Merge pull request #2999 from nipy/rel/1.2.1

REL: 1.2.1

Author: effigies

.circleci/config.yml

@@ -339,20 +339,22 @@ jobs:
       - run:
           name: Check pypi preconditions
           command: |
-            pip install --upgrade twine future wheel readme_renderer setuptools
+            pip install --upgrade pip twine future wheel readme_renderer setuptools
             python setup.py check -r -s
             python setup.py sdist bdist_wheel
       - run:
           name: Validate Python 2 installation
           command: |
             pyenv local 2.7.12
+            pip install --upgrade pip
             pip install dist/nipype-*-py2.py3-none-any.whl
             # Futures should install in Python 2
             pip show futures 2>/dev/null | grep "Name: futures"
       - run:
           name: Validate Python 3 installation
           command: |
             pyenv local 3.5.2
+            pip install --upgrade pip
             pip install dist/nipype-*-py2.py3-none-any.whl
             # Futures should not install in Python 3
             test $(pip show futures 2>/dev/null | wc -l) = "0"

.mailmap

@@ -139,6 +139,9 @@ Michael Clark <[email protected]> Clark <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> mick-d <mid2021@CHUCK.(none)>
+Michael Dayan <[email protected]>  Michael <[email protected]>
+Michael Joseph <[email protected]> mjoseph <[email protected]>
+Michael Joseph <[email protected]> Michael Joseph <[email protected]>
 Michael Philipp Notter <[email protected]> Michael Notter <[email protected]>
 Michael Philipp Notter <[email protected]> miykael <[email protected]>
 Michael Waskom <[email protected]> Michael Waskom <[email protected]>

.zenodo.json

@@ -30,16 +30,16 @@
       "name": "Jarecka, Dorota",
       "orcid": "0000-0003-1857-8129"
     },
-    {
-      "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
-      "name": "Notter, Michael Philipp",
-      "orcid": "0000-0002-5866-047X"
-    },
     {
       "affiliation": "University of Iowa",
       "name": "Johnson, Hans",
       "orcid": "0000-0001-9513-2660"
     },
+    {
+      "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
+      "name": "Notter, Michael Philipp",
+      "orcid": "0000-0002-5866-047X"
+    },
     {
       "name": "Burns, Christopher"
     },
@@ -79,16 +79,20 @@
       "name": "Wong, Jason"
     },
     {
-      "name": "Modat, Marc"
+      "affiliation": "Concordia University",
+      "name": "Benderoff, Erin"
     },
     {
-      "name": "Loney, Fred"
+      "name": "Modat, Marc"
     },
     {
       "affiliation": "Developer",
       "name": "Clark, Daniel",
       "orcid": "0000-0002-8121-8954"
     },
+    {
+      "name": "Loney, Fred"
+    },
     {
       "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
       "name": "Dewey, Blake E",
@@ -125,16 +129,16 @@
       "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",
       "orcid": "0000-0003-3554-043X"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "name": "Pinsard, Basile"
     },
@@ -166,11 +170,6 @@
       "name": "Guillon, Je\u0301re\u0301my",
       "orcid": "0000-0002-2672-7510"
     },
-    {
-      "affiliation": "Montreal Neurological Institute and Hospital",
-      "name": "Markello, Ross",
-      "orcid": "0000-0003-1057-1336"
-    },
     {
       "affiliation": "The University of Washington eScience Institute",
       "name": "Rokem, Ariel",
@@ -185,6 +184,11 @@
       "name": "DuPre, Elizabeth",
       "orcid": "0000-0003-1358-196X"
     },
+    {
+      "affiliation": "Montreal Neurological Institute and Hospital",
+      "name": "Markello, Ross",
+      "orcid": "0000-0003-1057-1336"
+    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -275,10 +279,6 @@
     {
       "name": "Dubois, Mathieu"
     },
-    {
-      "name": "Heinsfeld, Anibal S\u00f3lon",
-      "orcid": "0000-0002-2050-0614"
-    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Frohlich, Caroline"
@@ -293,12 +293,11 @@
       "orcid": "0000-0002-7796-8795"
     },
     {
-      "name": "Kent, James"
+      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "orcid": "0000-0002-2050-0614"
     },
     {
-      "affiliation": "University of Texas at Austin",
-      "name": "De La Vega, Alejandro",
-      "orcid": "0000-0001-9062-3778"
+      "name": "Kent, James"
     },
     {
       "name": "Watanabe, Aimi"
@@ -316,6 +315,11 @@
       "name": "Nichols, B. Nolan",
       "orcid": "0000-0003-1099-3328"
     },
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "De La Vega, Alejandro",
+      "orcid": "0000-0001-9062-3778"
+    },
     {
       "affiliation": "University College London",
       "name": "Eshaghi, Arman",
@@ -389,11 +393,6 @@
     {
       "name": "Haselgrove, Christian"
     },
-    {
-      "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",
-      "orcid": "0000-0003-2620-5883"
-    },
     {
       "name": "Renfro, Mandy"
     },
@@ -433,6 +432,11 @@
     {
       "name": "Hallquist, Michael"
     },
+    {
+      "affiliation": "Yale University; New Haven, CT, United States",
+      "name": "Sisk, Lucinda M.",
+      "orcid": "0000-0003-4900-9770"
+    },
     {
       "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
       "name": "Leinweber, Katrin",
@@ -469,6 +473,11 @@
     {
       "name": "Park, Anne"
     },
+    {
+      "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",
+      "orcid": "0000-0003-2620-5883"
+    },
     {
       "name": "Poldrack, Russell"
     },
@@ -485,10 +494,6 @@
       "name": "Cooper, Gavin",
       "orcid": "0000-0002-7186-5293"
     },
-    {
-      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
-      "name": "Weninger, Leon"
-    },
     {
       "name": "Inati, Souheil"
     },
@@ -501,6 +506,15 @@
       "name": "Lukas Snoek",
       "orcid": "0000-0001-8972-204X"
     },
+    {
+      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
+      "name": "Weninger, Leon"
+    },
+    {
+      "affiliation": "Stanford University",
+      "name": "Lerma-Usabiaga, Garikoitz",
+      "orcid": "0000-0001-9800-4816"
+    },
     {
       "name": "Marina, Ana"
     },
@@ -639,6 +653,11 @@
       "name": "Meyers, Benjamin",
       "orcid": "0000-0001-9137-4363"
     },
+    {
+      "affiliation": "Washington University in St Louis",
+      "name": "Van, Andrew",
+      "orcid": "0000-0002-8787-0943"
+    },
     {
       "name": "Davison, Andrew"
     },

doc/changelog/1.X.X-changelog

@@ -1,3 +1,30 @@
+1.2.1 (August 19, 2019)
+=======================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/32?closed=1)
+
+  * FIX: Resolve/rebase paths from/to results files (https://github.com/nipy/nipype/pull/2971)
+  * FIX: Use ``load_resultfile`` when loading a results pickle (https://github.com/nipy/nipype/pull/2985)
+  * FIX: Incorrect extension identified when checking ``File`` traits (https://github.com/nipy/nipype/pull/2987)
+  * FIX: Correctly pickle ``OuputMultiObject`` traits (https://github.com/nipy/nipype/pull/2983)
+  * FIX: Improve output handling in DWIDenoise and DWIBiasCorrect (https://github.com/nipy/nipype/pull/2978)
+  * FIX: Docker build (https://github.com/nipy/nipype/pull/2963)
+  * FIX: Remove '=' signs from EddyQuad argument specifications (https://github.com/nipy/nipype/pull/2941)
+  * FIX: Set input model to bedpostx for camino.TrackBedpostxProba (https://github.com/nipy/nipype/pull/2947)
+  * FIX: Allow ``max_sh``not to be set (auto mode) (https://github.com/nipy/nipype/pull/2940)
+  * ENH: Update mrtrix reconst.py EstimateFOD max_sh to be able to accept list (https://github.com/nipy/nipype/pull/2990)
+  * ENH: Let ``indirectory`` handle ``nipype.utils.filemanip.Path`` (https://github.com/nipy/nipype/pull/2989)
+  * ENH: Add resolve/rebase ``BasePath`` traits methods & tests (https://github.com/nipy/nipype/pull/2970)
+  * ENH: Modify ``Directory`` and ``File`` traits to get along with pathlib (https://github.com/nipy/nipype/pull/2962)
+  * REF: Update nipype2boutiques script (https://github.com/nipy/nipype/pull/2894)
+  * TST: Parametrize JoinNode expansion tests over config ``needed_outputs`` (https://github.com/nipy/nipype/pull/2981)
+  * MAINT: Pin lxml<4.4.0 for Python 3.4 (https://github.com/nipy/nipype/pull/2980)
+  * MAINT: Refactor ``aggregate_outputs`` for readability (https://github.com/nipy/nipype/pull/2969)
+  * MAINT: Bump neurodocker version (https://github.com/nipy/nipype/pull/2965)
+  * MAINT: Various minor improvements to complement previous PR (https://github.com/nipy/nipype/pull/2964)
+  * MAINT: Sort dependencies alphabetically (https://github.com/nipy/nipype/pull/2961)
+
+
 1.2.0 (May 09, 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 = "1.2.0"
+release = "1.2.1"
 
 # 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__ = '1.2.1-dev'
+__version__ = '1.2.1'
 
 
 def get_nipype_gitversion():
@@ -59,7 +59,9 @@ def get_nipype_gitversion():
     'Programming Language :: Python :: 2.7',
     'Programming Language :: Python :: 3.4',
     'Programming Language :: Python :: 3.5',
-    'Programming Language :: Python :: 3.6', 'Topic :: Scientific/Engineering'
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Topic :: Scientific/Engineering'
 ]
 
 description = 'Neuroimaging in Python: Pipelines and Interfaces'
@@ -107,7 +109,11 @@ def get_nipype_gitversion():
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
 NUMPY_MIN_VERSION_37 = '1.15.3'
 NUMPY_BAD_VERSION_27 = '1.16.0'
+# Numpy drops 2.7 support in 1.17
+NUMPY_MAX_VERSION_27 = '1.17.0'
 SCIPY_MIN_VERSION = '0.14'
+# Scipy drops 2.7 and 3.4 support in 1.3
+SCIPY_MAX_VERSION_34 = '1.3.0'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '2.2'
 FUTURE_MIN_VERSION = '0.16.0'
@@ -146,14 +152,17 @@ def get_nipype_gitversion():
     'nibabel>=%s' % NIBABEL_MIN_VERSION,
     'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
     'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
-    'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
+    'numpy>=%s,!=%s,<%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION,
+                                                      NUMPY_BAD_VERSION_27,
+                                                      NUMPY_MAX_VERSION_27),
     'packaging',
     'pathlib2; python_version <= "3.4"',
     'prov>=%s' % PROV_VERSION,
     'pydot>=%s' % PYDOT_MIN_VERSION,
     'pydotplus',
     'python-dateutil>=%s' % DATEUTIL_MIN_VERSION,
-    'scipy>=%s' % SCIPY_MIN_VERSION,
+    'scipy>=%s ; python_version >= "3.5"' % SCIPY_MIN_VERSION,
+    'scipy>=%s,<%s ; python_version <= "3.4"' % (SCIPY_MIN_VERSION, SCIPY_MAX_VERSION_34),
     'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
     'traits>=%s,!=5.0' % TRAITS_MIN_VERSION,
 ]

tools/update_changes.sh

@@ -12,7 +12,8 @@
 set -u         # Treat unset variables as an error when substituting.
 set -x         # Print command traces before executing command.
 
-CHANGES=../doc/changelog/1.X.X-changelog
+ROOT=$( git rev-parse --show-toplevel )
+CHANGES=$ROOT/doc/changelog/1.X.X-changelog
 
 # Check whether the Upcoming release header is present
 head -1 $CHANGES | grep -q Upcoming