sdcflows 2.13.2__tar.gz → 2.14.0__tar.gz

sdcflows-2.14.0/.circleci/version.py

@@ -0,0 +1,6 @@
+"""Get sdcflows version."""
+
+import sdcflows
+
+with open('/tmp/.docker-version.txt', 'w') as f:
+    f.write(sdcflows.__version__)

sdcflows-2.14.0/.git-blame-ignore-revs

@@ -0,0 +1,12 @@
+# Thu May 15 11:41:29 2025 -0400 - markiewicz@stanford.edu - chore: Manual ruff fixes [ignore-rev]
+e5153dbc00b089144b9f4b415234b27c58b2388b
+# Thu May 15 11:11:38 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
+2bb216b0a12612e31713b34d8ab2ee98fa2cc703
+# Thu May 15 09:34:34 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
+dc3706038661984718da079e24a863842407a837
+# Thu May 15 09:29:29 2025 -0400 - markiewicz@stanford.edu - run: ruff format [ignore-rev]
+d97ae316c0bdf71084a0732760ceed5221033fc2
+# Thu May 15 09:26:57 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
+cacd409cce71f2e530ad1bd1e8b79f397cab81d4
+# Thu May 15 09:22:00 2025 -0400 - markiewicz@stanford.edu - run: pre-commit run --all [ignore-rev]
+2b40bee0d6b2c88628760a8b1513851a439411e8

{sdcflows-2.13.2 → sdcflows-2.14.0}/.github/workflows/build-test-publish.yml

@@ -43,7 +43,7 @@ jobs:
       id-token: write
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - uses: hynek/build-and-inspect-python-package@v2
@@ -65,27 +65,27 @@ 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@v4
+    - uses: actions/checkout@v5
     - uses: actions/cache@v4
       with:
         path: /var/lib/apt
@@ -245,7 +245,7 @@ jobs:
 
     steps:
       - name: Download packages built by build-and-inspect-python-package
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: Packages
           path: dist

{sdcflows-2.13.2 → sdcflows-2.14.0}/.github/workflows/docs-build-update.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ssh-key: "${{ secrets.NIPREPS_DEPLOY }}"
         fetch-depth: 0
@@ -49,7 +49,7 @@ jobs:
         sudo apt-get install -y --no-install-recommends graphviz pandoc texlive
 
     - name: Set up Python 3
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: 3
 

{sdcflows-2.13.2 → sdcflows-2.14.0}/.github/workflows/validate.yml

@@ -20,12 +20,12 @@ jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: pipx run ruff check sdcflows/
     - run: pipx run ruff format --diff sdcflows/
 
   # codespell:
   #   runs-on: ubuntu-latest
   #   steps:
-  #   - uses: actions/checkout@v4
+  #   - uses: actions/checkout@v5
   #   - uses: codespell-project/actions-codespell@v2

{sdcflows-2.13.2 → sdcflows-2.14.0}/.maint/update_authors.py

@@ -57,7 +57,7 @@ def read_md_table(md_text):
             break
 
         values = [v.strip() or None for v in line.split('|')][1:-1]
-        retval.append({k: v for k, v in zip(keys, values) if v})
+        retval.append({k: v for k, v in zip(keys, values, strict=False) if v})
 
     return retval
 
@@ -130,10 +130,11 @@ def get_git_lines(fname='line-contributors.txt'):
     if not lines:
         raise RuntimeError(
             """\
-Could not find line-contributors from git repository.%s"""
-            % """ \
+Could not find line-contributors from git repository.{}""".format(
+                """ \
 git-line-summary not found, please install git-extras. """
-            * (cmd[0] is None)
+                * (cmd[0] is None)
+            )
         )
     return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
 
@@ -219,7 +220,7 @@ def zenodo(
         elif isinstance(creator['affiliation'], list):
             creator['affiliation'] = creator['affiliation'][0]
 
-    Path(zenodo_file).write_text('%s\n' % json.dumps(zenodo, indent=2, ensure_ascii=False))
+    Path(zenodo_file).write_text(f'{json.dumps(zenodo, indent=2, ensure_ascii=False)}\n')
 
 
 @cli.command()
@@ -266,10 +267,8 @@ def publication(
 
     aff_indexes = [
         ', '.join(
-            [
-                '%d' % (affiliations.index(a) + 1)
-                for a in _aslist(author.get('affiliation', 'Unaffiliated'))
-            ]
+            str(affiliations.index(a) + 1)
+            for a in _aslist(author.get('affiliation', 'Unaffiliated'))
         )
         for author in hits
     ]
@@ -280,15 +279,18 @@ def publication(
             file=sys.stderr,
         )
 
-    print('Authors (%d):' % len(hits))
+    print(f'Authors ({len(hits)}):')
     print(
-        '%s.'
-        % '; '.join(['%s \\ :sup:`%s`\\ ' % (i['name'], idx) for i, idx in zip(hits, aff_indexes)])
+        '; '.join(
+            [rf'{i["name"]} \ :sup:`{idx}`\ ' for i, idx in zip(hits, aff_indexes, strict=False)]
+        )
+        + '.'
     )
 
     print(
-        '\n\nAffiliations:\n%s'
-        % '\n'.join(['{0: >2}. {1}'.format(i + 1, a) for i, a in enumerate(affiliations)])
+        '\n\nAffiliations:\n{}'.format(
+            '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        )
     )
 
 

{sdcflows-2.13.2 → sdcflows-2.14.0}/.pre-commit-config.yaml

@@ -12,12 +12,9 @@ repos:
       - id: end-of-file-fixer
       - id: fix-byte-order-marker
       - id: trailing-whitespace
-  # Enable when no significant PRs are in progress
-  # - repo: https://github.com/psf/black
-  #   rev: 23.1.0
-  #   hooks:
-  #     - id: black
-  # - repo: https://github.com/pycqa/isort
-  #   rev: 5.12.0
-  #   hooks:
-  #     - id: isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.5
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

{sdcflows-2.13.2 → sdcflows-2.14.0}/CHANGES.rst

@@ -1,3 +1,14 @@
+2.14.0 (September 22, 2025)
+===========================
+Feature release in the 2.13.x series.
+
+This release requires a recent nitransforms release that in turn requires NumPy 2.
+Since this is a major dependency increment, a new feature release is justified.
+
+* fix: Adapt to transposed ndindex in nitransforms (#501)
+* fix: Adopt some more opinionated ruff rules, manual resolutions (#493)
+
+
 2.13.2 (July 28, 2025)
 ======================
 Patch release in the 2.13.x series.

{sdcflows-2.13.2 → sdcflows-2.14.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sdcflows
-Version: 2.13.2
+Version: 2.14.0
 Summary: Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes.
 Project-URL: Documentation, https://www.nipreps.org/sdcflows
 Project-URL: Home, https://github.com/nipreps/sdcflows
@@ -11,31 +11,30 @@ License-File: LICENSE
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.9
-Requires-Dist: acres>=0.2.0
+Requires-Python: >=3.10
+Requires-Dist: acres>=0.5.0
 Requires-Dist: attrs>=20.1.0
 Requires-Dist: migas>=0.4.0
-Requires-Dist: nibabel>=3.0
-Requires-Dist: nipype>=1.8.5
+Requires-Dist: nibabel>=5.1.1
+Requires-Dist: nipype>=1.9.0
 Requires-Dist: nireports>=25.0.1
-Requires-Dist: nitransforms>=24.1.0
+Requires-Dist: nitransforms>=25.0.1
 Requires-Dist: niworkflows>=1.11.0
-Requires-Dist: numpy>=1.23
+Requires-Dist: numpy>=2.0
 Requires-Dist: pybids>=0.16.4
-Requires-Dist: scikit-image>=0.18
-Requires-Dist: scipy>=1.8.1
+Requires-Dist: scikit-image>=0.23
+Requires-Dist: scipy>=1.10
 Requires-Dist: templateflow>=23.1
 Requires-Dist: toml>=0.10
 Provides-Extra: all
 Requires-Dist: attrs>=20.1.0; extra == 'all'
-Requires-Dist: coverage[toml]>=5.2.1; extra == 'all'
+Requires-Dist: coverage[toml]>=7; extra == 'all'
 Requires-Dist: furo; extra == 'all'
 Requires-Dist: importlib-resources; extra == 'all'
 Requires-Dist: ipykernel; extra == 'all'
@@ -49,7 +48,7 @@ Requires-Dist: pydotplus; extra == 'all'
 Requires-Dist: pytest-cov>=2.11; extra == 'all'
 Requires-Dist: pytest-env; extra == 'all'
 Requires-Dist: pytest-xdist>=2.5; extra == 'all'
-Requires-Dist: pytest>=6; extra == 'all'
+Requires-Dist: pytest>=8.1; extra == 'all'
 Requires-Dist: ruff; extra == 'all'
 Requires-Dist: sphinx-argparse; extra == 'all'
 Requires-Dist: sphinx>=7.2.2; extra == 'all'
@@ -86,17 +85,17 @@ Requires-Dist: sphinxcontrib-apidoc; extra == 'docs'
 Provides-Extra: mem
 Requires-Dist: psutil; extra == 'mem'
 Provides-Extra: test
-Requires-Dist: coverage[toml]>=5.2.1; extra == 'test'
+Requires-Dist: coverage[toml]>=7; extra == 'test'
 Requires-Dist: pytest-cov>=2.11; extra == 'test'
 Requires-Dist: pytest-env; extra == 'test'
 Requires-Dist: pytest-xdist>=2.5; extra == 'test'
-Requires-Dist: pytest>=6; extra == 'test'
+Requires-Dist: pytest>=8.1; extra == 'test'
 Provides-Extra: tests
-Requires-Dist: coverage[toml]>=5.2.1; extra == 'tests'
+Requires-Dist: coverage[toml]>=7; extra == 'tests'
 Requires-Dist: pytest-cov>=2.11; extra == 'tests'
 Requires-Dist: pytest-env; extra == 'tests'
 Requires-Dist: pytest-xdist>=2.5; extra == 'tests'
-Requires-Dist: pytest>=6; extra == 'tests'
+Requires-Dist: pytest>=8.1; extra == 'tests'
 Description-Content-Type: text/x-rst
 
 SDCFlows

{sdcflows-2.13.2 → sdcflows-2.14.0}/docs/notebooks/SDC - Theory and physics.ipynb

@@ -71,7 +71,7 @@
     "def get_centers(brain_slice):\n",
     "    samples_x = np.arange(6, brain_slice.shape[1] - 3, step=12).astype(int)\n",
     "    samples_y = np.arange(6, brain_slice.shape[0] - 3, step=12).astype(int)\n",
-    "    return zip(*product(samples_x, samples_y))\n",
+    "    return zip(*product(samples_x, samples_y), strict=False)\n",
     "\n",
     "\n",
     "def plot_brain(brain_slice, brain_cmap='RdPu_r', grid=False, voxel_centers_c=None):\n",

{sdcflows-2.13.2 → sdcflows-2.14.0}/docs/tools/apigen.py

@@ -27,7 +27,7 @@ from types import BuiltinFunctionType, FunctionType
 DEBUG = True
 
 
-class ApiDocWriter(object):
+class ApiDocWriter:
     """Class for automatic detection and parsing of API docs
     to Sphinx-parsable reST format"""
 
@@ -185,9 +185,8 @@ class ApiDocWriter(object):
             # nothing that we could handle here.
             return ([], [])
 
-        f = open(filename, 'rt')
-        functions, classes = self._parse_lines(f)
-        f.close()
+        with open(filename) as f:
+            functions, classes = self._parse_lines(f)
         return functions, classes
 
     def _parse_module_with_import(self, uri):
@@ -217,14 +216,10 @@ class ApiDocWriter(object):
                 continue
             obj = mod.__dict__[obj_str]
             # Check if function / class defined in module
-            if not self.other_defines and not getmodule(obj) == mod:
+            if not self.other_defines and getmodule(obj) != mod:
                 continue
             # figure out if obj is a function or class
-            if (
-                hasattr(obj, 'func_name')
-                or isinstance(obj, BuiltinFunctionType)
-                or isinstance(obj, FunctionType)
-            ):
+            if hasattr(obj, 'func_name') or isinstance(obj, (BuiltinFunctionType, FunctionType)):
                 functions.append(obj_str)
             else:
                 try:
@@ -278,7 +273,7 @@ class ApiDocWriter(object):
 
         # Make a shorter version of the uri that omits the package name for
         # titles
-        uri_short = re.sub(r'^%s\.' % self.package_name, '', uri)
+        uri_short = re.sub(rf'^{self.package_name}\.', '', uri)
 
         head = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n'
         body = ''
@@ -345,20 +340,12 @@ class ApiDocWriter(object):
         elif match_type == 'package':
             patterns = self.package_skip_patterns
         else:
-            raise ValueError('Cannot interpret match type "%s"' % match_type)
+            raise ValueError(f'Cannot interpret match type "{match_type}"')
         # Match to URI without package name
         L = len(self.package_name)
         if matchstr[:L] == self.package_name:
             matchstr = matchstr[L:]
-        for pat in patterns:
-            try:
-                pat.search
-            except AttributeError:
-                pat = re.compile(pat)
-            if pat.search(matchstr):
-                return False
-
-        return True
+        return not any(re.search(pat, matchstr) for pat in patterns)
 
     def discover_modules(self):
         r"""Return module sequence discovered from ``self.package_name``
@@ -417,7 +404,7 @@ class ApiDocWriter(object):
 
         module_by_ulm = OrderedDict()
 
-        for v, k in zip(modules, ulms):
+        for v, k in zip(modules, ulms, strict=False):
             if k in module_by_ulm:
                 module_by_ulm[k].append(v)
             else:
@@ -426,7 +413,7 @@ class ApiDocWriter(object):
         written_modules = []
 
         for ulm, mods in module_by_ulm.items():
-            print('Generating docs for %s:' % ulm)
+            print(f'Generating docs for {ulm}:')
             document_head = []
             document_body = []
 
@@ -438,11 +425,8 @@ class ApiDocWriter(object):
                 document_body.append(body)
 
             out_module = ulm + self.rst_extension
-            outfile = os.path.join(outdir, out_module)
-            fileobj = open(outfile, 'wt')
-
-            fileobj.writelines(document_head + document_body)
-            fileobj.close()
+            with open(os.path.join(outdir, out_module), 'w') as fileobj:
+                fileobj.writelines(document_head + document_body)
             written_modules.append(out_module)
 
         self.written_modules = written_modules
@@ -497,14 +481,13 @@ class ApiDocWriter(object):
             relpath = (outdir + os.path.sep).replace(relative_to + os.path.sep, '')
         else:
             relpath = outdir
-        idx = open(path, 'wt')
-        w = idx.write
-        w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
-
-        title = 'API Reference'
-        w(title + '\n')
-        w('=' * len(title) + '\n\n')
-        w('.. toctree::\n\n')
-        for f in self.written_modules:
-            w('   %s\n' % os.path.join(relpath, f))
-        idx.close()
+        with open(path, 'w') as idx:
+            w = idx.write
+            w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
+
+            title = 'API Reference'
+            w(title + '\n')
+            w('=' * len(title) + '\n\n')
+            w('.. toctree::\n\n')
+            for f in self.written_modules:
+                w(f'   {os.path.join(relpath, f)}\n')

{sdcflows-2.13.2 → sdcflows-2.14.0}/docs/tools/buildmodref.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 """Script to auto-generate API docs."""
 
-from __future__ import division, print_function
-
 # stdlib imports
 import sys
 
@@ -16,7 +14,7 @@ from apigen import ApiDocWriter
 
 
 def abort(error):
-    print('*WARNING* API documentation not generated: %s' % error)
+    print(f'*WARNING* API documentation not generated: {error}')
     exit()
 
 
@@ -43,13 +41,13 @@ def writeapi(package, outdir, source_version, other_defines=True):
     docwriter = ApiDocWriter(package, rst_extension='.rst', other_defines=other_defines)
 
     docwriter.package_skip_patterns += [
-        r'\.%s$' % package,
+        rf'\.{package}$',
         r'.*test.*$',
         r'\.version.*$',
     ]
     docwriter.write_api_docs(outdir)
     docwriter.write_index(outdir, 'index', relative_to=outdir)
-    print('%d files written' % len(docwriter.written_modules))
+    print(f'{len(docwriter.written_modules)} files written')
 
 
 if __name__ == '__main__':

{sdcflows-2.13.2 → sdcflows-2.14.0}/env.yml

@@ -9,13 +9,14 @@ dependencies:
   - mkl=2024.2.2
   - mkl-service=2.4.2
   # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.26
-  - scipy=1.15
-  - matplotlib=3.9
-  - pandas=2.2
-  - h5py=3.13
+  - numpy=2.3
+  - scipy=1.16
+  - matplotlib=3.10
+  - pandas=2.3
+  - h5py=3.14
   # Dependencies compiled against numpy, best to stick with conda
   - scikit-image=0.25
+  - scikit-learn=1.7
   # Utilities
   - graphviz=11.0
   # Workflow dependencies: ANTs

{sdcflows-2.13.2 → sdcflows-2.14.0}/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",
+    "acres >= 0.5.0",
     "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",
@@ -179,17 +178,22 @@ ignore = [
 line-length = 99
 
 [tool.ruff.lint]
-select = [
+extend-select = [
   "F",
   "E",
+  "C4",
   "W",
+  "B",
   "I",
+  "SIM",
+  "UP",
 ]
 ignore = [
   "E203",
   "B019",
   "SIM108",
   "C901",
+  "UP038",
 ]
 
 [tool.ruff.lint.flake8-quotes]
@@ -198,6 +202,9 @@ inline-quotes = "single"
 [tool.ruff.lint.extend-per-file-ignores]
 "*/__init__.py" = ["F401"]
 "docs/conf.py" = ["E265"]
+"*/test_*.py" = [
+  "B018",  # Unassigned expressions are fine
+]
 
 [tool.ruff.format]
 quote-style = "single"