Merge branch 'master' into master

Author: effigies

.codespellrc

@@ -5,8 +5,8 @@ skip = .git,*.pdf,*.svg,external
 # whos - smth used in matlab things
 # SMAL - Stanford CNI MRS Library
 # Suh - name
-# noo,crasher - field/var name used
+# noo,crasher,afile - field/var name used
 # Reson - short journal name
 # ALS, FWE - neuroimaging specific abbrevs
 # Comision - foreign word used
-ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision
+ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile

.github/workflows/tests.yml

@@ -90,16 +90,16 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-20.04']
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        os: ['ubuntu-22.04']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         check: ['test']
         pip-flags: ['']
         depends: ['REQUIREMENTS']
         deb-depends: [false]
         nipype-extras: ['doc,tests,profiler']
         include:
-          - os: ubuntu-20.04
-            python-version: 3.8
+          - os: ubuntu-22.04
+            python-version: '3.8'
             check: test
             pip-flags: ''
             depends: REQUIREMENTS

.pre-commit-config.yaml

@@ -1,14 +1,18 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
-    -   id: black
+      - id: black
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+    - id: codespell

.readthedocs.yml

@@ -4,6 +4,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: doc/conf.py
@@ -12,9 +18,10 @@ sphinx:
 formats:
   - htmlzip
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.7
   install:
     - requirements: doc/requirements.txt
     - method: pip

.zenodo.json

@@ -379,6 +379,11 @@
     {
       "name": "Schwartz, Yannick"
     },
+    {
+      "affiliation": "Medical College of Wisconsin",
+      "name": "Espana, Lezlie",
+      "orcid": "0000-0002-6466-4653"
+    },
     {
       "affiliation": "The University of Iowa",
       "name": "Ghayoor, Ali",

doc/conf.py

@@ -1,5 +1,3 @@
-# emacs: -*- coding: utf-8; mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set fileencoding=utf-8 ft=python sts=4 ts=4 sw=4 et:
 #
 # nipype documentation build configuration file, created by
 # sphinx-quickstart on Mon Jul 20 12:30:18 2009.
@@ -151,8 +149,8 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"nipype"
-copyright = u"2009-21, Neuroimaging in Python team"
+project = "nipype"
+copyright = "2009-21, Neuroimaging in Python team"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/devel/matlab_example1.py

@@ -1,6 +1,10 @@
 from nipype.interfaces.matlab import MatlabCommand
-from nipype.interfaces.base import TraitedSpec, \
-    BaseInterface, BaseInterfaceInputSpec, File
+from nipype.interfaces.base import (
+    TraitedSpec,
+    BaseInterface,
+    BaseInterfaceInputSpec,
+    File,
+)
 import os
 from string import Template
 
@@ -19,14 +23,15 @@ class ConmapTxt2Mat(BaseInterface):
     output_spec = ConmapTxt2MatOutputSpec
 
     def _run_interface(self, runtime):
-        d = dict(in_file=self.inputs.in_file,
-                 out_file=self.inputs.out_file)
+        d = dict(in_file=self.inputs.in_file, out_file=self.inputs.out_file)
         # This is your MATLAB code template
-        script = Template("""in_file = '$in_file';
+        script = Template(
+            """in_file = '$in_file';
                              out_file = '$out_file';
                              ConmapTxt2Mat(in_file, out_file);
                              exit;
-                          """).substitute(d)
+                          """
+        ).substitute(d)
 
         # mfile = True  will create an .m file with your script and executed.
         # Alternatively

doc/devel/matlab_example2.py

@@ -4,8 +4,7 @@
 
 
 class HelloWorldInputSpec(MatlabInputSpec):
-    name = traits.Str(mandatory=True,
-                      desc='Name of person to say hello to')
+    name = traits.Str(mandatory=True, desc='Name of person to say hello to')
 
 
 class HelloWorldOutputSpec(TraitedSpec):
@@ -29,6 +28,7 @@ class HelloWorld(MatlabCommand):
     >>> out = hello.run()
     >>> print out.outputs.matlab_output
     """
+
     input_spec = HelloWorldInputSpec
     output_spec = HelloWorldOutputSpec
 
@@ -37,7 +37,9 @@ def _my_script(self):
         script = """
         disp('Hello %s Python')
         two = 1 + 1
-        """ % (self.inputs.name)
+        """ % (
+            self.inputs.name
+        )
         return script
 
     def run(self, **inputs):

nipype/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
@@ -26,14 +25,14 @@
     import faulthandler
 
     faulthandler.enable()
-except (ImportError, IOError) as e:
+except (ImportError, OSError) as e:
     pass
 
 config = NipypeConfig()
 logging = Logging(config)
 
 
-class NipypeTester(object):
+class NipypeTester:
     def __call__(self, doctests=True, parallel=False):
         try:
             import pytest

nipype/algorithms/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """

nipype/algorithms/confounds.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
@@ -150,7 +149,7 @@ class ComputeDVARS(BaseInterface):
 
     def __init__(self, **inputs):
         self._results = {}
-        super(ComputeDVARS, self).__init__(**inputs)
+        super().__init__(**inputs)
 
     def _gen_fname(self, suffix, ext=None):
         fname, in_ext = op.splitext(op.basename(self.inputs.in_file))
@@ -165,7 +164,7 @@ def _gen_fname(self, suffix, ext=None):
         if ext.startswith("."):
             ext = ext[1:]
 
-        return op.abspath("{}_{}.{}".format(fname, suffix, ext))
+        return op.abspath(f"{fname}_{suffix}.{ext}")
 
     def _run_interface(self, runtime):
         dvars = compute_dvars(
@@ -466,12 +465,12 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
         "cosine",
         False,
         usedefault=True,
-        desc="Detrend time series prior to component " "extraction",
+        desc="Detrend time series prior to component extraction",
     )
     use_regress_poly = traits.Bool(
         deprecated="0.15.0",
         new_name="pre_filter",
-        desc=("use polynomial regression " "pre-component extraction"),
+        desc=("use polynomial regression pre-component extraction"),
     )
     regress_poly_degree = traits.Range(
         low=1, value=1, usedefault=True, desc="the degree polynomial to use"
@@ -584,7 +583,7 @@ class CompCor(SimpleInterface):
 
     def __init__(self, *args, **kwargs):
         """exactly the same as compcor except the header"""
-        super(CompCor, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._header = "CompCor"
 
     def _run_interface(self, runtime):
@@ -713,7 +712,7 @@ def _run_interface(self, runtime):
                 self.inputs.pre_filter
             ]
             ncols = filter_basis.shape[1] if filter_basis.size > 0 else 0
-            header = ["{}{:02d}".format(ftype, i) for i in range(ncols)]
+            header = [f"{ftype}{i:02d}" for i in range(ncols)]
             if skip_vols:
                 old_basis = filter_basis
                 # nrows defined above
@@ -724,7 +723,7 @@ def _run_interface(self, runtime):
                     filter_basis[skip_vols:, :ncols] = old_basis
                 filter_basis[:skip_vols, -skip_vols:] = np.eye(skip_vols)
                 header.extend(
-                    ["NonSteadyStateOutlier{:02d}".format(i) for i in range(skip_vols)]
+                    [f"NonSteadyStateOutlier{i:02d}" for i in range(skip_vols)]
                 )
             np.savetxt(
                 self._results["pre_filter_file"],
@@ -747,7 +746,7 @@ def _run_interface(self, runtime):
             not_retained = np.where(np.logical_not(metadata["retained"]))
             components_names[retained] = components_header
             components_names[not_retained] = [
-                "dropped{}".format(i) for i in range(len(not_retained[0]))
+                f"dropped{i}" for i in range(len(not_retained[0]))
             ]
             with open(self._results["metadata_file"], "w") as f:
                 f.write("\t".join(["component"] + list(metadata.keys())) + "\n")
@@ -768,7 +767,7 @@ def _make_headers(self, num_col):
             if isdefined(self.inputs.header_prefix)
             else self._header
         )
-        headers = ["{}{:02d}".format(header, i) for i in range(num_col)]
+        headers = [f"{header}{i:02d}" for i in range(num_col)]
         return headers
 
 
@@ -781,7 +780,7 @@ class ACompCor(CompCor):
 
     def __init__(self, *args, **kwargs):
         """exactly the same as compcor except the header"""
-        super(ACompCor, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._header = "aCompCor"
 
 
@@ -807,7 +806,7 @@ class TCompCorInputSpec(CompCorInputSpec):
 class TCompCorOutputSpec(CompCorOutputSpec):
     # and all the fields in CompCorOutputSpec
     high_variance_masks = OutputMultiPath(
-        File(exists=True), desc=(("voxels exceeding the variance" " threshold"))
+        File(exists=True), desc=("voxels exceeding the variance threshold")
     )
 
 
@@ -832,7 +831,7 @@ class TCompCor(CompCor):
 
     def __init__(self, *args, **kwargs):
         """exactly the same as compcor except the header"""
-        super(TCompCor, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._header = "tCompCor"
         self._mask_files = []
 
@@ -854,10 +853,10 @@ def _process_masks(self, mask_images, timeseries=None):
             out_image = nb.Nifti1Image(mask_data, affine=img.affine, header=img.header)
 
             # save mask
-            mask_file = os.path.abspath("mask_{:03d}.nii.gz".format(i))
+            mask_file = os.path.abspath(f"mask_{i:03d}.nii.gz")
             out_image.to_filename(mask_file)
             IFLOGGER.debug(
-                "tCompcor computed and saved mask of shape %s to " "mask_file %s",
+                "tCompcor computed and saved mask of shape %s to mask_file %s",
                 str(mask.shape),
                 mask_file,
             )
@@ -866,7 +865,7 @@ def _process_masks(self, mask_images, timeseries=None):
         return out_images
 
     def _list_outputs(self):
-        outputs = super(TCompCor, self)._list_outputs()
+        outputs = super()._list_outputs()
         outputs["high_variance_masks"] = self._mask_files
         return outputs
 
@@ -1136,7 +1135,7 @@ def plot_confound(tseries, figsize, name, units=None, series_tr=None, normalize=
 
     xlabel = "Frame #"
     if series_tr is not None:
-        xlabel = "Frame # ({} sec TR)".format(series_tr)
+        xlabel = f"Frame # ({series_tr} sec TR)"
     ax.set_xlabel(xlabel)
     ylim = ax.get_ylim()
 
@@ -1280,19 +1279,15 @@ def combine_mask_files(mask_files, mask_method=None, mask_index=None):
                 mask_index = 0
             else:
                 raise ValueError(
-                    (
-                        "When more than one mask file is provided, "
-                        "one of merge_method or mask_index must be "
-                        "set"
-                    )
+                    "When more than one mask file is provided, "
+                    "one of merge_method or mask_index must be "
+                    "set"
                 )
         if mask_index < len(mask_files):
             mask = nb.load(mask_files[mask_index])
             return [mask]
         raise ValueError(
-            ("mask_index {0} must be less than number of mask " "files {1}").format(
-                mask_index, len(mask_files)
-            )
+            f"mask_index {mask_index} must be less than number of mask files {len(mask_files)}"
         )
     masks = []
     if mask_method == "none":

nipype/algorithms/icc.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import os
 from functools import lru_cache
 import numpy as np