Merge pull request #2600 from effigies/ci/travis_python

CI: Stop using Miniconda on Travis

Author: effigies

.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 +53,12 @@ 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 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

nipype/interfaces/base/core.py

@@ -692,13 +692,8 @@ class SimpleInterface(BaseInterface):
     Examples
     --------
 
-    .. testsetup::
-
-    >>> from .specs import TraitedSpec
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to a temporary directory
-
-    .. doctest::
+    >>> from nipype.interfaces.base import (
+    ...     SimpleInterface, BaseInterfaceInputSpec, TraitedSpec)
 
     >>> def double(x):
     ...    return 2 * x
@@ -721,11 +716,6 @@ class SimpleInterface(BaseInterface):
     >>> dbl.inputs.x = 2
     >>> dbl.run().outputs.doubled
     4.0
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
     """
 
     def __init__(self, from_file=None, resource_monitor=None, **inputs):

nipype/interfaces/dcm2nii.py

@@ -106,26 +106,14 @@ class Dcm2nii(CommandLine):
     Examples
     ========
 
-    .. testsetup::
-
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to a temporary directory
-
-    .. doctest::
-
     >>> from nipype.interfaces.dcm2nii import Dcm2nii
     >>> converter = Dcm2nii()
-    >>> converter.inputs.source_names = [os.path.join(datadir, 'functional_1.dcm'), os.path.join(datadir, 'functional_2.dcm')]
+    >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
     >>> converter.inputs.gzip_output = True
     >>> converter.inputs.output_dir = '.'
-    >>> converter.cmdline #doctest: +ELLIPSIS
-    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n ...functional_1.dcm'
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
-    """
+    >>> converter.cmdline  # doctest: +ELLIPSIS
+    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
+"""
 
     input_spec = Dcm2niiInputSpec
     output_spec = Dcm2niiOutputSpec

nipype/interfaces/image.py

@@ -110,58 +110,63 @@ class ReorientOutputSpec(TraitedSpec):
 class Reorient(SimpleInterface):
     """Conform an image to a given orientation
 
-    Flips and reorder the image data array so that the axes match the
-    directions indicated in ``orientation``.
-    The default ``RAS`` orientation corresponds to the first axis being ordered
-    from left to right, the second axis from posterior to anterior, and the
-    third axis from inferior to superior.
+Flips and reorder the image data array so that the axes match the
+directions indicated in ``orientation``.
+The default ``RAS`` orientation corresponds to the first axis being ordered
+from left to right, the second axis from posterior to anterior, and the
+third axis from inferior to superior.
 
-    For oblique images, the original orientation is considered to be the
-    closest plumb orientation.
+For oblique images, the original orientation is considered to be the
+closest plumb orientation.
 
-    No resampling is performed, and thus the output image is not de-obliqued
-    or registered to any other image or template.
+No resampling is performed, and thus the output image is not de-obliqued
+or registered to any other image or template.
 
-    The effective transform is calculated from the original affine matrix to
-    the reoriented affine matrix.
+The effective transform is calculated from the original affine matrix to
+the reoriented affine matrix.
 
-    Examples
-    --------
+Examples
+--------
 
-    If an image is not reoriented, the original file is not modified
+If an image is not reoriented, the original file is not modified
 
-    >>> import numpy as np
-    >>> from nipype.interfaces.image import Reorient
-    >>> reorient = Reorient(orientation='LPS')
-    >>> reorient.inputs.in_file = 'segmentation0.nii.gz'
-    >>> res = reorient.run()
-    >>> res.outputs.out_file
-    'segmentation0.nii.gz'
+.. testsetup::
 
-    >>> print(np.loadtxt(res.outputs.transform))
-    [[1. 0. 0. 0.]
-     [0. 1. 0. 0.]
-     [0. 0. 1. 0.]
-     [0. 0. 0. 1.]]
+    >>> def print_affine(matrix):
+    ...     print(str(matrix).replace(']', ' ').replace('[', ' '))
 
-    >>> reorient.inputs.orientation = 'RAS'
-    >>> res = reorient.run()
-    >>> res.outputs.out_file  # doctest: +ELLIPSIS
-    '.../segmentation0_ras.nii.gz'
+>>> import numpy as np
+>>> from nipype.interfaces.image import Reorient
+>>> reorient = Reorient(orientation='LPS')
+>>> reorient.inputs.in_file = 'segmentation0.nii.gz'
+>>> res = reorient.run()
+>>> res.outputs.out_file
+'segmentation0.nii.gz'
 
-    >>> print(np.loadtxt(res.outputs.transform))
-    [[-1.  0.  0. 60.]
-     [ 0. -1.  0. 72.]
-     [ 0.  0.  1.  0.]
-     [ 0.  0.  0.  1.]]
+>>> print_affine(np.loadtxt(res.outputs.transform))
+1.  0.  0.  0.
+0.  1.  0.  0.
+0.  0.  1.  0.
+0.  0.  0.  1.
 
-    .. testcleanup::
+>>> reorient.inputs.orientation = 'RAS'
+>>> res = reorient.run()
+>>> res.outputs.out_file  # doctest: +ELLIPSIS
+'.../segmentation0_ras.nii.gz'
 
-        >>> import os
-        >>> os.unlink(res.outputs.out_file)
-        >>> os.unlink(res.outputs.transform)
+>>> print_affine(np.loadtxt(res.outputs.transform))
+-1.   0.   0.  60.
+ 0.  -1.   0.  72.
+ 0.   0.   1.   0.
+ 0.   0.   0.   1.
 
-    """
+.. testcleanup::
+
+    >>> import os
+    >>> os.unlink(res.outputs.out_file)
+    >>> os.unlink(res.outputs.transform)
+
+"""
     input_spec = ReorientInputSpec
     output_spec = ReorientOutputSpec
 

nipype/interfaces/io.py

@@ -2585,13 +2585,6 @@ class JSONFileGrabber(IOBase):
     Example
     -------
 
-    .. testsetup::
-
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to a temporary directory
-
-    .. doctest::
-
     >>> import pprint
     >>> from nipype.interfaces.io import JSONFileGrabber
     >>> jsonSource = JSONFileGrabber()
@@ -2603,11 +2596,6 @@ class JSONFileGrabber(IOBase):
     >>> res = jsonSource.run()
     >>> pprint.pprint(res.outputs.get())  # doctest:, +ELLIPSIS
     {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
     """
     input_spec = JSONFileGrabberInputSpec
     output_spec = DynamicTraitedSpec

nipype/interfaces/niftyreg/regutils.py

@@ -450,13 +450,6 @@ class RegAverage(NiftyRegCommand):
     Examples
     --------
 
-    .. testsetup::
-
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to temporary file
-
-    .. doctest::
-
     >>> from nipype.interfaces import niftyreg
     >>> node = niftyreg.RegAverage()
     >>> one_file = 'im1.nii'
@@ -465,11 +458,6 @@ class RegAverage(NiftyRegCommand):
     >>> node.inputs.avg_files = [one_file, two_file, three_file]
     >>> node.cmdline  # doctest: +ELLIPSIS
     'reg_average --cmd_file .../reg_average_cmd'
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
     """
     _cmd = get_custom_path('reg_average')
     input_spec = RegAverageInputSpec