nibabies.types import Anatomical
 
 
 def prepare_timing_parameters(metadata: dict):

nibabies/workflows/bold/registration.py

@@ -20,7 +20,7 @@
 from nipype.pipeline import engine as pe
 
 from nibabies import config, data
-from nibabies.types import AffineDOF, RegistrationInit
+from nibabies._types import AffineDOF, RegistrationInit
 
 DEFAULT_MEMORY_MIN_GB = config.DEFAULT_MEMORY_MIN_GB
 LOGGER = logging.getLogger('nipype.workflow')

nibabies/workflows/bold/stc.py

@@ -115,7 +115,7 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'):
     slice_timing_correction = pe.Node(
         TShift(
             outputtype='NIFTI_GZ',
-            tr=f"{metadata['RepetitionTime']}s",
+            tr=f'{metadata["RepetitionTime"]}s',
             slice_timing=metadata['SliceTiming'],
             slice_encoding_direction=metadata.get('SliceEncodingDirection', 'k'),
             tzero=tzero,

scripts/fetch_templates.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-'Pre-emptive caching of commonly used TemplateFlow templates'
+'Preemptive caching of commonly used TemplateFlow templates'
 import templateflow.api as tf