Merge remote-tracking branch 'upstream/master' into addSPMrealingUnwarp

Author: effigies

.circleci/config.yml

@@ -339,9 +339,25 @@ jobs:
  - run:
  name: Check pypi preconditions
  command: |
- pip install twine future wheel readme_renderer
+ pip install --upgrade 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 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 dist/nipype-*-py2.py3-none-any.whl
+ # Futures should not install in Python 3
+ test $(pip show futures 2>/dev/null | wc -l) = "0"
+ - store_artifacts:
+ path: /home/circleci/nipype/dist
 
  deploy_pypi:
  machine: *machine_kwds
@@ -352,7 +368,7 @@ jobs:
  - run:
  name: Deploy to PyPI
  command: |
- pip install twine future wheel readme_renderer
+ pip install --upgrade twine future wheel readme_renderer setuptools
  python setup.py check -r -s
  python setup.py sdist bdist_wheel
  twine upload dist/*
@@ -393,6 +409,7 @@ workflows:
  version: 2
  build_test_deploy:
  jobs:
+ - pypi_precheck
  - compare_base_dockerfiles:
  filters:
  tags:
@@ -428,6 +445,7 @@ workflows:
  tags:
  only: /.*/
  requires:
+ - pypi_precheck
  - test_pytest
  - update_feedstock:
  context: nipybot
@@ -436,7 +454,3 @@ workflows:
  only: /rel\/.*/
  tags:
  only: /.*/
- - pypi_precheck:
- filters:
- branches:
- only: /rel\/.*/

nipype/interfaces/io.py

@@ -42,10 +42,16 @@
 
 have_pybids = True
 try:
- from bids import grabbids as gb
+ import bids
 except ImportError:
  have_pybids = False
 
+if have_pybids:
+ try:
+ from bids import layout as bidslayout
+ except ImportError:
+ from bids import grabbids as bidslayout
+
 try:
  import pyxnat
 except:
@@ -2810,7 +2816,7 @@ def __init__(self, infields=None, **kwargs):
 
  # If infields is empty, use all BIDS entities
  if infields is None and have_pybids:
- bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
+ bids_config = join(dirname(bidslayout.__file__), 'config', 'bids.json')
  bids_config = json.load(open(bids_config, 'r'))
  infields = [i['name'] for i in bids_config['entities']]
 
@@ -2835,7 +2841,7 @@ def _list_outputs(self):
  exclude = None
  if self.inputs.strict:
  exclude = ['derivatives/', 'code/', 'sourcedata/']
- layout = gb.BIDSLayout(self.inputs.base_dir, exclude=exclude)
+ layout = bidslayout.BIDSLayout(self.inputs.base_dir, exclude=exclude)
 
  # If infield is not given nm input value, silently ignore
  filters = {}

nipype/interfaces/tests/test_io.py

@@ -77,7 +77,6 @@
 have_pybids = True
 try:
  import bids
- from bids import grabbids as gb
  filepath = os.path.realpath(os.path.dirname(bids.__file__))
  datadir = os.path.realpath(os.path.join(filepath, 'tests/data/'))
 except ImportError: