Skip to content

Commit c6c9093

Browse files
mgxdmgxd
committed
Merge branch 'master' of https://github.com/nipy/nipype into doc-enhs [skip ci]
2 parents 6a1e2e6 + 4b576d8 commit c6c9093

File tree

888 files changed

+723
-7113
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

888 files changed

+723
-7113
lines changed

‎.circleci/config.yml

+19-1
Original file line numberDiff line numberDiff line change
@@ -330,6 +330,19 @@ jobs:
330330
- /tmp/docker/cache/Dockerfile.base-pruned
331331
key: dockerfile-cache-v1-{{ .Branch }}-{{ checksum "/tmp/docker/cache/Dockerfile.base-pruned" }}
332332

333+
pypi_precheck:
334+
machine: *machine_kwds
335+
working_directory: /home/circleci/nipype
336+
steps:
337+
- checkout:
338+
path: /home/circleci/nipype
339+
- run:
340+
name: Check pypi preconditions
341+
command: |
342+
pip install twine future wheel readme_renderer
343+
python setup.py check -r -s
344+
python setup.py sdist bdist_wheel
345+
333346
deploy_pypi:
334347
machine: *machine_kwds
335348
working_directory: /home/circleci/nipype
@@ -339,7 +352,8 @@ jobs:
339352
- run:
340353
name: Deploy to PyPI
341354
command: |
342-
pip install twine future wheel
355+
pip install twine future wheel readme_renderer
356+
python setup.py check -r -s
343357
python setup.py sdist bdist_wheel
344358
twine upload dist/*
345359
@@ -422,3 +436,7 @@ workflows:
422436
only: /rel\/.*/
423437
tags:
424438
only: /.*/
439+
- pypi_precheck:
440+
filters:
441+
branches:
442+
only: /rel\/.*/

‎.travis.yml

+20-16
Original file line numberDiff line numberDiff line change
@@ -10,10 +10,24 @@ python:
1010
- 3.6
1111

1212
env:
13-
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
14-
- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
15-
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1
16-
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
13+
global:
14+
- EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
15+
- PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
16+
- EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
17+
matrix:
18+
- INSTALL_DEB_DEPENDECIES=true
19+
NIPYPE_EXTRAS="doc,tests,fmri,profiler"
20+
CI_SKIP_TEST=1
21+
- INSTALL_DEB_DEPENDECIES=false
22+
NIPYPE_EXTRAS="doc,tests,fmri,profiler"
23+
CI_SKIP_TEST=1
24+
- INSTALL_DEB_DEPENDECIES=true
25+
NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh"
26+
CI_SKIP_TEST=1
27+
- INSTALL_DEB_DEPENDECIES=true
28+
NIPYPE_EXTRAS="doc,tests,fmri,profiler"
29+
EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
30+
CI_SKIP_TEST=1
1731

1832
addons:
1933
apt:
@@ -39,23 +53,13 @@ before_install:
3953
export FSLOUTPUTTYPE=NIFTI_GZ;
4054
fi;
4155

42-
# handle python operations separately to reduce timeouts
43-
- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
44-
-O /home/travis/.cache/conda.sh
45-
- bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
46-
- export PATH=${HOME}/conda/bin:$PATH
47-
- hash -r
48-
- conda config --set always_yes yes --set changeps1 no
49-
- travis_retry conda update -q conda
50-
- conda config --add channels conda-forge
51-
- travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu
5256
- travis_retry pip install -r requirements.txt
57+
- travis_retry pip install grabbit==0.1.2
5358
- travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids &&
5459
pip install -e ${HOME}/pybids
55-
- travis_retry pip install codecov
5660

5761
install:
58-
- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
62+
- travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]
5963

6064
script:
6165
- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype

‎docker/generate_dockerfiles.sh

+3-1
Original file line numberDiff line numberDiff line change
@@ -106,8 +106,10 @@ function generate_main_dockerfile() {
106106
pandas psutil scikit-learn scipy traits=4.6.0' \
107107
pip_opts="-e" \
108108
pip_install="/src/nipype[all]" \
109+
--miniconda env_name=neuro \
110+
pip_install="grabbit==0.1.2" \
109111
--run-bash "mkdir -p /src/pybids
110-
&& curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/master
112+
&& curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1
111113
| tar -xz -C /src/pybids --strip-components 1
112114
&& source activate neuro
113115
&& pip install --no-cache-dir -e /src/pybids" \

‎nipype/algorithms/confounds.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
2424
from ..utils import NUMPY_MMAP
2525
from ..utils.misc import normalize_mc_params
2626

27-
IFLOGGER = logging.getLogger('interface')
27+
IFLOGGER = logging.getLogger('nipype.interface')
2828

2929

3030
class ComputeDVARSInputSpec(BaseInterfaceInputSpec):

‎nipype/algorithms/mesh.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@
1717
BaseInterfaceInputSpec)
1818
from ..interfaces.vtkbase import tvtk
1919
from ..interfaces import vtkbase as VTKInfo
20-
IFLOGGER = logging.getLogger('interface')
20+
IFLOGGER = logging.getLogger('nipype.interface')
2121

2222

2323
class TVTKBaseInterface(BaseInterface):

‎nipype/algorithms/metrics.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
isdefined)
2727
from ..interfaces.nipy.base import NipyBaseInterface
2828

29-
iflogger = logging.getLogger('interface')
29+
iflogger = logging.getLogger('nipype.interface')
3030

3131

3232
class DistanceInputSpec(BaseInterfaceInputSpec):

‎nipype/algorithms/misc.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131

3232
from . import confounds
3333

34-
iflogger = logging.getLogger('interface')
34+
iflogger = logging.getLogger('nipype.interface')
3535

3636

3737
class PickAtlasInputSpec(BaseInterfaceInputSpec):

‎nipype/algorithms/modelgen.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@
2929
from ..utils.filemanip import ensure_list
3030
from ..utils.misc import normalize_mc_params
3131
from .. import config, logging
32-
iflogger = logging.getLogger('interface')
32+
iflogger = logging.getLogger('nipype.interface')
3333

3434

3535
def gcd(a, b):

‎nipype/algorithms/rapidart.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131
from ..utils.filemanip import ensure_list, save_json, split_filename
3232
from ..utils.misc import find_indices, normalize_mc_params
3333
from .. import logging, config
34-
iflogger = logging.getLogger('interface')
34+
iflogger = logging.getLogger('nipype.interface')
3535

3636

3737
def _get_affine_matrix(params, source):

‎nipype/algorithms/tests/test_auto_ACompCor.py

-5
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,6 @@ def test_ACompCor_inputs():
88
components_file=dict(usedefault=True, ),
99
header_prefix=dict(),
1010
high_pass_cutoff=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
13-
nohash=True,
14-
usedefault=True,
15-
),
1611
ignore_initial_volumes=dict(usedefault=True, ),
1712
mask_files=dict(),
1813
mask_index=dict(

‎nipype/algorithms/tests/test_auto_ActivationCount.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_ActivationCount_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
in_files=dict(mandatory=True, ),
149
threshold=dict(mandatory=True, ),
1510
)

‎nipype/algorithms/tests/test_auto_AddCSVRow.py

-5
Original file line numberDiff line numberDiff line change
@@ -6,11 +6,6 @@
66
def test_AddCSVRow_inputs():
77
input_map = dict(
88
_outputs=dict(usedefault=True, ),
9-
ignore_exception=dict(
10-
deprecated='1.0.0',
11-
nohash=True,
12-
usedefault=True,
13-
),
149
in_file=dict(mandatory=True, ),
1510
)
1611
inputs = AddCSVRow.input_spec()

‎nipype/algorithms/tests/test_auto_ArtifactDetect.py

-5
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,6 @@ def test_ArtifactDetect_inputs():
77
input_map = dict(
88
bound_by_brainmask=dict(usedefault=True, ),
99
global_threshold=dict(usedefault=True, ),
10-
ignore_exception=dict(
11-
deprecated='1.0.0',
12-
nohash=True,
13-
usedefault=True,
14-
),
1510
intersect_mask=dict(usedefault=True, ),
1611
mask_file=dict(),
1712
mask_threshold=dict(),

‎nipype/algorithms/tests/test_auto_CalculateMedian.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_CalculateMedian_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
in_files=dict(),
149
median_file=dict(),
1510
median_per_file=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_ComputeDVARS.py

-5
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,6 @@ def test_ComputeDVARS_inputs():
88
figdpi=dict(usedefault=True, ),
99
figformat=dict(usedefault=True, ),
1010
figsize=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
13-
nohash=True,
14-
usedefault=True,
15-
),
1611
in_file=dict(mandatory=True, ),
1712
in_mask=dict(mandatory=True, ),
1813
intensity_normalization=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_ComputeMeshWarp.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_ComputeMeshWarp_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
metric=dict(usedefault=True, ),
149
out_file=dict(usedefault=True, ),
1510
out_warp=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_CreateNifti.py

-5
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,6 @@ def test_CreateNifti_inputs():
88
affine=dict(),
99
data_file=dict(mandatory=True, ),
1010
header_file=dict(mandatory=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
13-
nohash=True,
14-
usedefault=True,
15-
),
1611
)
1712
inputs = CreateNifti.input_spec()
1813

‎nipype/algorithms/tests/test_auto_Distance.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_Distance_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
mask_volume=dict(),
149
method=dict(usedefault=True, ),
1510
volume1=dict(mandatory=True, ),

‎nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

-5
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,6 @@ def test_FramewiseDisplacement_inputs():
77
input_map = dict(
88
figdpi=dict(usedefault=True, ),
99
figsize=dict(usedefault=True, ),
10-
ignore_exception=dict(
11-
deprecated='1.0.0',
12-
nohash=True,
13-
usedefault=True,
14-
),
1510
in_file=dict(mandatory=True, ),
1611
normalize=dict(usedefault=True, ),
1712
out_figure=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_FuzzyOverlap.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_FuzzyOverlap_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
in_mask=dict(),
149
in_ref=dict(mandatory=True, ),
1510
in_tst=dict(mandatory=True, ),

‎nipype/algorithms/tests/test_auto_Gunzip.py

+1-8
Original file line numberDiff line numberDiff line change
@@ -4,14 +4,7 @@
44

55

66
def test_Gunzip_inputs():
7-
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
13-
in_file=dict(mandatory=True, ),
14-
)
7+
input_map = dict(in_file=dict(mandatory=True, ), )
158
inputs = Gunzip.input_spec()
169

1710
for key, metadata in list(input_map.items()):

‎nipype/algorithms/tests/test_auto_ICC.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_ICC_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
mask=dict(mandatory=True, ),
149
subjects_sessions=dict(mandatory=True, ),
1510
)

‎nipype/algorithms/tests/test_auto_MeshWarpMaths.py

-5
Original file line numberDiff line numberDiff line change
@@ -6,11 +6,6 @@
66
def test_MeshWarpMaths_inputs():
77
input_map = dict(
88
float_trait=dict(),
9-
ignore_exception=dict(
10-
deprecated='1.0.0',
11-
nohash=True,
12-
usedefault=True,
13-
),
149
in_surf=dict(mandatory=True, ),
1510
operation=dict(usedefault=True, ),
1611
operator=dict(

‎nipype/algorithms/tests/test_auto_ModifyAffine.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_ModifyAffine_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
transformation_matrix=dict(usedefault=True, ),
149
volumes=dict(mandatory=True, ),
1510
)

‎nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py

+1-8
Original file line numberDiff line numberDiff line change
@@ -4,14 +4,7 @@
44

55

66
def test_NonSteadyStateDetector_inputs():
7-
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
13-
in_file=dict(mandatory=True, ),
14-
)
7+
input_map = dict(in_file=dict(mandatory=True, ), )
158
inputs = NonSteadyStateDetector.input_spec()
169

1710
for key, metadata in list(input_map.items()):

‎nipype/algorithms/tests/test_auto_P2PDistance.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_P2PDistance_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
metric=dict(usedefault=True, ),
149
out_file=dict(usedefault=True, ),
1510
out_warp=dict(usedefault=True, ),

‎nipype/algorithms/tests/test_auto_PickAtlas.py

-5
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,6 @@ def test_PickAtlas_inputs():
88
atlas=dict(mandatory=True, ),
99
dilation_size=dict(usedefault=True, ),
1010
hemi=dict(usedefault=True, ),
11-
ignore_exception=dict(
12-
deprecated='1.0.0',
13-
nohash=True,
14-
usedefault=True,
15-
),
1611
labels=dict(mandatory=True, ),
1712
output_file=dict(),
1813
)

‎nipype/algorithms/tests/test_auto_Similarity.py

-5
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,6 @@
55

66
def test_Similarity_inputs():
77
input_map = dict(
8-
ignore_exception=dict(
9-
deprecated='1.0.0',
10-
nohash=True,
11-
usedefault=True,
12-
),
138
mask1=dict(),
149
mask2=dict(),
1510
metric=dict(usedefault=True, ),

0 commit comments

Comments
 (0)