Merge remote-tracking branch 'upstream/master' into enh/workflow_syntax

Author: effigies

.circleci/config.yml

@@ -330,6 +330,19 @@ jobs:
             - /tmp/docker/cache/Dockerfile.base-pruned
           key: dockerfile-cache-v1-{{ .Branch }}-{{ checksum "/tmp/docker/cache/Dockerfile.base-pruned" }}
 
+  pypi_precheck:
+    machine: *machine_kwds
+    working_directory: /home/circleci/nipype
+    steps:
+      - checkout:
+          path: /home/circleci/nipype
+      - run:
+          name: Check pypi preconditions
+          command: |
+            pip install twine future wheel readme_renderer
+            python setup.py check -r -s
+            python setup.py sdist bdist_wheel
+
   deploy_pypi:
     machine: *machine_kwds
     working_directory: /home/circleci/nipype
@@ -339,7 +352,8 @@ jobs:
       - run:
           name: Deploy to PyPI
           command: |
-            pip install twine future wheel
+            pip install twine future wheel readme_renderer
+            python setup.py check -r -s
             python setup.py sdist bdist_wheel
             twine upload dist/*
 
@@ -422,3 +436,7 @@ workflows:
               only: /rel\/.*/
             tags:
               only: /.*/
+      - pypi_precheck:
+          filters:
+            branches:
+              only: /rel\/.*/

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,15 +1,23 @@
-Pull-request guidelines (Remove this section after reading):
+<!--
+
+Pull-request guidelines
+-----------------------
 
 1. If you would like to list yourself as a Nipype contributor and your name is not mentioned please modify .zenodo.json file.
 2. By submitting this request you acknowledge that your contributions are available under the Apache 2 license.
 3. Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
-4. The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
-5. Run `make check-before-commit` before submitting the PR.
+4. Run `make check-before-commit` before submitting the PR.
 
------ REMOVE TILL HERE -----
+-->
+## Summary
+<!-- Please reference any related issue and use fixes/close to automatically
+close them, if pertinent -->
 
 Fixes # .
 
-Changes proposed in this pull request
--
--
+## List of changes proposed in this PR (pull-request)
+<!-- We suggest using bullets (indicated by * or -) and filled checkboxes [x] here -->
+
+## Acknowledgment
+
+- [ ] \(Mandatory\) I acknowledge that this contribution will be available under the Apache 2 license.

.travis.yml

@@ -54,6 +54,7 @@ before_install:
   fi;
 
 - travis_retry pip install -r requirements.txt
+- travis_retry pip install grabbit==0.1.2
 - travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids &&
   pip install -e ${HOME}/pybids
 

doc/changelog/1.X.X-changelog

@@ -1,3 +1,20 @@
+1.1.0 (July 04, 2018)
+=====================
+
+###### [Full changelog](https://github.com/nipy/nipype/milestone/21?closed=1)
+
+  * RF: Futures-based MultiProc (https://github.com/nipy/nipype/pull/2598)
+  * FIX: Avoid closing file descriptors on Windows (https://github.com/nipy/nipype/pull/2617)
+  * MAINT: Play nice with external logging (https://github.com/nipy/nipype/pull/2611)
+  * MAINT: Remove ignore_exception and terminal_output traits from input specs (https://github.com/nipy/nipype/pull/2618)
+  * MAINT: Converge autotest names (https://github.com/nipy/nipype/pull/2610)
+  * ENH: Add versioning metadata to crash files (https://github.com/nipy/nipype/pull/2626)
+  * ENH add -dsort option to TProject (https://github.com/nipy/nipype/pull/2623)
+  * ENH: Add Rescale interface (https://github.com/nipy/nipype/pull/2599)
+  * DOC: Improve documentation for ANTs/FSL interfaces (https://github.com/nipy/nipype/pull/2593)
+  * CI: Stop using Miniconda on Travis (https://github.com/nipy/nipype/pull/2600)
+  * CI: Add PyPI validation on rel/* branches (https://github.com/nipy/nipype/pull/2603)
+
 1.0.4 (May 29, 2018)
 ====================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.0.4"
+release = "1.1.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/generate_dockerfiles.sh

@@ -106,8 +106,10 @@ function generate_main_dockerfile() {
                              pandas psutil scikit-learn scipy traits=4.6.0' \
               pip_opts="-e" \
               pip_install="/src/nipype[all]" \
+  --miniconda env_name=neuro \
+              pip_install="grabbit==0.1.2" \
   --run-bash "mkdir -p /src/pybids
-         && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/master
+         && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1
          | tar -xz -C /src/pybids --strip-components 1
          && source activate neuro
          && pip install --no-cache-dir -e /src/pybids" \

nipype/algorithms/confounds.py

@@ -24,7 +24,7 @@
 from ..utils import NUMPY_MMAP
 from ..utils.misc import normalize_mc_params
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class ComputeDVARSInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/mesh.py

@@ -17,7 +17,7 @@
                                BaseInterfaceInputSpec)
 from ..interfaces.vtkbase import tvtk
 from ..interfaces import vtkbase as VTKInfo
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class TVTKBaseInterface(BaseInterface):

nipype/algorithms/metrics.py

@@ -26,7 +26,7 @@
     isdefined)
 from ..interfaces.nipy.base import NipyBaseInterface
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class DistanceInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/misc.py

@@ -31,7 +31,7 @@
 
 from . import confounds
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class PickAtlasInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/modelgen.py

@@ -29,7 +29,7 @@
 from ..utils.filemanip import ensure_list
 from ..utils.misc import normalize_mc_params
 from .. import config, logging
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def gcd(a, b):

nipype/algorithms/rapidart.py

@@ -31,7 +31,7 @@
 from ..utils.filemanip import ensure_list, save_json, split_filename
 from ..utils.misc import find_indices, normalize_mc_params
 from .. import logging, config
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def _get_affine_matrix(params, source):

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -8,11 +8,6 @@ def test_ACompCor_inputs():
         components_file=dict(usedefault=True, ),
         header_prefix=dict(),
         high_pass_cutoff=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         ignore_initial_volumes=dict(usedefault=True, ),
         mask_files=dict(),
         mask_index=dict(

nipype/algorithms/tests/test_auto_ActivationCount.py

@@ -5,11 +5,6 @@
 
 def test_ActivationCount_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_files=dict(mandatory=True, ),
         threshold=dict(mandatory=True, ),
     )

nipype/algorithms/tests/test_auto_AddCSVRow.py

@@ -6,11 +6,6 @@
 def test_AddCSVRow_inputs():
     input_map = dict(
         _outputs=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file=dict(mandatory=True, ),
     )
     inputs = AddCSVRow.input_spec()

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -7,11 +7,6 @@ def test_ArtifactDetect_inputs():
     input_map = dict(
         bound_by_brainmask=dict(usedefault=True, ),
         global_threshold=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         intersect_mask=dict(usedefault=True, ),
         mask_file=dict(),
         mask_threshold=dict(),

nipype/algorithms/tests/test_auto_CalculateMedian.py

@@ -5,11 +5,6 @@
 
 def test_CalculateMedian_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_files=dict(),
         median_file=dict(),
         median_per_file=dict(usedefault=True, ),

nipype/algorithms/tests/test_auto_ComputeDVARS.py

@@ -8,11 +8,6 @@ def test_ComputeDVARS_inputs():
         figdpi=dict(usedefault=True, ),
         figformat=dict(usedefault=True, ),
         figsize=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file=dict(mandatory=True, ),
         in_mask=dict(mandatory=True, ),
         intensity_normalization=dict(usedefault=True, ),

nipype/algorithms/tests/test_auto_ComputeMeshWarp.py

@@ -5,11 +5,6 @@
 
 def test_ComputeMeshWarp_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         metric=dict(usedefault=True, ),
         out_file=dict(usedefault=True, ),
         out_warp=dict(usedefault=True, ),

nipype/algorithms/tests/test_auto_CreateNifti.py

@@ -8,11 +8,6 @@ def test_CreateNifti_inputs():
         affine=dict(),
         data_file=dict(mandatory=True, ),
         header_file=dict(mandatory=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
     )
     inputs = CreateNifti.input_spec()
 

nipype/algorithms/tests/test_auto_Distance.py

@@ -5,11 +5,6 @@
 
 def test_Distance_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         mask_volume=dict(),
         method=dict(usedefault=True, ),
         volume1=dict(mandatory=True, ),

nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

@@ -7,11 +7,6 @@ def test_FramewiseDisplacement_inputs():
     input_map = dict(
         figdpi=dict(usedefault=True, ),
         figsize=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_file=dict(mandatory=True, ),
         normalize=dict(usedefault=True, ),
         out_figure=dict(usedefault=True, ),

nipype/algorithms/tests/test_auto_FuzzyOverlap.py

@@ -5,11 +5,6 @@
 
 def test_FuzzyOverlap_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_mask=dict(),
         in_ref=dict(mandatory=True, ),
         in_tst=dict(mandatory=True, ),

nipype/algorithms/tests/test_auto_Gunzip.py

@@ -4,14 +4,7 @@
 
 
 def test_Gunzip_inputs():
-    input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
-        in_file=dict(mandatory=True, ),
-    )
+    input_map = dict(in_file=dict(mandatory=True, ), )
     inputs = Gunzip.input_spec()
 
     for key, metadata in list(input_map.items()):

nipype/algorithms/tests/test_auto_ICC.py

@@ -5,11 +5,6 @@
 
 def test_ICC_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         mask=dict(mandatory=True, ),
         subjects_sessions=dict(mandatory=True, ),
     )

nipype/algorithms/tests/test_auto_MeshWarpMaths.py

@@ -6,11 +6,6 @@
 def test_MeshWarpMaths_inputs():
     input_map = dict(
         float_trait=dict(),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         in_surf=dict(mandatory=True, ),
         operation=dict(usedefault=True, ),
         operator=dict(

nipype/algorithms/tests/test_auto_ModifyAffine.py

@@ -5,11 +5,6 @@
 
 def test_ModifyAffine_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         transformation_matrix=dict(usedefault=True, ),
         volumes=dict(mandatory=True, ),
     )

nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py

@@ -4,14 +4,7 @@
 
 
 def test_NonSteadyStateDetector_inputs():
-    input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
-        in_file=dict(mandatory=True, ),
-    )
+    input_map = dict(in_file=dict(mandatory=True, ), )
     inputs = NonSteadyStateDetector.input_spec()
 
     for key, metadata in list(input_map.items()):

nipype/algorithms/tests/test_auto_P2PDistance.py

@@ -5,11 +5,6 @@
 
 def test_P2PDistance_inputs():
     input_map = dict(
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         metric=dict(usedefault=True, ),
         out_file=dict(usedefault=True, ),
         out_warp=dict(usedefault=True, ),

nipype/algorithms/tests/test_auto_PickAtlas.py

@@ -8,11 +8,6 @@ def test_PickAtlas_inputs():
         atlas=dict(mandatory=True, ),
         dilation_size=dict(usedefault=True, ),
         hemi=dict(usedefault=True, ),
-        ignore_exception=dict(
-            deprecated='1.0.0',
-            nohash=True,
-            usedefault=True,
-        ),
         labels=dict(mandatory=True, ),
         output_file=dict(),
     )