From b9cfbb5df1d762a7858748cebefbf92b3aad081f Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 11:21:28 -0400
Subject: [PATCH 1/9] FIX: Permit newer coverage

---
 nipype/info.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/info.py b/nipype/info.py
index b6e6245511..f96e1783d5 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -152,7 +152,7 @@ def get_nipype_gitversion():
 
 TESTS_REQUIRES = [
     "codecov",
-    "coverage<5",
+    "coverage",
     "pytest",
     "pytest-cov",
     "pytest-env",

From 6f3ed28738961b0cee72f8caf5693dd42cbebbc7 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 11:21:38 -0400
Subject: [PATCH 2/9] FIX: make specs

---
 nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py  | 4 ++--
 nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py | 4 ++--
 nipype/interfaces/tests/test_auto_Dcm2niix.py        | 3 +--
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py
index aae5d80c57..c841391efc 100644
--- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py
+++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py
@@ -90,13 +90,13 @@ def test_ProbTrackX_inputs():
             argstr="--randfib=%d",
         ),
         random_seed=dict(
-            argstr="--rseed",
+            argstr="--rseed=%d",
         ),
         s2tastext=dict(
             argstr="--s2tastext",
         ),
         sample_random_points=dict(
-            argstr="--sampvox",
+            argstr="--sampvox=%.3f",
         ),
         samples_base_name=dict(
             argstr="--samples=%s",
diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py
index 1813bd3c9c..f1941f036d 100644
--- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py
+++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py
@@ -116,13 +116,13 @@ def test_ProbTrackX2_inputs():
             argstr="--randfib=%d",
         ),
         random_seed=dict(
-            argstr="--rseed",
+            argstr="--rseed=%d",
         ),
         s2tastext=dict(
             argstr="--s2tastext",
         ),
         sample_random_points=dict(
-            argstr="--sampvox",
+            argstr="--sampvox=%.3f",
         ),
         samples_base_name=dict(
             argstr="--samples=%s",
diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py
index dec95abcff..328067806f 100644
--- a/nipype/interfaces/tests/test_auto_Dcm2niix.py
+++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py
@@ -41,8 +41,7 @@ def test_Dcm2niix_inputs():
             argstr="-i",
         ),
         merge_imgs=dict(
-            argstr="-m",
-            usedefault=True,
+            argstr="-m %d",
         ),
         out_filename=dict(
             argstr="-f %s",

From d473dcbcf676303d2c0e16fa5884506baa52dac1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 11:22:01 -0400
Subject: [PATCH 3/9] FIX: Remove unused decorators that depended on deprecated
 numpy module

---
 nipype/testing/__init__.py   |  3 --
 nipype/testing/decorators.py | 98 ------------------------------------
 2 files changed, 101 deletions(-)
 delete mode 100644 nipype/testing/decorators.py

diff --git a/nipype/testing/__init__.py b/nipype/testing/__init__.py
index c22de2cc7a..4a0ab306f6 100644
--- a/nipype/testing/__init__.py
+++ b/nipype/testing/__init__.py
@@ -16,11 +16,8 @@
 template = funcfile
 transfm = funcfile
 
-from . import decorators
 from .utils import package_check, TempFATFS
 
-skipif = decorators.dec.skipif
-
 
 def example_data(infile="functional.nii"):
     """returns path to empty example data files for doc tests
diff --git a/nipype/testing/decorators.py b/nipype/testing/decorators.py
deleted file mode 100644
index a0e4c2ede1..0000000000
--- a/nipype/testing/decorators.py
+++ /dev/null
@@ -1,98 +0,0 @@
-# -*- 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:
-"""
-Extend numpy's decorators to use nipype's gui and data labels.
-"""
-from numpy.testing import dec
-
-from nibabel.data import DataError
-
-
-def make_label_dec(label, ds=None):
-    """Factory function to create a decorator that applies one or more labels.
-
-    Parameters
-    ----------
-    label : str or sequence
-        One or more labels that will be applied by the decorator to the
-        functions it decorates. Labels are attributes of the decorated function
-        with their value set to True.
-    ds : str
-        An optional docstring for the resulting decorator. If not given, a
-        default docstring is auto-generated.
-
-    Returns
-    -------
-    ldec : function
-        A decorator.
-
-    Examples
-    --------
-    >>> slow = make_label_dec('slow')
-    >>> slow.__doc__
-    "Labels a test as 'slow'"
-
-    >>> rare = make_label_dec(['slow','hard'],
-    ... "Mix labels 'slow' and 'hard' for rare tests")
-    >>> @rare
-    ... def f(): pass
-    ...
-    >>>
-    >>> f.slow
-    True
-    >>> f.hard
-    True
-    """
-    if isinstance(label, str):
-        labels = [label]
-    else:
-        labels = label
-    # Validate that the given label(s) are OK for use in setattr() by doing a
-    # dry run on a dummy function.
-    tmp = lambda: None
-    for label in labels:
-        setattr(tmp, label, True)
-    # This is the actual decorator we'll return
-
-    def decor(f):
-        for label in labels:
-            setattr(f, label, True)
-        return f
-
-    # Apply the user's docstring
-    if ds is None:
-        ds = "Labels a test as %r" % label
-        decor.__doc__ = ds
-    return decor
-
-
-# For tests that need further review
-
-
-def needs_review(msg):
-    """Skip a test that needs further review.
-
-    Parameters
-    ----------
-    msg : string
-        msg regarding the review that needs to be done
-    """
-
-    def skip_func(func):
-        return dec.skipif(True, msg)(func)
-
-    return skip_func
-
-
-# Easier version of the numpy knownfailure
-def knownfailure(f):
-    return dec.knownfailureif(True)(f)
-
-
-def if_datasource(ds, msg):
-    try:
-        ds.get_filename()
-    except DataError:
-        return dec.skipif(True, msg)
-    return lambda f: f

From 8dd46d3b613c2151cd9df9ec490d60605f8e07be Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 09:56:14 -0400
Subject: [PATCH 4/9] MNT: Add afile to codespell ignores

---
 .codespellrc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.codespellrc b/.codespellrc
index fcf6e648ca..4bc57b6662 100644
--- a/.codespellrc
+++ b/.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

From 3b89ca85faf2428ecf7844de9c0db4aa7c329c93 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 11:30:42 -0400
Subject: [PATCH 5/9] STY: black

---
 nipype/interfaces/dcm2nii.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py
index 8a268f951a..41321855c5 100644
--- a/nipype/interfaces/dcm2nii.py
+++ b/nipype/interfaces/dcm2nii.py
@@ -329,7 +329,9 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
         desc="Gzip compress images - [y=pigz, i=internal, n=no, 3=no,3D]",
     )
     merge_imgs = traits.Enum(
-        0, 1, 2,
+        0,
+        1,
+        2,
         argstr="-m %d",
         desc="merge 2D slices from same series regardless of echo, exposure, etc. - [0=no, 1=yes, 2=auto]",
     )

From fc43d6521ecb72787c40fc1c1f350f606efbaa74 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 11:32:31 -0400
Subject: [PATCH 6/9] MNT: Build docs on Python 3.10

---
 .readthedocs.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 5a32188317..33b5e91a58 100644
--- a/.readthedocs.yml
+++ b/.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

From fec8cd950c66a2f29c896ad69c0fe3f3e0e3a193 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 12:08:51 -0400
Subject: [PATCH 7/9] MNT: Avoid looseversion 1.2

---
 nipype/info.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/info.py b/nipype/info.py
index f96e1783d5..0dd048e38a 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -147,7 +147,7 @@ def get_nipype_gitversion():
     "traits>=%s,<%s,!=5.0" % (TRAITS_MIN_VERSION, TRAITS_MAX_VERSION),
     "filelock>=3.0.0",
     "etelemetry>=0.2.0",
-    "looseversion",
+    "looseversion!=1.2",
 ]
 
 TESTS_REQUIRES = [

From 6bf5f7a89fefc4b5225c5f46b4e4168a60930ff7 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 12:29:45 -0400
Subject: [PATCH 8/9] FIX: dcm2niix -m arguments

---
 nipype/interfaces/dcm2nii.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py
index 41321855c5..6b6de041bf 100644
--- a/nipype/interfaces/dcm2nii.py
+++ b/nipype/interfaces/dcm2nii.py
@@ -332,6 +332,8 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
         0,
         1,
         2,
+        default=0,
+        usedefault=True,
         argstr="-m %d",
         desc="merge 2D slices from same series regardless of echo, exposure, etc. - [0=no, 1=yes, 2=auto]",
     )
@@ -395,7 +397,7 @@ class Dcm2niix(CommandLine):
     >>> converter.inputs.compression = 5
     >>> converter.inputs.output_dir = 'ds005'
     >>> converter.cmdline
-    'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir'
+    'dcm2niix -b y -z y -5 -x n -t n -m 0 -o ds005 -s n -v n dicomdir'
     >>> converter.run() # doctest: +SKIP
 
     In the example below, we note that the current version of dcm2niix
@@ -408,7 +410,7 @@ class Dcm2niix(CommandLine):
     >>> converter.inputs.compression = 5
     >>> converter.inputs.output_dir = 'ds005'
     >>> converter.cmdline
-    'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n .'
+    'dcm2niix -b y -z y -5 -x n -t n -m 0 -o ds005 -s n -v n .'
     >>> converter.run() # doctest: +SKIP
     """
 
@@ -423,7 +425,6 @@ def version(self):
     def _format_arg(self, opt, spec, val):
         bools = [
             "bids_format",
-            "merge_imgs",
             "single_file",
             "verbose",
             "crop",

From 5e2fd1cdeda57b21940271eb9393f000b810690b Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 5 Jul 2023 12:32:58 -0400
Subject: [PATCH 9/9] TEST: make specs

---
 nipype/interfaces/tests/test_auto_Dcm2niix.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py
index 328067806f..7563f0ddb2 100644
--- a/nipype/interfaces/tests/test_auto_Dcm2niix.py
+++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py
@@ -42,6 +42,7 @@ def test_Dcm2niix_inputs():
         ),
         merge_imgs=dict(
             argstr="-m %d",
+            usedefault=True,
         ),
         out_filename=dict(
             argstr="-f %s",