Merge remote-tracking branch 'upstream/master' into dev/2.0

Curated by CJM

Author: effigies

.zenodo.json

@@ -73,10 +73,6 @@
       "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
       "name": "Wong, Jason"
     },
-    {
-      "affiliation": "Concordia University",
-      "name": "Benderoff, Erin"
-    },
     {
       "affiliation": "Developer",
       "name": "Clark, Daniel",
@@ -142,6 +138,10 @@
       "name": "Gramfort, Alexandre",
       "orcid": "0000-0001-9791-4404"
     },
+    {
+      "affiliation": "Concordia University",
+      "name": "Benderoff, Erin"
+    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
@@ -274,6 +274,11 @@
     {
       "name": "Dubois, Mathieu"
     },
+    {
+      "affiliation": "Holland Bloorview Kids Rehabilitation Hospital",
+      "name": "Tilley II, Steven",
+      "orcid": "0000-0003-4853-5082"
+    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Frohlich, Caroline"
@@ -313,10 +318,6 @@
       "name": "Eshaghi, Arman",
       "orcid": "0000-0002-6652-3512"
     },
-    {
-      "name": "Heinsfeld, Anibal S\u00f3lon",
-      "orcid": "0000-0002-2050-0614"
-    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -330,6 +331,10 @@
       "name": "Kastman, Erik",
       "orcid": "0000-0001-7221-9042"
     },
+    {
+      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "orcid": "0000-0002-2050-0614"
+    },
     {
       "affiliation": "Washington University in St Louis",
       "name": "Acland, Benjamin",
@@ -376,9 +381,6 @@
     {
       "name": "Millman, Jarrod"
     },
-    {
-      "name": "Lai, Jeff"
-    },
     {
       "name": "Zhou, Dale"
     },
@@ -388,11 +390,6 @@
     {
       "name": "Haselgrove, Christian"
     },
-    {
-      "affiliation": "Holland Bloorview Kids Rehabilitation Hospital",
-      "name": "Tilley II, Steven",
-      "orcid": "0000-0003-4853-5082"
-    },
     {
       "name": "Renfro, Mandy"
     },
@@ -405,11 +402,6 @@
       "name": "Kahn, Ari E.",
       "orcid": "0000-0002-2127-0507"
     },
-    {
-      "affiliation": "Yale University; New Haven, CT, United States",
-      "name": "Sisk, Lucinda M.",
-      "orcid": "0000-0003-4900-9770"
-    },
     {
       "affiliation": "Korea Advanced Institute of Science and Technology",
       "name": "Kim, Sin",
@@ -437,6 +429,11 @@
     {
       "name": "Hallquist, Michael"
     },
+    {
+      "affiliation": "Yale University; New Haven, CT, United States",
+      "name": "Sisk, Lucinda M.",
+      "orcid": "0000-0003-4900-9770"
+    },
     {
       "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
       "name": "Chetverikov, Andrey",
@@ -484,11 +481,6 @@
     {
       "name": "Hinds, Oliver"
     },
-    {
-      "affiliation": "National Institute on Aging, Baltimore, MD, USA",
-      "name": "Bilgel, Murat",
-      "orcid": "0000-0001-5042-7422"
-    },
     {
       "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
       "name": "Leinweber, Katrin",
@@ -501,15 +493,6 @@
       "affiliation": "Boston University",
       "name": "Perkins, L. Nathan"
     },
-    {
-      "affiliation": "University of Amsterdam",
-      "name": "Snoek, Lukas",
-      "orcid": "0000-0001-8972-204X"
-    },
-    {
-      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
-      "name": "Weninger, Leon"
-    },
     {
       "affiliation": "University of Newcastle, Australia",
       "name": "Cooper, Gavin",
@@ -524,16 +507,20 @@
     {
       "name": "Noel, Maxime"
     },
+    {
+      "affiliation": "University of Amsterdam",
+      "name": "Snoek, Lukas",
+      "orcid": "0000-0001-8972-204X"
+    },
+    {
+      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
+      "name": "Weninger, Leon"
+    },
     {
       "affiliation": "University of Pennsylvania",
       "name": "Junhao WEN",
       "orcid": "0000-0003-2077-3070"
     },
-    {
-      "affiliation": "Leibniz Institute for Neurobiology",
-      "name": "Stadler, J\u00f6rg",
-      "orcid": "0000-0003-4313-129X"
-    },
     {
       "name": "Cheung, Brian"
     },
@@ -549,6 +536,11 @@
       "name": "Durnez, Joke",
       "orcid": "0000-0001-9030-2202"
     },
+    {
+      "affiliation": "Leibniz Institute for Neurobiology",
+      "name": "Stadler, J\u00f6rg",
+      "orcid": "0000-0003-4313-129X"
+    },
     {
       "affiliation": "CNRS, UMS3552 IRMaGe",
       "name": "Condamine, Eric",
@@ -600,10 +592,12 @@
       "name": "Khanuja, Ranjeet"
     },
     {
-      "name": "Schlamp, Kai"
+      "affiliation": "National Institute on Aging, Baltimore, MD, USA",
+      "name": "Bilgel, Murat",
+      "orcid": "0000-0001-5042-7422"
     },
     {
-      "name": "Arias, Jaime"
+      "name": "Schlamp, Kai"
     },
     {
       "affiliation": "CEA",
@@ -671,6 +665,12 @@
     {
       "name": "Davison, Andrew"
     },
+    {
+      "name": "Lai, Jeff"
+    },
+    {
+      "name": "Arias, Jaime"
+    },
     {
       "name": "Bielievtsov, Dmytro",
       "orcid": "0000-0003-3846-7696"

doc/changelog/1.X.X-changelog

@@ -1,11 +1,16 @@
-1.3.0 (To Be Determined)
-========================
+1.3.0 (November 11, 2019)
+=========================
 
 ##### [Full changelog](https://github.com/nipy/nipype/milestone/34?closed=1)
 
+  * FIX: Fixed typo in QwarpInputSpec Trait description (https://github.com/nipy/nipype/pull/3079)
   * FIX: Restore ``AFNICommand._get_fname``, required by some interfaces (https://github.com/nipy/nipype/pull/3071)
   * FIX: Remove asynchronous chdir callback (https://github.com/nipy/nipype/pull/3060)
   * FIX: Minimize scope for directory changes while loading results file (https://github.com/nipy/nipype/pull/3061)
+  * ENH: Minimize the number of calls to ``_load_results`` when populating inputs (https://github.com/nipy/nipype/pull/3075)
+  * ENH: Refactor savepkl/loadpkl - add a window for loadpkl to wait for the file (https://github.com/nipy/nipype/pull/3089)
+  * ENH: Add "ExportFile" interface as simple alternative to "DataSink" (https://github.com/nipy/nipype/pull/3054)
+  * ENH: Allow nipype.cfg in cwd to be read even if ~/.nipype does not exist (https://github.com/nipy/nipype/pull/3072)
   * ENH: Add precommit information for contributors and pre-commit style (https://github.com/nipy/nipype/pull/3063)
   * ENH: Delay etelemetry for non-interactive sessions, report bad versions (https://github.com/nipy/nipype/pull/3049)
   * ENH: Run memoized check_version at REPL import, Node/Workflow/Interface init (https://github.com/nipy/nipype/pull/30)

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.2.3 <http://nipype.readthedocs.io/en/1.2.3/>`_ `1.2.2 <http://nipype.readthedocs.io/en/1.2.2/>`_
+Previous versions: `1.3.0 <http://nipype.readthedocs.io/en/1.3.0/>`_ `1.2.3 <http://nipype.readthedocs.io/en/1.2.3/>`_
 
 
 .. container:: doc2

nipype/info.py

@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = '2.0.0-dev'
+__version__ = '1.4.0-dev'
 
 
 def get_nipype_gitversion():
@@ -97,7 +97,7 @@ def get_nipype_gitversion():
 NIBABEL_MIN_VERSION = '2.1.0'
 NETWORKX_MIN_VERSION = '1.9'
 NETWORKX_MAX_VERSION_27 = '2.2'
-NUMPY_MIN_VERSION = '1.9.0'
+NUMPY_MIN_VERSION = '1.12'
 # 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/afni/preprocess.py

@@ -3384,11 +3384,11 @@ class QwarpInputSpec(AFNICommandInputSpec):
         exists=True,
         copyfile=False)
     noXdis = traits.Bool(
-        desc='Warp will not displace in x directoin', argstr='-noXdis')
+        desc='Warp will not displace in x direction', argstr='-noXdis')
     noYdis = traits.Bool(
-        desc='Warp will not displace in y directoin', argstr='-noYdis')
+        desc='Warp will not displace in y direction', argstr='-noYdis')
     noZdis = traits.Bool(
-        desc='Warp will not displace in z directoin', argstr='-noZdis')
+        desc='Warp will not displace in z direction', argstr='-noZdis')
     iniwarp = traits.List(
         File(exists=True, copyfile=False),
         desc='A dataset with an initial nonlinear warp to use.'

nipype/interfaces/io.py

@@ -28,12 +28,12 @@
 from .. import config, logging
 from ..utils.filemanip import (
     copyfile, simplify_list, ensure_list,
-    get_related_files)
+    get_related_files, split_filename)
 from ..utils.misc import human_order_sorted, str2bool
 from .base import (
     TraitedSpec, traits, Str, File, Directory, BaseInterface, InputMultiPath,
     isdefined, OutputMultiPath, DynamicTraitedSpec, Undefined, BaseInterfaceInputSpec,
-    LibraryBaseInterface)
+    LibraryBaseInterface, SimpleInterface)
 
 iflogger = logging.getLogger('nipype.interface')
 
@@ -2859,3 +2859,51 @@ def _list_outputs(self):
 
     def _add_output_traits(self, base):
         return add_traits(base, list(self.inputs.output_query.keys()))
+
+
+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')
+    clobber = traits.Bool(desc='Permit overwriting existing files')
+
+
+class ExportFileOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='Output file name')
+
+
+class ExportFile(SimpleInterface):
+    """ Export a file to an absolute path
+
+    This interface copies an input file to a named output file.
+    This is useful to save individual files to a specific location,
+    instead of more flexible interfaces like DataSink.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.io import ExportFile
+    >>> import os.path as op
+    >>> ef = ExportFile()
+    >>> ef.inputs.in_file = "T1.nii.gz"
+    >>> os.mkdir("output_folder")
+    >>> ef.inputs.out_file = op.abspath("output_folder/sub1_out.nii.gz")
+    >>> res = ef.run()
+    >>> os.path.exists(res.outputs.out_file)
+    True
+
+    """
+    input_spec = ExportFileInputSpec
+    output_spec = ExportFileOutputSpec
+
+    def _run_interface(self, runtime):
+        if not self.inputs.clobber and op.exists(self.inputs.out_file):
+            raise FileExistsError(self.inputs.out_file)
+        if not op.isabs(self.inputs.out_file):
+            raise ValueError('Out_file must be an absolute path.')
+        if (self.inputs.check_extension and
+                split_filename(self.inputs.in_file)[2] != split_filename(self.inputs.out_file)[2]):
+            raise RuntimeError('%s and %s have different extensions' % (self.inputs.in_file, self.inputs.out_file))
+        shutil.copy(str(self.inputs.in_file), str(self.inputs.out_file))
+        self._results['out_file'] = self.inputs.out_file
+        return runtime

nipype/interfaces/tests/test_auto_ExportFile.py

@@ -0,0 +1,29 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..io import ExportFile
+
+
+def test_ExportFile_inputs():
+    input_map = dict(
+        check_extension=dict(),
+        clobber=dict(),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        out_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+    )
+    inputs = ExportFile.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_ExportFile_outputs():
+    output_map = dict(out_file=dict(extensions=None, ), )
+    outputs = ExportFile.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/tests/test_io.py

@@ -15,7 +15,7 @@
 import nipype.interfaces.io as nio
 from nipype.interfaces.base.traits_extension import isdefined
 from nipype.interfaces.base import Undefined, TraitError
-from nipype.utils.filemanip import dist_is_editable
+from nipype.utils.filemanip import dist_is_editable, FileExistsError
 
 # Check for boto
 noboto = False
@@ -674,3 +674,26 @@ def _mock_get_ssh_client(self):
             .check(file=True, exists=True)) # exists?
 
     old_cwd.chdir()
+
+
+def test_ExportFile(tmp_path):
+    testin = tmp_path / 'in.txt'
+    testin.write_text('test string')
+    i = nio.ExportFile()
+    i.inputs.in_file = str(testin)
+    i.inputs.out_file = str(tmp_path / 'out.tsv')
+    i.inputs.check_extension = True
+    with pytest.raises(RuntimeError):
+        i.run()
+    i.inputs.check_extension = False
+    i.run()
+    assert (tmp_path / 'out.tsv').read_text() == 'test string'
+    i.inputs.out_file = str(tmp_path / 'out.txt')
+    i.inputs.check_extension = True
+    i.run()
+    assert (tmp_path / 'out.txt').read_text() == 'test string'
+    with pytest.raises(FileExistsError):
+        i.run()
+    i.inputs.clobber = True
+    i.run()
+    assert (tmp_path / 'out.txt').read_text() == 'test string'