Merge pull request #501 from effigies/fix/nitransforms-25.0.1

fix: Adapt to transposed ndindex in nitransforms

Author: effigies

.github/workflows/build-test-publish.yml

@@ -65,24 +65,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         dependencies:  ["latest", "pre"]
         marks: ["fast"]
         include:
-          - python-version: "3.9"
+          - python-version: "3.10"
             dependencies: "min"
             marks: "fast"
-          - python-version: "3.9"
+          - python-version: "3.10"
             dependencies: "latest"
             marks: "slow"
-          - python-version: "3.12"
+          - python-version: "3.13"
             dependencies: "latest"
             marks: "veryslow"
         exclude:
-          - python-version: "3.9"
-            dependencies: "pre"
           - python-version: "3.10"
             dependencies: "pre"
+          - python-version: "3.11"
+            dependencies: "pre"
 
     steps:
     - uses: actions/checkout@v5

pyproject.toml

@@ -13,27 +13,26 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Image Recognition",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
 license = "Apache-2.0"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "acres >= 0.2.0",
     "attrs >= 20.1.0",
-    "nibabel >= 3.0",
-    "nipype >= 1.8.5",
+    "nibabel >= 5.1.1",
+    "nipype >= 1.9.0",
     "migas >= 0.4.0",
     "nireports >= 25.0.1",
     "niworkflows >= 1.11.0",
-    "nitransforms >= 24.1.0",
-    "numpy >= 1.23",
+    "nitransforms >= 25.0.1",
+    "numpy >= 2.0",
     "pybids >= 0.16.4",
-    "scikit-image >= 0.18",
-    "scipy >= 1.8.1",
+    "scikit-image >= 0.23",
+    "scipy >= 1.10",
     "templateflow >= 23.1",
     "toml >= 0.10",
 ]
@@ -70,8 +69,8 @@ dev = [
 ]
 
 test = [
-    "coverage[toml] >=5.2.1",
-    "pytest >= 6",
+    "coverage[toml] >=7",
+    "pytest >= 8.1",
     "pytest-cov >= 2.11",
     "pytest-env",
     "pytest-xdist >= 2.5",
@@ -194,6 +193,7 @@ ignore = [
   "B019",
   "SIM108",
   "C901",
+  "UP038",
 ]
 
 [tool.ruff.lint.flake8-quotes]

sdcflows/interfaces/epi.py

@@ -120,14 +120,15 @@ def _run_interface(self, runtime):
                 blips,
                 self.inputs.readout_times,
                 self.inputs.in_data,
+                strict=False,
             )
         )
 
         (
             self._results['pe_dirs_fsl'],
             self._results['readout_times'],
             self._results['out_data'],
-        ) = zip(*sorted_inputs)
+        ) = zip(*sorted_inputs, strict=False)
 
         # Put sign back last
         self._results['pe_dirs_fsl'] = [

sdcflows/interfaces/fmap.py

@@ -289,7 +289,7 @@ def _run_interface(self, runtime):
         fmap_imgs = [nb.load(fname) for fname in fmap_files]
 
         # Baseline check: paired magnitude/phase maps are basically the same
-        for mag, fmap in zip(mag_imgs, fmap_imgs):
+        for mag, fmap in zip(mag_imgs, fmap_imgs, strict=False):
             msg = _check_gross_geometry(mag, fmap)
             if msg is not None:
                 LOGGER.critical(msg)

sdcflows/interfaces/utils.py

@@ -81,13 +81,15 @@ class Flatten(SimpleInterface):
 
     def _run_interface(self, runtime):
         self._results['out_list'] = _flatten(
-            zip(self.inputs.in_data, self.inputs.in_meta),
+            zip(self.inputs.in_data, self.inputs.in_meta, strict=False),
             max_trs=self.inputs.max_trs,
             out_dir=runtime.cwd,
         )
 
         # Unzip out_data, out_meta outputs.
-        self._results['out_data'], self._results['out_meta'] = zip(*self._results['out_list'])
+        self._results['out_data'], self._results['out_meta'] = zip(
+            *self._results['out_list'], strict=False
+        )
         return runtime
 
 
@@ -449,7 +451,11 @@ def _deoblique(in_file, in_affine=None, newpath=None):
     if in_affine is None:
         orientation = nb.aff2axcodes(nii.affine)
         directions = (
-            np.array([int(l1 == l2) for l1, l2 in zip(orientation, 'RAS')], dtype='float32') * 2
+            np.array(
+                [int(l1 == l2) for l1, l2 in zip(orientation, 'RAS', strict=False)],
+                dtype='float32',
+            )
+            * 2
             - 1
         )
         newaff = np.eye(4)

sdcflows/tests/test_transform.py

@@ -48,7 +48,7 @@ def generate_oracle(
     data[19:22, ...] = 0
     data = np.pad(data + nd.binary_erosion(data, ball(3)), 8)
 
-    zooms = [z if not f else -z for z, f in zip(zooms, flip)]
+    zooms = [z if not f else -z for z, f in zip(zooms, flip, strict=False)]
     affine = np.diag(zooms + [1])
     affine[:3, 3] = -affine[:3, :3] @ ((np.array(data.shape) - 1) * 0.5)
 
@@ -123,7 +123,9 @@ def test_displacements_field(tmpdir, testdata_dir, outdir, pe_dir, rotation, fli
     assert np.all((np.sqrt(((ours - theirs) ** 2).sum()) / ours.size) < 1e-1)
 
     if outdir:
-        orientation = ''.join([ax[bool(f)] for ax, f in zip(('RL', 'AP', 'SI'), flip)])
+        orientation = ''.join(
+            [ax[bool(f)] for ax, f in zip(('RL', 'AP', 'SI'), flip, strict=False)]
+        )
 
         SimpleBeforeAfter(
             after_label='Theirs (ANTs)',

sdcflows/transform.py

@@ -49,10 +49,9 @@
 
 import asyncio
 import os
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from functools import partial
 from pathlib import Path
-from typing import Callable
 from warnings import warn
 
 import attr
@@ -492,7 +491,7 @@ def apply(
             ro_time *= n_volumes
 
         pe_info = []
-        for vol_pe_dir, vol_ro_time in zip(pe_dir, ro_time):
+        for vol_pe_dir, vol_ro_time in zip(pe_dir, ro_time, strict=False):
             pe_axis = 'ijk'.index(vol_pe_dir[0])
             # Displacements are reversed if either is true (after ensuring positive cosines)
             flip = (axcodes[pe_axis] in 'LPI') ^ vol_pe_dir.endswith('-')
@@ -502,7 +501,7 @@ def apply(
         # Reference image's voxel coordinates (in voxel units)
         voxcoords = (
             nt.linear.Affine(reference=moving)
-            .reference.ndindex.reshape((ndim, *data.shape[:ndim]))
+            .reference.ndindex.T.reshape((ndim, *data.shape[:ndim]))
             .astype('float32')
         )
 

sdcflows/utils/wrangler.py

@@ -488,7 +488,7 @@ def find_estimators(
                 targets = all_targets
                 intent_map = [[target] for target in all_targets]
 
-            for target, intent in zip(targets, intent_map):
+            for target, intent in zip(targets, intent_map, strict=False):
                 logger.debug('Found single PE target %s', target.relpath)
                 # The new estimator is IntendedFor the individual targets,
                 # even if the EPI file is IntendedFor multiple

sdcflows/workflows/fit/tests/test_syn.py

@@ -304,7 +304,10 @@ def test_mm2vox(tmp_path, fixed_ornt, moving_ornt, ijk, index):
 
     vox_params = _mm2vox(str(moving_path), str(fixed_path), ijk, config)
     vox_values = [level[2] for level in vox_params]
-    assert [mm_level[:2] == vox_level[:2] for mm_level, vox_level in zip(params, vox_params)]
+    assert all(
+        mm_level[:2] == vox_level[:2]
+        for mm_level, vox_level in zip(params, vox_params, strict=False)
+    )
     assert np.array_equal(vox_values, mm_values / [2, 3, 4][index])
 
 

tox.ini

@@ -3,8 +3,8 @@ requires =
   tox>=4
   tox-uv
 envlist =
-  py3{9,10,11,12,13}-latest-{fast,slow,veryslow}
-  py39-min-fast
+  py3{10,11,12,13}-latest-{fast,slow,veryslow}
+  py310-min-fast
   py3{11,12,13}-pre-{fast,slow,veryslow}
   style
   spellcheck