Merge branch 'master' of https://github.com/nipy/nipype into update-nipype2boutiques

Author: erinb90

.mailmap

@@ -26,6 +26,7 @@ Basille Pinsard <[email protected]> bpinsard <basile.pinsard@umontreal
 Basille Pinsard <[email protected]> bpinsard <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
 Benjamin Acland <[email protected]> Ben Acland <[email protected]>
+Benjamin Meyers <[email protected]> BenjaminMey <[email protected]>
 Benjamin Yvernault <[email protected]> Benjamin Yvernault <[email protected]>
 Benjamin Yvernault <[email protected]> byvernault <[email protected]>
 Blake Dewey <[email protected]> Blake Dewey <[email protected]>
@@ -93,8 +94,8 @@ Jérémy Guillon <[email protected]> GUILLON Jeremy <jeremy.guillon@etu.
 Joerg Stadler <[email protected]> Joerg Stadler <[email protected]>
 Joerg Stadler <[email protected]> Joerg Stadler <[email protected]>
 Joerg Stadler <[email protected]> Jörg Stadler <[email protected]>
-John Lee <[email protected]> john anthony lee <[email protected]>
-John Lee <[email protected]> leej3 <[email protected]>
+John A. Lee <[email protected]> john anthony lee <[email protected]>
+John A. Lee <[email protected]> leej3 <[email protected]>
 Joke Durnez <[email protected]> jokedurnez <[email protected]>
 Josh Warner <[email protected]> JDWarner <[email protected]>
 Josh Warner <[email protected]> Josh Warner (Mac) <[email protected]>
@@ -133,6 +134,7 @@ Matteo Mancini <[email protected]> matteomancini <ingmatteomancini@gmai
 Matteo Visconti di Oleggio Castello <[email protected]> Matteo Visconti dOC <[email protected]>
 Matteo Visconti di Oleggio Castello <[email protected]> Matteo Visconti dOC <[email protected]>
 Matteo Visconti di Oleggio Castello <[email protected]> mvdoc <[email protected]>
+Matthew Cieslak <[email protected]> Matt Cieslak <[email protected]>
 Michael Clark <[email protected]> Clark <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
@@ -153,6 +155,8 @@ 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 +166,7 @@ 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 +181,7 @@ 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.",
@@ -330,11 +344,6 @@
       "name": "Liem, Franz",
       "orcid": "0000-0003-0646-4810"
     },
-    {
-      "affiliation": "The Centre for Addiction and Mental Health",
-      "name": "Joseph, Michael",
-      "orcid": "0000-0002-0068-230X"
-    },
     {
       "affiliation": "UniversityHospital Heidelberg, Germany",
       "name": "Kleesiek, Jens"
@@ -346,6 +355,11 @@
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
     },
+    {
+      "affiliation": "NIMH IRP",
+      "name": "Lee, John A.",
+      "orcid": "0000-0001-5884-4247"
+    },
     {
       "name": "Correa, Carlos"
     },
@@ -419,11 +433,6 @@
     {
       "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",
@@ -439,6 +448,16 @@
       "name": "Grignard, Martin",
       "orcid": "0000-0001-5549-1861"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Ma, Feilong",
+      "orcid": "0000-0002-6838-3971"
+    },
+    {
+      "affiliation": "Department of Neuropsychiatry, University of Pennsylvania",
+      "name": "Cieslak, Matthew",
+      "orcid": "0000-0002-1931-4734"
+    },
     {
       "affiliation": "INRIA-Saclay, Team Parietal",
       "name": "Chawla, Kshitij",
@@ -582,6 +601,10 @@
     {
       "name": "Nickson, Thomas"
     },
+    {
+      "name": "Crusoe, Michael R.",
+      "orcid": "0000-0002-2961-9670"
+    },
     {
       "name": "Brett, Matthew"
     },
@@ -611,6 +634,11 @@
       "name": "McNamee, Daniel",
       "orcid": "0000-0001-9928-4960"
     },
+    {
+      "affiliation": "University of Pittsburgh",
+      "name": "Meyers, Benjamin",
+      "orcid": "0000-0001-9137-4363"
+    },
     {
       "name": "Davison, Andrew"
     },

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.

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.1.9 <http://nipype.readthedocs.io/en/1.1.9/>`_ `1.1.8 <http://nipype.readthedocs.io/en/1.1.8/>`_
+Previous versions: `1.2.0 <http://nipype.readthedocs.io/en/1.2.0/>`_ `1.1.9 <http://nipype.readthedocs.io/en/1.1.9/>`_
 
 
 .. container:: doc2

docker/generate_dockerfiles.sh

@@ -90,8 +90,8 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                               icu=58.1 libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
-                               pandas psutil scikit-learn scipy traits=4.6.0' \
+                               libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
+                               pandas psutil scikit-learn scipy traits' \
                 pip_install="pytest-xdist" \
                 activate=true \
     --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \