Merge pull request #3066 from effigies/ci/make_checks

CI: make check-before-commit on Travis

Author: effigies

.travis.yml

@@ -16,6 +16,7 @@ env:
     - 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"
+    - CHECK_TYPE=test
   matrix:
     - INSTALL_DEB_DEPENDECIES=true
       NIPYPE_EXTRAS="doc,tests,nipy,profiler"
@@ -31,6 +32,13 @@ env:
       EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
       CI_SKIP_TEST=1
 
+matrix:
+  include:
+    - python: 3.7
+      env:
+        - NIPYPE_EXTRAS=dev
+          CHECK_TYPE=specs
+
 addons:
   apt:
     packages:
@@ -64,7 +72,16 @@ install:
 - travis_retry pip install pytest-xdist
 
 script:
-- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
+- |
+    if [ "$CHECK_TYPE" = "test" ]; then
+        py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
+    fi
+- |
+    if [ "$CHECK_TYPE" = "specs" ]; then
+        make specs
+        git add nipype
+        test "$( git diff --cached | wc -l )" -eq 0 || ( git diff --cached && false )
+    fi
 
 after_script:
 - codecov --file cov.xml --flags unittests -e TRAVIS_JOB_NUMBER

nipype/interfaces/afni/tests/test_auto_Remlfit.py

@@ -46,6 +46,7 @@ def test_Remlfit_inputs():
             extensions=None,
         ),
         gltsym=dict(argstr='-gltsym "%s" %s...', ),
+        goforit=dict(argstr='-GOFORIT', ),
         in_files=dict(
             argstr='-input "%s"',
             copyfile=False,

nipype/interfaces/afni/utils.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft = python sts = 4 ts = 4 sw = 4 et:
+# vi: set ft=python sts=4 ts=4 sw=4 et:
 """
 AFNI utility interfaces.
 
@@ -213,9 +213,9 @@ class Autobox(AFNICommand):
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
         outputs = super(Autobox, self).aggregate_outputs(
             runtime, needed_outputs)
-        pattern = 'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+)  '\
-                  'y=(?P<y_min>-?\d+)\.\.(?P<y_max>-?\d+)  '\
-                  'z=(?P<z_min>-?\d+)\.\.(?P<z_max>-?\d+)'
+        pattern = r'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+)  '\
+                  r'y=(?P<y_min>-?\d+)\.\.(?P<y_max>-?\d+)  '\
+                  r'z=(?P<z_min>-?\d+)\.\.(?P<z_max>-?\d+)'
         for line in runtime.stderr.split('\n'):
             m = re.search(pattern, line)
             if m:

nipype/interfaces/diffusion_toolkit/dti.py

@@ -94,7 +94,7 @@ class DTIRecon(CommandLine):
     def _create_gradient_matrix(self, bvecs_file, bvals_file):
         _gradient_matrix_file = 'gradient_matrix.txt'
         with open(bvals_file) as fbvals:
-            bvals = [val for val in re.split('\s+', fbvals.readline().strip())]
+            bvals = [val for val in re.split(r'\s+', fbvals.readline().strip())]
         with open(bvecs_file) as fbvecs:
           bvecs_x = fbvecs.readline().split()
           bvecs_y = fbvecs.readline().split()

nipype/interfaces/dipy/tracks.py

@@ -5,7 +5,6 @@
 import os.path as op
 import numpy as np
 import nibabel as nb
-import nibabel.trackvis as nbt
 from distutils.version import LooseVersion
 
 from ... import logging
@@ -89,6 +88,7 @@ class TrackDensityMap(DipyBaseInterface):
     def _run_interface(self, runtime):
         from numpy import min_scalar_type
         from dipy.tracking.utils import density_map
+        import nibabel.trackvis as nbt
 
         tracks, header = nbt.read(self.inputs.in_file)
         streams = ((ii[0]) for ii in tracks)

nipype/interfaces/fsl/utils.py

@@ -858,18 +858,18 @@ def _run_interface(self, runtime):
         runtime = super(AvScale, self)._run_interface(runtime)
 
         expr = re.compile(
-            'Rotation\ &\ Translation\ Matrix:\n(?P<rot_tran_mat>[0-9\.\ \n-]+)[\s\n]*'
-            '(Rotation\ Angles\ \(x,y,z\)\ \[rads\]\ =\ (?P<rot_angles>[0-9\.\ -]+))?[\s\n]*'
-            '(Translations\ \(x,y,z\)\ \[mm\]\ =\ (?P<translations>[0-9\.\ -]+))?[\s\n]*'
-            'Scales\ \(x,y,z\)\ =\ (?P<scales>[0-9\.\ -]+)[\s\n]*'
-            'Skews\ \(xy,xz,yz\)\ =\ (?P<skews>[0-9\.\ -]+)[\s\n]*'
-            'Average\ scaling\ =\ (?P<avg_scaling>[0-9\.-]+)[\s\n]*'
-            'Determinant\ =\ (?P<determinant>[0-9\.-]+)[\s\n]*'
-            'Left-Right\ orientation:\ (?P<lr_orientation>[A-Za-z]+)[\s\n]*'
-            'Forward\ half\ transform\ =[\s]*\n'
-            '(?P<fwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*'
-            'Backward\ half\ transform\ =[\s]*\n'
-            '(?P<bwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*')
+            r'Rotation & Translation Matrix:\n(?P<rot_tran_mat>[0-9\. \n-]+)[\s\n]*'
+            r'(Rotation Angles \(x,y,z\) \[rads\] = (?P<rot_angles>[0-9\. -]+))?[\s\n]*'
+            r'(Translations \(x,y,z\) \[mm\] = (?P<translations>[0-9\. -]+))?[\s\n]*'
+            r'Scales \(x,y,z\) = (?P<scales>[0-9\. -]+)[\s\n]*'
+            r'Skews \(xy,xz,yz\) = (?P<skews>[0-9\. -]+)[\s\n]*'
+            r'Average scaling = (?P<avg_scaling>[0-9\.-]+)[\s\n]*'
+            r'Determinant = (?P<determinant>[0-9\.-]+)[\s\n]*'
+            r'Left-Right orientation: (?P<lr_orientation>[A-Za-z]+)[\s\n]*'
+            r'Forward half transform =[\s]*\n'
+            r'(?P<fwd_half_xfm>[0-9\. \n-]+)[\s\n]*'
+            r'Backward half transform =[\s]*\n'
+            r'(?P<bwd_half_xfm>[0-9\. \n-]+)[\s\n]*')
         out = expr.search(runtime.stdout).groupdict()
         outputs = {}
         outputs['rotation_translation_matrix'] = [[

nipype/interfaces/image.py

@@ -43,8 +43,8 @@ class Rescale(SimpleInterface):
     Examples
     --------
 
-    To use a high-resolution T1w image as a registration target for a T2\*
-    image, it may be useful to invert the T1w image and rescale to the T2\*
+    To use a high-resolution T1w image as a registration target for a T2\\*
+    image, it may be useful to invert the T1w image and rescale to the T2\\*
     range.
     Using the 1st and 99th percentiles may reduce the impact of outlier
     voxels.

nipype/interfaces/io.py

@@ -1466,7 +1466,7 @@ class DataFinder(IOBase):
     >>> from nipype.interfaces.io import DataFinder
     >>> df = DataFinder()
     >>> df.inputs.root_paths = '.'
-    >>> df.inputs.match_regex = '.+/(?P<series_dir>.+(qT1|ep2d_fid_T1).+)/(?P<basename>.+)\.nii.gz'
+    >>> df.inputs.match_regex = r'.+/(?P<series_dir>.+(qT1|ep2d_fid_T1).+)/(?P<basename>.+)\.nii.gz'
     >>> result = df.run() # doctest: +SKIP
     >>> result.outputs.out_paths  # doctest: +SKIP
     ['./027-ep2d_fid_T1_Gd4/acquisition.nii.gz',

nipype/interfaces/tests/test_io.py

@@ -524,7 +524,7 @@ def test_datafinder_unpack(tmpdir):
 
     df = nio.DataFinder()
     df.inputs.root_paths = outdir
-    df.inputs.match_regex = '.+/(?P<basename>.+)\.txt'
+    df.inputs.match_regex = r'.+/(?P<basename>.+)\.txt'
     df.inputs.unpack_single = True
     result = df.run()
     print(result.outputs.out_paths)

nipype/interfaces/utility/base.py

@@ -254,7 +254,7 @@ class Rename(SimpleInterface, IOBase):
 
     >>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii")
     >>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii")
-    >>> rename3.inputs.parse_string = "func_(?P<seq>\w*)_.*"
+    >>> rename3.inputs.parse_string = r"func_(?P<seq>\w*)_.*"
     >>> rename3.inputs.subject_id = "subj_201"
     >>> rename3.inputs.run = 2
     >>> res = rename3.run()          # doctest: +SKIP

nipype/pipeline/engine/utils.py

@@ -235,7 +235,7 @@ def save_resultfile(result, cwd, name, rebase=None):
     logger.debug("Saving results file: '%s'", resultsfile)
 
     if result.outputs is None:
-        logger.warn('Storing result file without outputs')
+        logger.warning('Storing result file without outputs')
         savepkl(resultsfile, result)
         return
     try: