nipy · effigies · Jul 5, 2023 · Jul 5, 2023 · Jul 5, 2023 · Jul 5, 2023
diff --git 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
diff --git 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

diff --git a/nipype/info.py b/nipype/info.py
@@ -147,12 +147,12 @@ 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 = [
     "codecov",
-    "coverage<5",
+    "coverage",
     "pytest",
     "pytest-cov",
     "pytest-env",

diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py
@@ -329,7 +329,11 @@ 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,
+        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]",
     )
@@ -393,7 +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
@@ -406,7 +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
     """
 
@@ -421,7 +425,6 @@ def version(self):
     def _format_arg(self, opt, spec, val):
         bools = [
             "bids_format",
-            "merge_imgs",
             "single_file",
             "verbose",
             "crop",

diff --git 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
@@ -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
@@ -41,7 +41,7 @@ def test_Dcm2niix_inputs():
             argstr="-i",
         ),
         merge_imgs=dict(
-            argstr="-m",
+            argstr="-m %d",
             usedefault=True,
         ),
         out_filename=dict(

diff --git 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