Merge pull request #2930 from nipy/rel/1.2.0

REL: 1.2.0

Author: effigies

.mailmap

@@ -153,6 +153,8 @@ Pablo Polosecki <[email protected]> pipolose <[email protected]
 Pablo Polosecki <[email protected]> pipolose <[email protected]>
 Paul Sharp <[email protected]> psharp1289 <[email protected]>
 Ranjit Khanuja <[email protected]> RanjitK <[email protected]>
+Rastko Ćirić <[email protected]> rciric <[email protected]>
+Rastko Ćirić <[email protected]> Rastko Ćirić <[email protected]>
 Ross Markello <[email protected]> Ross Markello <[email protected]>
 Russell Poldrack <[email protected]> Russ Poldrack <[email protected]>
 Russell Poldrack <[email protected]> poldrack <[email protected]>
@@ -162,6 +164,7 @@ Salma Bougacha <[email protected]> salma1601 <[email protected]>
 Sami Kristian Andberg <[email protected]> Sami Andberg <[email protected]>
 Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
 Sebastian Urchs <[email protected]> sebastian <[email protected]>
+Serge Koudoro <[email protected]> skoudoro <[email protected]>
 Sharad Sikka <[email protected]> ssikka <[email protected]>
 Shariq Iqbal <[email protected]> shariqiqbal2810 <[email protected]>
 Shariq Iqbal <[email protected]> shariqiqbal2810 <[email protected]>
@@ -176,6 +179,7 @@ Steven Giavasis <[email protected]> sgiavasis <[email protected]>
 Steven Giavasis <[email protected]> sgiavasis <[email protected]>
 Tristan Glatard <[email protected]> Tristan Glatard <[email protected]>
 Victor Saase <[email protected]> vsaase <[email protected]>
+Weijie Huang <[email protected]> forwho <[email protected]>
 William Triplett <[email protected]> William Triplett <[email protected]>
 Wolfgang Pauli <[email protected]> Wolfgang Pauli <[email protected]>
 Xiangzhen Kong <[email protected]> bnucon <[email protected]>

.zenodo.json

@@ -89,23 +89,28 @@
       "name": "Clark, Daniel",
       "orcid": "0000-0002-8121-8954"
     },
-    {
-      "affiliation": "National Institute of Mental Health",
-      "name": "Nielson, Dylan M.",
-      "orcid": "0000-0003-4613-6643"
-    },
     {
       "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
       "name": "Dewey, Blake E",
       "orcid": "0000-0003-4554-5058"
     },
+    {
+      "affiliation": "National Institute of Mental Health",
+      "name": "Nielson, Dylan M.",
+      "orcid": "0000-0003-4613-6643"
+    },
     {
       "name": "Madison, Cindee"
     },
     {
       "affiliation": "Molecular Imaging Research Center, CEA, France",
       "name": "Bougacha, Salma"
     },
+    {
+      "affiliation": "Stanford University",
+      "name": "\u0106iri\u0107 , Rastko",
+      "orcid": "0000-0001-6347-7939"
+    },
     {
       "affiliation": "National Institutes of Health",
       "name": "Clark, Michael G. "
@@ -115,16 +120,16 @@
       "name": "Dayan, Michael",
       "orcid": "0000-0002-2666-0969"
     },
-    {
-      "affiliation": "Dartmouth College",
-      "name": "Visconti di Oleggio Castello, Matteo",
-      "orcid": "0000-0001-7931-5272"
-    },
     {
       "affiliation": "UC Berkeley",
       "name": "Clark, Dav",
       "orcid": "0000-0002-3982-4416"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
       "name": "Keshavan, Anisha",
@@ -141,16 +146,16 @@
     {
       "name": "Berleant, Shoshana"
     },
-    {
-      "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": "UC San Diego",
       "name": "Cipollini, Ben",
@@ -171,6 +176,10 @@
       "name": "Rokem, Ariel",
       "orcid": "0000-0003-0679-1985"
     },
+    {
+      "affiliation": "Indiana University, IN, USA",
+      "name": "Koudoro, Serge"
+    },
     {
       "affiliation": "Montreal Neurological Institute and Hospital",
       "name": "DuPre, Elizabeth",
@@ -189,6 +198,11 @@
       "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",
@@ -245,14 +259,14 @@
       "name": "Iqbal, Shariq",
       "orcid": "0000-0003-2766-8425"
     },
+    {
+      "name": "Schwartz, Yannick"
+    },
     {
       "affiliation": "University of Washington",
       "name": "Richie-Halford, Adam",
       "orcid": "0000-0001-9276-9084"
     },
-    {
-      "name": "Schwartz, Yannick"
-    },
     {
       "affiliation": "University College London",
       "name": "Malone, Ian B.",
@@ -330,16 +344,6 @@
       "name": "Liem, Franz",
       "orcid": "0000-0003-0646-4810"
     },
-    {
-      "affiliation": "Stanford University",
-      "name": "Ciric, Rastko",
-      "orcid": "0000-0001-6347-7939"
-    },
-    {
-      "affiliation": "The Centre for Addiction and Mental Health",
-      "name": "Joseph, Michael",
-      "orcid": "0000-0002-0068-230X"
-    },
     {
       "affiliation": "UniversityHospital Heidelberg, Germany",
       "name": "Kleesiek, Jens"
@@ -380,10 +384,6 @@
     {
       "name": "Haselgrove, Christian"
     },
-    {
-      "name": "Koudoro, Serge",
-      "affiliation": "Indiana University, IN, USA"
-    },
     {
       "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
       "name": "Glatard, Tristan",
@@ -428,11 +428,6 @@
     {
       "name": "Hallquist, Michael"
     },
-    {
-      "affiliation": "Dartmouth College",
-      "name": "Ma, Feilong",
-      "orcid": "0000-0002-6838-3971"
-    },
     {
       "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
       "name": "Leinweber, Katrin",
@@ -448,6 +443,11 @@
       "name": "Grignard, Martin",
       "orcid": "0000-0001-5549-1861"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Ma, Feilong",
+      "orcid": "0000-0002-6838-3971"
+    },
     {
       "affiliation": "INRIA-Saclay, Team Parietal",
       "name": "Chawla, Kshitij",
@@ -591,6 +591,10 @@
     {
       "name": "Nickson, Thomas"
     },
+    {
+      "name": "Crusoe, Michael R.",
+      "orcid": "0000-0002-2961-9670"
+    },
     {
       "name": "Brett, Matthew"
     },

doc/changelog/1.X.X-changelog

@@ -1,3 +1,22 @@
+1.2.0 (May 09, 2019)
+====================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/31?closed=1)
+
+  * FIX: Parsing of filename in AlignEpiAnatPy when filename does not have + (https://github.com/nipy/nipype/pull/2909)
+  * FIX: Import nibabel reorientation bug fix (https://github.com/nipy/nipype/pull/2912)
+  * FIX: Update FNIRT outputs for warped_file log_file to include cwd (https://github.com/nipy/nipype/pull/2900)
+  * FIX: Sort conditions in bids_gen_info to ensure consistent order (https://github.com/nipy/nipype/pull/2867)
+  * FIX: Some traits-5.0.0 don't work with Python 2.7 (https://github.com/nipy/nipype/pull/1)
+  * ENH: CompCor enhancement (https://github.com/nipy/nipype/pull/2878)
+  * ENH: Do not override caught exceptions with FileNotFoundError from unfinished hashfile (https://github.com/nipy/nipype/pull/2919)
+  * ENH: More verbose description when a faulty results file is loaded (https://github.com/nipy/nipype/pull/2920)
+  * ENH: Add all DIPY workflows dynamically  (https://github.com/nipy/nipype/pull/2905)
+  * ENH: Add mrdegibbs and dwibiascorrect from mrtrix3 (https://github.com/nipy/nipype/pull/2904)
+  * TEST: Fix CI builds (https://github.com/nipy/nipype/pull/2927)
+  * MAINT: Reduce deprecation warnings (https://github.com/nipy/nipype/pull/2903)
+
+
 1.1.9 (February 25, 2019)
 =========================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.9"
+release = "1.2.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

nipype/info.py

@@ -11,7 +11,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.2.0-dev'
+__version__ = '1.2.0'
 
 
 def get_nipype_gitversion():
@@ -101,6 +101,7 @@ def get_nipype_gitversion():
 # versions
 NIBABEL_MIN_VERSION = '2.1.0'
 NETWORKX_MIN_VERSION = '1.9'
+NETWORKX_MAX_VERSION_27 = '2.2'
 NUMPY_MIN_VERSION = '1.9.0'
 # Numpy bug in python 3.7:
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
@@ -135,7 +136,8 @@ def get_nipype_gitversion():
 PROVIDES = ['nipype']
 REQUIRES = [
     'nibabel>=%s' % NIBABEL_MIN_VERSION,
-    'networkx>=%s' % NETWORKX_MIN_VERSION,
+    'networkx>=%s,<=%s ; python_version < "3.0"' % (NETWORKX_MIN_VERSION, NETWORKX_MAX_VERSION_27),
+    'networkx>=%s ; python_version >= "3.0"' % NETWORKX_MIN_VERSION,
     'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
     'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
     'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,