Merge branch 'rel/1.5.0'

Author: effigies

.travis.yml

@@ -4,7 +4,6 @@ dist: xenial
 language: python
 # our build matrix
 python:
-- 3.5
 - 3.6
 - 3.7
 

.zenodo.json

@@ -157,11 +157,6 @@
       "name": "De La Vega, Alejandro",
       "orcid": "0000-0001-9062-3778"
     },
-    {
-      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
-      "name": "Waller, Lea",
-      "orcid": "0000-0002-3239-6957"
-    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -183,6 +178,11 @@
     {
       "name": "Erickson, Drew"
     },
+    {
+      "affiliation": "Neuroscience Program, University of Iowa",
+      "name": "Kent, James D.",
+      "orcid": "0000-0002-4892-2659"
+    },
     {
       "affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
       "name": "Hanke, Michael",
@@ -195,11 +195,6 @@
     {
       "name": "Moloney, Brendan"
     },
-    {
-      "affiliation": "Neuroscience Program, University of Iowa",
-      "name": "Kent, James D.",
-      "orcid": "0000-0002-4892-2659"
-    },
     {
       "affiliation": "SRI International",
       "name": "Nichols, B. Nolan",
@@ -246,6 +241,11 @@
     {
       "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",
@@ -291,16 +291,16 @@
     {
       "name": "Salvatore, John"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Mancini, Matteo",
-      "orcid": "0000-0001-7194-4568"
-    },
     {
       "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay",
       "name": "Gramfort, Alexandre",
       "orcid": "0000-0001-9791-4404"
     },
+    {
+      "affiliation": "Department of Psychology, University of Bielefeld, Bielefeld, Germany.",
+      "name": "Doll, Anna",
+      "orcid": "0000-0002-0799-0831"
+    },
     {
       "name": "Buchanan, Colin"
     },
@@ -393,9 +393,14 @@
       "orcid": "0000-0003-2766-8425"
     },
     {
-      "affiliation": "Department of Psychology, University of Bielefeld, Bielefeld, Germany.",
-      "name": "Doll, Anna",
-      "orcid": "0000-0002-0799-0831"
+      "affiliation": "NIMH, Scientific and Statistical Computing Core",
+      "name": "Glen, Daniel",
+      "orcid": "0000-0001-8456-5647"
+    },
+    {
+      "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
+      "name": "Geisler, Daniel",
+      "orcid": "0000-0003-2076-5329"
     },
     {
       "affiliation": "University of Iowa",
@@ -406,6 +411,11 @@
       "name": "Triplett, William",
       "orcid": "0000-0002-9546-1306"
     },
+    {
+      "affiliation": "The University of Iowa",
+      "name": "Ghayoor, Ali",
+      "orcid": "0000-0002-8858-1254"
+    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Craddock, R. Cameron",
@@ -450,12 +460,12 @@
       "name": "Rothmei, Simon"
     },
     {
-      "name": "Weinstein, Alejandro"
+      "affiliation": "Korea Advanced Institute of Science and Technology",
+      "name": "Kim, Sin",
+      "orcid": "0000-0003-4652-3758"
     },
     {
-      "affiliation": "The University of Iowa",
-      "name": "Ghayoor, Ali",
-      "orcid": "0000-0002-8858-1254"
+      "name": "Weinstein, Alejandro"
     },
     {
       "affiliation": "University of Pennsylvania",
@@ -508,6 +518,11 @@
       "name": "Linkersd\u00f6rfer, Janosch",
       "orcid": "0000-0002-1577-1233"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "name": "Renfro, Mandy"
     },
@@ -521,11 +536,6 @@
     {
       "name": "K\u00fcttner, Ren\u00e9"
     },
-    {
-      "affiliation": "Korea Advanced Institute of Science and Technology",
-      "name": "Kim, Sin",
-      "orcid": "0000-0003-4652-3758"
-    },
     {
       "affiliation": "California Institute of Technology",
       "name": "Pauli, Wolfgang M.",
@@ -536,6 +546,11 @@
       "name": "Glen, Daniel",
       "orcid": "0000-0001-8456-5647"
     },
+    {
+      "affiliation": "Florida International University",
+      "name": "Kimbler, Adam",
+      "orcid": "0000-0001-5885-9596"
+    },
     {
       "affiliation": "University of Pittsburgh",
       "name": "Meyers, Benjamin",
@@ -544,11 +559,6 @@
     {
       "name": "Tarbert, Claire"
     },
-    {
-      "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
-      "name": "Geisler, Daniel",
-      "orcid": "0000-0003-2076-5329"
-    },
     {
       "name": "Ginsburg, Daniel"
     },

doc/changelog/1.X.X-changelog.rst

@@ -1,3 +1,29 @@
+1.5.0 (To be determined)
+=========================
+
+New feature release in the 1.5.x series.
+
+In this release, the example scripts have been split out into their own package:
+`niflow-nipype1-examples <https://github.com/niflows/nipype1-examples>`__.
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.5.0?closed=1>`__)
+
+  * FIX: Partial rollback of N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3188)
+  * FIX: ANTs' tools maintenance overhaul (https://github.com/nipy/nipype/pull/3180)
+  * FIX: load_resultfile crashes if open resultsfile from crashed job (https://github.com/nipy/nipype/pull/3182)
+  * FIX: FSL model.py make multiple F-tests (https://github.com/nipy/nipype/pull/3166)
+  * ENH: Improve workflow connect performance (https://github.com/nipy/nipype/pull/3184)
+  * ENH: Add ``ConstrainedSphericalDeconvolution`` interface to replace ``EstimateFOD`` for MRtrix3's ``dwi2fod`` (https://github.com/nipy/nipype/pull/3176)
+  * ENH: Detect values for EulerNumber interface (https://github.com/nipy/nipype/pull/3173)
+  * ENH: Remove examples from repository (https://github.com/nipy/nipype/pull/3172)
+  * REF: Prefer math.gcd to hand-rolled Euclid's algorithm (https://github.com/nipy/nipype/pull/3177)
+  * REF: Removed all uses of numpy_mmap (https://github.com/nipy/nipype/pull/3121)
+  * DOC: Update links, typos in contributing guide (https://github.com/nipy/nipype/pull/3160)
+  * DOC: Update SelectFiles docstring to match actual behavior (https://github.com/nipy/nipype/pull/3041)
+  * DOC: Updated .zenodo.json file (https://github.com/nipy/nipype/pull/3167)
+  * DOC: Update .zenodo.json (https://github.com/nipy/nipype/pull/3165)
+  * MNT: Update Zenodo ordering based on commit count (https://github.com/nipy/nipype/pull/3169)
+
 1.4.2 (February 14, 2020)
 =========================
 (`Full changelog <https://github.com/nipy/nipype/milestone/1.4.2?closed=1>`__)

nipype/info.py

@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = "1.5.0-dev"
+__version__ = "1.5.0-rc1.post-dev"
 
 
 def get_nipype_gitversion():
@@ -54,12 +54,11 @@ def get_nipype_gitversion():
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.5",
     "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Topic :: Scientific/Engineering",
 ]
-PYTHON_REQUIRES = ">= 3.5"
+PYTHON_REQUIRES = ">= 3.6"
 
 description = "Neuroimaging in Python: Pipelines and Interfaces"
 
@@ -100,7 +99,7 @@ def get_nipype_gitversion():
 # versions
 NIBABEL_MIN_VERSION = "2.1.0"
 NETWORKX_MIN_VERSION = "1.9"
-NUMPY_MIN_VERSION = "1.12"
+NUMPY_MIN_VERSION = "1.13"
 # Numpy bug in python 3.7:
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
 NUMPY_MIN_VERSION_37 = "1.15.3"

nipype/interfaces/base/traits_extension.py

@@ -26,6 +26,7 @@
 import traits.api as traits
 from traits.api import TraitType, Unicode
 from traits.trait_base import _Undefined
+
 try:
     # Moved in traits 6.0
     from traits.trait_type import NoDefaultSpecified

nipype/interfaces/freesurfer/utils.py

@@ -2592,8 +2592,10 @@ class EulerNumberInputSpec(FSTraitedSpec):
 
 
 class EulerNumberOutputSpec(TraitedSpec):
-    euler = traits.Int(desc="Euler number of cortical surface. A value of 2 signals a "
-                            "topologically correct surface model with no holes")
+    euler = traits.Int(
+        desc="Euler number of cortical surface. A value of 2 signals a "
+        "topologically correct surface model with no holes"
+    )
     defects = traits.Int(desc="Number of defects")
 
 
@@ -2621,7 +2623,7 @@ def _run_interface(self, runtime):
 
     def _parse_output(self, stdout, stderr):
         """Parse stdout / stderr and extract defects"""
-        m = re.search(r'(?<=total defect index = )\d+', stdout or stderr)
+        m = re.search(r"(?<=total defect index = )\d+", stdout or stderr)
         if m is None:
             raise RuntimeError("Could not fetch defect index")
         self._defects = int(m.group())

nipype/interfaces/fsl/tests/test_model.py

@@ -7,18 +7,25 @@
 import nipype.interfaces.fsl.model as fsl
 from nipype.interfaces.fsl import no_fsl
 from pathlib import Path
-from ....pipeline import engine as pe 
+from ....pipeline import engine as pe
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_MultipleRegressDesign(tmpdir):
-    designer = pe.Node(fsl.MultipleRegressDesign(), name='designer', base_dir=str(tmpdir))
+    designer = pe.Node(
+        fsl.MultipleRegressDesign(), name="designer", base_dir=str(tmpdir)
+    )
     designer.inputs.regressors = dict(
         voice_stenght=[1, 1, 1], age=[0.2, 0.4, 0.5], BMI=[1, -1, 2]
     )
     con1 = ["voice_and_age", "T", ["age", "voice_stenght"], [0.5, 0.5]]
     con2 = ["just_BMI", "T", ["BMI"], [1]]
-    designer.inputs.contrasts = [con1, con2, ["con3", "F", [con1, con2]], ["con4", "F", [con2]]]
+    designer.inputs.contrasts = [
+        con1,
+        con2,
+        ["con3", "F", [con1, con2]],
+        ["con4", "F", [con2]],
+    ]
     res = designer.run()
     outputs = res.outputs.get_traitsfree()
 
@@ -27,7 +34,9 @@ def test_MultipleRegressDesign(tmpdir):
 
     expected_content = {}
 
-    expected_content["design_mat"] = """/NumWaves       3
+    expected_content[
+        "design_mat"
+    ] = """/NumWaves       3
 /NumPoints      3
 /PPheights      3.000000e+00 5.000000e-01 1.000000e+00
 
@@ -37,7 +46,9 @@ def test_MultipleRegressDesign(tmpdir):
 2.000000e+00 5.000000e-01 1.000000e+00
 """
 
-    expected_content["design_con"] = """/ContrastName1   voice_and_age
+    expected_content[
+        "design_con"
+    ] = """/ContrastName1   voice_and_age
 /ContrastName2   just_BMI
 /NumWaves       3
 /NumContrasts   2
@@ -49,15 +60,19 @@ def test_MultipleRegressDesign(tmpdir):
 1.000000e+00 0.000000e+00 0.000000e+00
 """
 
-    expected_content["design_fts"] = """/NumWaves       2
+    expected_content[
+        "design_fts"
+    ] = """/NumWaves       2
 /NumContrasts   2
 
 /Matrix
 1 1
 0 1
 """
 
-    expected_content["design_grp"] = """/NumWaves       1
+    expected_content[
+        "design_grp"
+    ] = """/NumWaves       1
 /NumPoints      3
 
 /Matrix

nipype/interfaces/io.py

@@ -450,7 +450,7 @@ def _check_s3_base_dir(self):
 
         s3_flag = base_directory.lower().startswith(s3_str)
         if s3_flag:
-            bucket_name = base_directory[len(s3_str):].partition('/')[0]
+            bucket_name = base_directory[len(s3_str) :].partition("/")[0]
 
         return s3_flag, bucket_name
 
@@ -610,7 +610,7 @@ def _upload_to_s3(self, bucket, src, dst):
 
         # Explicitly lower-case the "s3"
         if dst.lower().startswith(s3_str):
-            dst = s3_str + dst[len(s3_str):]
+            dst = s3_str + dst[len(s3_str) :]
 
         # If src is a directory, collect files (this assumes dst is a dir too)
         if os.path.isdir(src):
@@ -3005,7 +3005,9 @@ class ExportFileInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc="Input file name")
     out_file = File(mandatory=True, desc="Output file name")
     check_extension = traits.Bool(
-        True, desc="Ensure that the input and output file extensions match"
+        True,
+        usedefault=True,
+        desc="Ensure that the input and output file extensions match",
     )
     clobber = traits.Bool(desc="Permit overwriting existing files")
 

nipype/interfaces/tests/test_auto_ExportFile.py

@@ -4,7 +4,7 @@
 
 def test_ExportFile_inputs():
     input_map = dict(
-        check_extension=dict(),
+        check_extension=dict(usedefault=True,),
         clobber=dict(),
         in_file=dict(extensions=None, mandatory=True,),
         out_file=dict(extensions=None, mandatory=True,),

nipype/pipeline/engine/workflows.py

@@ -803,7 +803,8 @@ def _check_is_already_connected(workflow, node, attrname):
             if subtype == "in":
                 hierattrname = ".".join(hierarchy + [nodename, attrname])
                 if not _check_is_already_connected(
-                        targetworkflow, workflow, hierattrname):
+                    targetworkflow, workflow, hierattrname
+                ):
                     return False
             targetworkflow = workflow
 
@@ -828,8 +829,7 @@ def _check_is_already_connected(workflow, node, attrname):
         # Verify input does not already have an incoming connection
         # in the target workflow
         if subtype == "in":
-            if not _check_is_already_connected(
-                    targetworkflow, targetnode, attrname):
+            if not _check_is_already_connected(targetworkflow, targetnode, attrname):
                 return False
 
         return True