Merge remote-tracking branch 'upstream/master' into update_eddy

Author: josephmje

.mailmap

@@ -1,10 +1,5 @@
 {
   "creators": [
-    {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Gorgolewski, Krzysztof J.",
-      "orcid": "0000-0003-3321-7583"
-    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Esteban, Oscar",
@@ -150,15 +145,20 @@
       "affiliation": "Concordia University",
       "name": "Benderoff, Erin"
     },
+    {
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "name": "Halchenko, Yaroslav O.",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
       "orcid": "0000-0001-7037-2449"
     },
     {
-      "affiliation": "Dartmouth College: Hanover, NH, United States",
-      "name": "Halchenko, Yaroslav O.",
-      "orcid": "0000-0003-3456-2493"
+      "affiliation": "The Centre for Addiction and Mental Health",
+      "name": "Joseph, Michael",
+      "orcid": "0000-0002-0068-230X"
     },
     {
       "affiliation": "UC San Diego",
@@ -202,11 +202,6 @@
       "name": "Varoquaux, Gael",
       "orcid": "0000-0003-1076-5122"
     },
-    {
-      "affiliation": "The Centre for Addiction and Mental Health",
-      "name": "Joseph, Michael",
-      "orcid": "0000-0002-0068-230X"
-    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann, Demian",
@@ -250,14 +245,14 @@
       "affiliation": "Nathan s Kline institute for psychiatric research",
       "name": "Sikka, Sharad"
     },
+    {
+      "name": "Forbes, Jessica"
+    },
     {
       "affiliation": "University College London",
       "name": "Mancini, Matteo",
       "orcid": "0000-0001-7194-4568"
     },
-    {
-      "name": "Forbes, Jessica"
-    },
     {
       "affiliation": "Duke University",
       "name": "Iqbal, Shariq",
@@ -295,10 +290,6 @@
     {
       "name": "Kent, James"
     },
-    {
-      "name": "Heinsfeld, Anibal S\u00f3lon",
-      "orcid": "0000-0002-2050-0614"
-    },
     {
       "name": "Watanabe, Aimi"
     },
@@ -325,6 +316,10 @@
       "name": "Eshaghi, Arman",
       "orcid": "0000-0002-6652-3512"
     },
+    {
+      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "orcid": "0000-0002-2050-0614"
+    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -352,14 +347,14 @@
       "affiliation": "UniversityHospital Heidelberg, Germany",
       "name": "Kleesiek, Jens"
     },
-    {
-      "name": "Erickson, Drew"
-    },
     {
       "affiliation": "NIMH IRP",
       "name": "Lee, John A.",
       "orcid": "0000-0001-5884-4247"
     },
+    {
+      "name": "Erickson, Drew"
+    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
@@ -378,6 +373,9 @@
     {
       "name": "K\u00fcttner, Ren\u00e9"
     },
+    {
+      "name": "Perez-Guevara, Martin"
+    },
     {
       "name": "Millman, Jarrod"
     },
@@ -412,6 +410,11 @@
       "name": "Stadler, J\u00f6rg",
       "orcid": "0000-0003-4313-129X"
     },
+    {
+      "affiliation": "Korea Advanced Institute of Science and Technology",
+      "name": "Kim, Sin",
+      "orcid": "0000-0003-4652-3758"
+    },
     {
       "affiliation": "University College London",
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
@@ -524,6 +527,11 @@
     {
       "name": "Matsubara, K"
     },
+    {
+      "affiliation": "University of Pennsylvania",
+      "name": "Junhao WEN",
+      "orcid": "0000-0003-2077-3070"
+    },
     {
       "name": "Cheung, Brian"
     },
@@ -679,9 +687,6 @@
       "name": "Pellman, John",
       "orcid": "0000-0001-6810-4461"
     },
-    {
-      "name": "Perez-Guevara, Martin"
-    },
     {
       "name": "Khanuja, Ranjeet"
     },
@@ -701,6 +706,11 @@
     {
       "name": "Lai, Jeff"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Gorgolewski, Krzysztof J.",
+      "orcid": "0000-0003-3321-7583"
+    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",

.zenodo.json

@@ -1,3 +1,24 @@
+1.2.3 (September 23, 2019)
+==========================
+
+Python 1.2.3 will be the last version to support Python 3.4.
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/35?closed=1)
+
+  * FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037)
+  * FIX: Drop deprecated message argument to ``FileNotFoundError`` (https://github.com/nipy/nipype/pull/3035)
+  * FIX: Handle NIFTI extensions in ``afni.Qwarp`` (https://github.com/nipy/nipype/pull/3028)
+  * FIX: Disallow returning ``None`` in ``pipeline.utils.load_resultfile`` (https://github.com/nipy/nipype/pull/3023)
+  * ENH: Allow afni.CatMatvec to accept empty string opkeys (https://github.com/nipy/nipype/pull/2943)
+  * ENH: Add ``mrrtrix3.MRResize`` interface (https://github.com/nipy/nipype/pull/3031)
+  * ENH: Add version check / telemetry to Nipype (https://github.com/nipy/nipype/pull/3027)
+  * ENH: Update MCFLIRT outputs for FSL 6+ (https://github.com/nipy/nipype/pull/3029)
+  * ENH: Lightweight node cache checking (https://github.com/nipy/nipype/pull/3026)
+  * ENH: Avoid loading result from file when writing reports (https://github.com/nipy/nipype/pull/3024)
+  * ENH: replace portalocker with filelock (https://github.com/nipy/nipype/pull/3025)
+  * MAINT: Set minimum yapf for `checkspecs` to 0.27 (https://github.com/nipy/nipype/pull/3033)
+
+
 1.2.2 (September 07, 2019)
 ==========================
 

doc/changelog/1.X.X-changelog

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.2.2"
+release = "1.2.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/conf.py

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.2.2 <http://nipype.readthedocs.io/en/1.2.2/>`_ `1.2.1 <http://nipype.readthedocs.io/en/1.2.1/>`_
+Previous versions: `1.2.3 <http://nipype.readthedocs.io/en/1.2.3/>`_ `1.2.2 <http://nipype.readthedocs.io/en/1.2.2/>`_
 
 
 .. container:: doc2

doc/documentation.rst

@@ -68,10 +68,11 @@ function generate_base_dockerfile() {
     --spm12 version=r7219 \
     --env 'LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
     --freesurfer version=6.0.0-min \
+    --dcm2niix version=v1.0.20190902 method=source \
     --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tCjUxNzIKICpDdnVtdkVWM3pUZmcKRlM1Si8yYzFhZ2c0RQoiID4gL29wdC9mcmVlc3VyZmVyLTYuMC4wLW1pbi9saWNlbnNlLnR4dA==" | base64 -d | sh' \
     --install afni ants apt-utils bzip2 convert3d file fsl-core \
               fsl-mni152-templates fusefat g++ git graphviz make python ruby \
-              unzip xvfb \
+              unzip xvfb git-annex-standalone liblzma-dev \
     --add-to-entrypoint "source /etc/fsl/fsl.sh && source /etc/afni/afni.sh" \
     --env ANTSPATH='/usr/lib/ants' \
           PATH='/usr/lib/ants:$PATH' \

docker/generate_dockerfiles.sh

@@ -9,7 +9,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = '1.2.3-dev'
+__version__ = '1.3.0-dev'
 
 
 def get_nipype_gitversion():
@@ -182,6 +182,7 @@ def get_nipype_gitversion():
 ]
 
 EXTRA_REQUIRES = {
+    'data': ['datalad'],
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
     'duecredit': ['duecredit'],
     'nipy': ['nitime', 'nilearn<0.5.0', 'dipy', 'nipy', 'matplotlib'],

nipype/info.py

@@ -541,6 +541,10 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         desc='turns on more progress messages, including memory usage '
         'progress reports at various stages',
         argstr='-verb')
+    goforit = traits.Bool(
+        desc='With potential issues flagged in the design matrix, an attempt '
+        'will nevertheless be made to fit the model',
+        argstr='-GOFORIT')
     ovar = File(
         desc='dataset for OLSQ st.dev. parameter (kind of boring)',
         argstr='-Ovar %s')

nipype/interfaces/afni/model.py

@@ -619,8 +619,9 @@ class CatMatvec(AFNICommand):
 
     def _format_arg(self, name, spec, value):
         if name == 'in_file':
-            return spec.argstr % (' '.join([i[0] + ' -' + i[1]
-                                            for i in value]))
+            # Concatenate a series of filenames, with optional opkeys
+            return ' '.join('%s -%s' % (mfile, opkey) if opkey else mfile
+                           for mfile, opkey in value)
         return super(CatMatvec, self)._format_arg(name, spec, value)
 
 

nipype/interfaces/afni/utils.py

@@ -476,9 +476,9 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
                 setattr(outputs, key, val)
             except TraitError as error:
                 if 'an existing' in getattr(error, 'info', 'default'):
-                    msg = "No such file or directory for output '%s' of a %s interface" % \
-                        (key, self.__class__.__name__)
-                    raise FileNotFoundError(val, message=msg)
+                    msg = "No such file or directory '%s' for output '%s' of a %s interface" % \
+                        (val, key, self.__class__.__name__)
+                    raise FileNotFoundError(msg)
                 raise error
         return outputs