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

Reviewed by CJM

.circleci/config.yml

@@ -317,13 +317,14 @@ jobs:
           name: Check pypi preconditions
           command: |
             pyenv local 3.5.2
-            pip install --upgrade twine 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 3 installation
           command: |
             pyenv local 3.5.2
+            pip install --upgrade pip
             pip install dist/nipype-*-py3-none-any.whl
       - run:
           name: Validate Python 3.7 installation

.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]>
@@ -138,6 +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"
     },
@@ -634,6 +648,16 @@
       "name": "McNamee, Daniel",
       "orcid": "0000-0001-9928-4960"
     },
+    {
+      "affiliation": "University of Pittsburgh",
+      "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"
     },

Makefile

@@ -56,7 +56,7 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	py.test --doctest-module nipype
+	py.test --doctest-modules nipype
 
 test-coverage: clean-tests in
 	py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype

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.

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.2.0 <http://nipype.readthedocs.io/en/1.2.0/>`_ `1.1.9 <http://nipype.readthedocs.io/en/1.1.9/>`_
+Previous versions: `1.2.1 <http://nipype.readthedocs.io/en/1.2.1/>`_ `1.2.0 <http://nipype.readthedocs.io/en/1.2.0/>`_
 
 
 .. container:: doc2

docker/generate_dockerfiles.sh

@@ -52,8 +52,8 @@ do
   esac
 done
 
-# neurodocker version 0.4.1-22-g7c44e01
-NEURODOCKER_IMAGE="kaczmarj/neurodocker:master@sha256:858632a7533cac100f70932749b4cfc77fc40f667f41fca208f406215cff8a27"
+# neurodocker version 0.5.0-3-g1788917
+NEURODOCKER_IMAGE="kaczmarj/neurodocker:master@sha256:ac2085702daac716481daae5da055e2062be52075f8f3881672e958e0cd53e6b"
 # neurodebian:stretch-non-free pulled on September 19, 2018
 BASE_IMAGE="neurodebian:stretch-non-free@sha256:7cd978427d7ad215834fee221d0536ed7825b3cddebc481eba2d792dfc2f7332"
 
@@ -88,6 +88,7 @@ function generate_main_dockerfile() {
           OMP_NUM_THREADS=1 \
     --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
     --user neuro \
+    --workdir /home/neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
                                libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko

nipype/algorithms/misc.py

@@ -722,7 +722,7 @@ def _list_outputs(self):
 
 
 class AddCSVRowInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
-    in_file = traits.File(
+    in_file = File(
         mandatory=True, desc='Input comma-separated value (CSV) files')
     _outputs = traits.Dict(traits.Any, value={}, usedefault=True)
 

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -21,7 +21,10 @@ def test_ACompCor_inputs():
         ),
         num_components=dict(xor=['variance_threshold'], ),
         pre_filter=dict(usedefault=True, ),
-        realigned_file=dict(mandatory=True, ),
+        realigned_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
         regress_poly_degree=dict(usedefault=True, ),
         repetition_time=dict(),
         save_metadata=dict(usedefault=True, ),
@@ -39,9 +42,9 @@ def test_ACompCor_inputs():
             assert getattr(inputs.traits()[key], metakey) == value
 def test_ACompCor_outputs():
     output_map = dict(
-        components_file=dict(),
-        metadata_file=dict(),
-        pre_filter_file=dict(),
+        components_file=dict(extensions=None, ),
+        metadata_file=dict(extensions=None, ),
+        pre_filter_file=dict(extensions=None, ),
     )
     outputs = ACompCor.output_spec()
 

nipype/algorithms/tests/test_auto_ActivationCount.py

@@ -14,9 +14,9 @@ def test_ActivationCount_inputs():
             assert getattr(inputs.traits()[key], metakey) == value
 def test_ActivationCount_outputs():
     output_map = dict(
-        acm_neg=dict(),
-        acm_pos=dict(),
-        out_file=dict(),
+        acm_neg=dict(extensions=None, ),
+        acm_pos=dict(extensions=None, ),
+        out_file=dict(extensions=None, ),
     )
     outputs = ActivationCount.output_spec()
 

nipype/algorithms/tests/test_auto_AddCSVColumn.py

@@ -6,16 +6,22 @@ def test_AddCSVColumn_inputs():
     input_map = dict(
         extra_column_heading=dict(),
         extra_field=dict(),
-        in_file=dict(mandatory=True, ),
-        out_file=dict(usedefault=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
+        out_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
     )
     inputs = AddCSVColumn.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_AddCSVColumn_outputs():
-    output_map = dict(csv_file=dict(), )
+    output_map = dict(csv_file=dict(extensions=None, ), )
     outputs = AddCSVColumn.output_spec()
 
     for key, metadata in list(output_map.items()):