Merge branch 'master' of https://github.com/nipy/nipype into doc-enhs [skip ci]

Author: mgxd

.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\/.*/

.travis.yml

@@ -10,10 +10,24 @@ python:
 - 3.6
 
 env:
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
+  global:
+    - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+    - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
+    - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
+  matrix:
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=false
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+      CI_SKIP_TEST=1
 
 addons:
   apt:
@@ -39,23 +53,13 @@ before_install:
     export FSLOUTPUTTYPE=NIFTI_GZ;
   fi;
 
-# handle python operations separately to reduce timeouts
-- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
-    -O /home/travis/.cache/conda.sh
-- bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
-- export PATH=${HOME}/conda/bin:$PATH
-- hash -r
-- conda config --set always_yes yes --set changeps1 no
-- travis_retry conda update -q conda
-- conda config --add channels conda-forge
-- travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu
 - 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
-- travis_retry pip install codecov
 
 install:
-- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]
 
 script:
 - py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype

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(