Merge pull request #3238 from nipy/rel/1.5.1

effigies · web-flow · commit 071523a5069b · 2020-08-16T14:10:45.000-04:00
REL: 1.5.1
diff --git a/.zenodo.json b/.zenodo.json
@@ -115,16 +115,16 @@
       "name": "Hamalainen, Carlo",
       "orcid": "0000-0001-7655-3830"
     },
-    {
-      "affiliation": "Stanford University",
-      "name": "\u0106iri\u0107 , Rastko",
-      "orcid": "0000-0001-6347-7939"
-    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
       "orcid": "0000-0001-7037-2449"
     },
+    {
+      "affiliation": "Stanford University",
+      "name": "\u0106iri\u0107 , Rastko",
+      "orcid": "0000-0001-6347-7939"
+    },
     {
       "name": "Dubois, Mathieu"
     },
@@ -225,6 +225,11 @@
     {
       "name": "Millman, Jarrod"
     },
+    {
+      "affiliation": "University College London",
+      "name": "Mancini, Matteo",
+      "orcid": "0000-0001-7194-4568"
+    },
     {
       "affiliation": "National Institute of Mental Health",
       "name": "Nielson, Dylan M.",
@@ -241,11 +246,6 @@
     {
       "name": "Mordom, David"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Mancini, Matteo",
-      "orcid": "0000-0001-7194-4568"
-    },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
       "name": "Guillon, Je\u0301re\u0301my",
diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst
@@ -1,5 +1,21 @@
+1.5.1 (August 16, 2020)
+=======================
+
+Bug-fix release in the 1.5.x series.
+
+This release includes small updates to ANTs utilities that lie somewhere
+between bug fixes and enhancements.
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.5.1?closed=1>`__)
+
+  * FIX: Warn for min/max_ver traits when tool version can't be parsed (https://github.com/nipy/nipype/pull/3241)
+  * FIX: Serialize all interface arguments when exporting workflows (https://github.com/nipy/nipype/pull/3240)
+  * FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (https://github.com/nipy/nipype/pull/3237)
+  * FIX: ANTs' utilities revision - bug fixes and add more operations to ``ants.ImageMath`` (https://github.com/nipy/nipype/pull/3236)
+  * DOC: Skip BIDSDataGrabber doctest if pybids is missing (https://github.com/nipy/nipype/pull/3224)
+
 1.5.0 (June 03, 2020)
-=========================
+=====================
 
 New feature release in the 1.5.x series.
 
diff --git a/doc/interfaces.rst b/doc/interfaces.rst
@@ -8,7 +8,7 @@ Interfaces and Workflows
 :Release: |version|
 :Date: |today|
 
-Previous versions: `1.4.2 <http://nipype.readthedocs.io/en/1.4.2/>`_ `1.4.1 <http://nipype.readthedocs.io/en/1.4.1/>`_
+Previous versions: `1.5.0 <http://nipype.readthedocs.io/en/1.5.0/>`_ `1.4.2 <http://nipype.readthedocs.io/en/1.4.2/>`_
 
 Workflows
 ---------
diff --git a/nipype/info.py b/nipype/info.py
@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = "1.5.1-dev"
+__version__ = "1.5.1"
 
 
 def get_nipype_gitversion():
diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py
@@ -592,7 +592,8 @@ class RegistrationOutputSpec(TraitedSpec):
         File(exists=True), desc="List of output transforms for forward registration"
     )
     reverse_forward_transforms = traits.List(
-        File(exists=True), desc="List of output transforms for forward registration reversed for antsApplyTransform"
+        File(exists=True),
+        desc="List of output transforms for forward registration reversed for antsApplyTransform",
     )
     reverse_transforms = traits.List(
         File(exists=True), desc="List of output transforms for reverse registration"
@@ -601,7 +602,8 @@ class RegistrationOutputSpec(TraitedSpec):
         traits.Bool(), desc="List of flags corresponding to the forward transforms"
     )
     reverse_forward_invert_flags = traits.List(
-        traits.Bool(), desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform"
+        traits.Bool(),
+        desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform",
     )
     reverse_invert_flags = traits.List(
         traits.Bool(), desc="List of flags corresponding to the reverse transforms"
diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py
@@ -543,6 +543,7 @@ def _list_outputs(self):
             outputs["bias_image"] = os.path.abspath(self._out_bias_file)
         return outputs
 
+
 class CorticalThicknessInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(
         3, 2, argstr="-d %d", usedefault=True, desc="image dimension (2 or 3)"
diff --git a/nipype/interfaces/ants/utils.py b/nipype/interfaces/ants/utils.py
@@ -138,18 +138,18 @@ class ImageMath(ANTSCommand, CopyHeaderInterface):
 
     def __init__(self, **inputs):
         super(ImageMath, self).__init__(**inputs)
-        if self.inputs.operation in ("PadImage", ):
+        if self.inputs.operation in ("PadImage",):
             self.inputs.copy_header = False
 
         self.inputs.on_trait_change(self._operation_update, "operation")
         self.inputs.on_trait_change(self._copyheader_update, "copy_header")
 
     def _operation_update(self):
-        if self.inputs.operation in ("PadImage", ):
+        if self.inputs.operation in ("PadImage",):
             self.inputs.copy_header = False
 
     def _copyheader_update(self):
-        if self.inputs.copy_header and self.inputs.operation in ("PadImage", ):
+        if self.inputs.copy_header and self.inputs.operation in ("PadImage",):
             warn("copy_header cannot be updated to True with PadImage as operation.")
             self.inputs.copy_header = False
 
diff --git a/nipype/interfaces/freesurfer/base.py b/nipype/interfaces/freesurfer/base.py
@@ -76,7 +76,7 @@ def looseversion(cls):
                 vstr = "6.0.0-dev" + githash
             elif vinfo[5][0] == "v":
                 vstr = vinfo[5][1:]
-            elif len([1 for val in vinfo[3] if val == '.']) == 2:
+            elif len([1 for val in vinfo[3] if val == "."]) == 2:
                 "version string: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b"
                 vstr = vinfo[3]
             else:
diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
@@ -727,7 +727,10 @@ def cmdline(self):
         outdir = self._get_outdir()
         cmd = []
         if not os.path.exists(outdir):
-            cmdstr = "%s -c \"import os; os.makedirs('%s')\"" % (op.basename(sys.executable), outdir)
+            cmdstr = "%s -c \"import os; os.makedirs('%s')\"" % (
+                op.basename(sys.executable),
+                outdir,
+            )
             cmd.extend([cmdstr])
         infofile = os.path.join(outdir, "shortinfo.txt")
         if not os.path.exists(infofile):
diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
@@ -174,9 +174,9 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = self._gen_outfilename()
 
-        basename = os.path.basename(outputs['out_file'])
-        cwd = os.path.dirname(outputs['out_file'])
-        kwargs = {'basename': basename, 'cwd': cwd}
+        basename = os.path.basename(outputs["out_file"])
+        cwd = os.path.dirname(outputs["out_file"])
+        kwargs = {"basename": basename, "cwd": cwd}
 
         if (isdefined(self.inputs.mesh) and self.inputs.mesh) or (
             isdefined(self.inputs.surfaces) and self.inputs.surfaces
@@ -189,9 +189,7 @@ def _list_outputs(self):
         ):
             outputs["mask_file"] = self._gen_fname(suffix="_mask", **kwargs)
         if isdefined(self.inputs.outline) and self.inputs.outline:
-            outputs["outline_file"] = self._gen_fname(
-                suffix="_overlay", **kwargs
-            )
+            outputs["outline_file"] = self._gen_fname(suffix="_overlay", **kwargs)
         if isdefined(self.inputs.surfaces) and self.inputs.surfaces:
             outputs["inskull_mask_file"] = self._gen_fname(
                 suffix="_inskull_mask", **kwargs
@@ -211,13 +209,9 @@ def _list_outputs(self):
             outputs["outskin_mesh_file"] = self._gen_fname(
                 suffix="_outskin_mesh", **kwargs
             )
-            outputs["skull_mask_file"] = self._gen_fname(
-                suffix="_skull_mask", **kwargs
-            )
+            outputs["skull_mask_file"] = self._gen_fname(suffix="_skull_mask", **kwargs)
         if isdefined(self.inputs.skull) and self.inputs.skull:
-            outputs["skull_file"] = self._gen_fname(
-                suffix="_skull", **kwargs
-            )
+            outputs["skull_file"] = self._gen_fname(suffix="_skull", **kwargs)
         if isdefined(self.inputs.no_output) and self.inputs.no_output:
             outputs["out_file"] = Undefined
         return outputs
diff --git a/nipype/interfaces/niftyreg/base.py b/nipype/interfaces/niftyreg/base.py
@@ -19,8 +19,7 @@
 import os
 
 from ... import logging
-from ..base import (CommandLine, CommandLineInputSpec, traits, Undefined,
-                    PackageInfo)
+from ..base import CommandLine, CommandLineInputSpec, traits, Undefined, PackageInfo
 from ...utils.filemanip import split_filename
 
 iflogger = logging.getLogger("nipype.interface")
@@ -31,7 +30,7 @@ def get_custom_path(command, env_dir="NIFTYREGDIR"):
 
 
 class Info(PackageInfo):
-    version_cmd = get_custom_path('reg_aladin') + ' --version'
+    version_cmd = get_custom_path("reg_aladin") + " --version"
 
     @staticmethod
     def parse_version(raw_info):
diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py
@@ -1884,7 +1884,7 @@ class MultiChannelNewSegmentInputSpec(SPMCommandInputSpec):
                     - FWHM of Gaussian smoothness of bias
                     - which maps to save (Field, Corrected) - a tuple of two boolean values""",
                 field="channel",
-            )
+            ),
         ),
         desc="""A list of tuples (one per each channel) with the following fields:
             - a list of channel files (only 1rst channel files will be segmented)
diff --git a/nipype/pipeline/plugins/tests/test_legacymultiproc_nondaemon.py b/nipype/pipeline/plugins/tests/test_legacymultiproc_nondaemon.py
@@ -134,7 +134,9 @@ def run_multiproc_nondaemon_with_flag(nondaemon_flag):
     return result
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_run_multiproc_nondaemon_false():
     """
     This is the entry point for the test. Two times a pipe of several
@@ -153,7 +155,9 @@ def test_run_multiproc_nondaemon_false():
     assert shouldHaveFailed
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_run_multiproc_nondaemon_true():
     # with nondaemon_flag = True, the execution should succeed
     result = run_multiproc_nondaemon_with_flag(True)
diff --git a/nipype/pipeline/plugins/tests/test_multiproc.py b/nipype/pipeline/plugins/tests/test_multiproc.py
@@ -34,7 +34,9 @@ def _list_outputs(self):
         return outputs
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_run_multiproc(tmpdir):
     tmpdir.chdir()
 
@@ -116,7 +118,9 @@ def test_no_more_threads_than_specified(tmpdir):
         pipe.run(plugin="MultiProc", plugin_args={"n_procs": max_threads})
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_hold_job_until_procs_available(tmpdir):
     tmpdir.chdir()
 
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
@@ -655,12 +655,15 @@ def test_pickle(tmp_path, save_versioning):
     assert outobj == testobj
 
 
-@pytest.mark.parametrize("items,expected", [
-    ('', ' \n\n'),
-    ('A string', ' A string\n\n'),
-    (['A list', 'Of strings'], ' A list\n Of strings\n\n'),
-    (None, TypeError),
-])
+@pytest.mark.parametrize(
+    "items,expected",
+    [
+        ("", " \n\n"),
+        ("A string", " A string\n\n"),
+        (["A list", "Of strings"], " A list\n Of strings\n\n"),
+        (None, TypeError),
+    ],
+)
 def test_write_rst_list(tmp_path, items, expected):
     if items is not None:
         assert write_rst_list(items) == expected

Original file line number	Diff line number	Diff line change
`@@ -592,7 +592,8 @@ class RegistrationOutputSpec(TraitedSpec):`
`592`	`592`	`File(exists=True), desc="List of output transforms for forward registration"`
`593`	`593`	`)`
`594`	`594`	`reverse_forward_transforms = traits.List(`
`595`		`- File(exists=True), desc="List of output transforms for forward registration reversed for antsApplyTransform"`
	`595`	`+ File(exists=True),`
	`596`	`+ desc="List of output transforms for forward registration reversed for antsApplyTransform",`
`596`	`597`	`)`
`597`	`598`	`reverse_transforms = traits.List(`
`598`	`599`	`File(exists=True), desc="List of output transforms for reverse registration"`
`@@ -601,7 +602,8 @@ class RegistrationOutputSpec(TraitedSpec):`
`601`	`602`	`traits.Bool(), desc="List of flags corresponding to the forward transforms"`
`602`	`603`	`)`
`603`	`604`	`reverse_forward_invert_flags = traits.List(`
`604`		`- traits.Bool(), desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform"`
	`605`	`+ traits.Bool(),`
	`606`	`+ desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform",`
`605`	`607`	`)`
`606`	`608`	`reverse_invert_flags = traits.List(`
`607`	`609`	`traits.Bool(), desc="List of flags corresponding to the reverse transforms"`