Merge remote-tracking branch 'upstream/master' into rel/1.5.0

Author: effigies

.travis.yml

@@ -1,21 +1,19 @@
+os: linux
 dist: xenial
-sudo: true
 
 language: python
 # our build matrix
 python:
 - 3.6
 - 3.7
 
-# NOTE: Any changes to the matrix section should be duplicated below for
-#       Python 3.4
 env:
   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"
     - CHECK_TYPE=test
-  matrix:
+  jobs:
     - INSTALL_DEB_DEPENDECIES=true
       NIPYPE_EXTRAS="doc,tests,nipy,profiler"
       CI_SKIP_TEST=1
@@ -30,7 +28,7 @@ env:
       EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS --upgrade"
       CI_SKIP_TEST=1
 
-matrix:
+jobs:
   include:
     - python: 3.7
       env:

nipype/__init__.py

@@ -83,41 +83,9 @@ def check_latest_version(raise_exception=False):
     import etelemetry
 
     logger = logging.getLogger("nipype.utils")
-
-    INIT_MSG = "Running {packname} version {version} (latest: {latest})".format
-
-    latest = {"version": "Unknown", "bad_versions": []}
-    result = None
-    try:
-        result = etelemetry.get_project("nipy/nipype")
-    except Exception as e:
-        logger.warning("Could not check for version updates: \n%s", e)
-    finally:
-        if result:
-            latest.update(**result)
-            if LooseVersion(__version__) != LooseVersion(latest["version"]):
-                logger.info(
-                    INIT_MSG(
-                        packname="nipype", version=__version__, latest=latest["version"]
-                    )
-                )
-            else:
-                logger.info("No new version available.")
-            if latest["bad_versions"] and any(
-                [
-                    LooseVersion(__version__) == LooseVersion(ver)
-                    for ver in latest["bad_versions"]
-                ]
-            ):
-                message = (
-                    "You are using a version of Nipype with a critical "
-                    "bug. Please use a different version."
-                )
-                if raise_exception:
-                    raise RuntimeError(message)
-                else:
-                    logger.critical(message)
-    return latest
+    return etelemetry.check_available_version(
+        "nipy/nipype", __version__, logger, raise_exception
+    )
 
 
 # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL

nipype/algorithms/tests/test_TSNR.py

@@ -7,7 +7,7 @@
 
 import pytest
 import numpy.testing as npt
-import mock
+from unittest import mock
 import nibabel as nb
 import numpy as np
 import os
@@ -16,9 +16,7 @@
 class TestTSNR:
     """ Note: Tests currently do a poor job of testing functionality """
 
-    in_filenames = {
-        "in_file": "tsnrinfile.nii",
-    }
+    in_filenames = {"in_file": "tsnrinfile.nii"}
 
     out_filenames = {  # default output file names
         "detrended_file": "detrend.nii.gz",

nipype/info.py

@@ -147,7 +147,7 @@ def get_nipype_gitversion():
     "simplejson>=%s" % SIMPLEJSON_MIN_VERSION,
     "traits>=%s,!=5.0" % TRAITS_MIN_VERSION,
     "filelock>=3.0.0",
-    "etelemetry",
+    "etelemetry>=0.2.0",
 ]
 
 # neurdflib has to come after prov
@@ -157,7 +157,6 @@ def get_nipype_gitversion():
 TESTS_REQUIRES = [
     "codecov",
     "coverage<5",
-    "mock",
     "pytest",
     "pytest-cov",
     "pytest-env",

nipype/interfaces/ants/registration.py

@@ -591,12 +591,18 @@ class RegistrationOutputSpec(TraitedSpec):
     forward_transforms = traits.List(
         File(exists=True), desc="List of output transforms for forward registration"
     )
+    reverse_forward_transforms = traits.List(
+        File(exists=True), desc="List of output transforms for forward registration reversed for antsApplyTransform"
+    )
     reverse_transforms = traits.List(
         File(exists=True), desc="List of output transforms for reverse registration"
     )
     forward_invert_flags = traits.List(
         traits.Bool(), desc="List of flags corresponding to the forward transforms"
     )
+    reverse_forward_invert_flags = traits.List(
+        traits.Bool(), desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform"
+    )
     reverse_invert_flags = traits.List(
         traits.Bool(), desc="List of flags corresponding to the reverse transforms"
     )
@@ -797,6 +803,8 @@ class Registration(ANTSCommand):
      'inverse_composite_transform': '...data/output_InverseComposite.h5',
      'inverse_warped_image': <undefined>,
      'metric_value': <undefined>,
+     'reverse_forward_invert_flags': [],
+     'reverse_forward_transforms': [],
      'reverse_invert_flags': [],
      'reverse_transforms': [],
      'save_state': '...data/trans.mat',
@@ -826,6 +834,9 @@ class Registration(ANTSCommand):
      'inverse_composite_transform': <undefined>,
      'inverse_warped_image': <undefined>,
      'metric_value': <undefined>,
+     'reverse_forward_invert_flags': [False, False],
+     'reverse_forward_transforms': ['...data/output_1Warp.nii.gz',
+     '...data/output_0GenericAffine.mat'],
      'reverse_invert_flags': [True, False],
      'reverse_transforms': ['...data/output_0GenericAffine.mat', \
     '...data/output_1InverseWarp.nii.gz'],
@@ -1472,6 +1483,10 @@ def _list_outputs(self):
             outputs["metric_value"] = self._metric_value
         if self._elapsed_time:
             outputs["elapsed_time"] = self._elapsed_time
+
+        outputs["reverse_forward_transforms"] = outputs["forward_transforms"][::-1]
+        outputs["reverse_forward_invert_flags"] = outputs["forward_invert_flags"][::-1]
+
         return outputs
 
 

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -97,6 +97,8 @@ def test_Registration_outputs():
         inverse_composite_transform=dict(extensions=None,),
         inverse_warped_image=dict(extensions=None,),
         metric_value=dict(),
+        reverse_forward_invert_flags=dict(),
+        reverse_forward_transforms=dict(),
         reverse_invert_flags=dict(),
         reverse_transforms=dict(),
         save_state=dict(extensions=None,),

nipype/interfaces/base/tests/test_core.py

@@ -5,6 +5,7 @@
 import simplejson as json
 
 import pytest
+from unittest import mock
 
 from .... import config
 from ....testing import example_data
@@ -456,17 +457,18 @@ def test_global_CommandLine_output(tmpdir):
     ci = BET()
     assert ci.terminal_output == "stream"  # default case
 
-    nib.CommandLine.set_default_terminal_output("allatonce")
-    ci = nib.CommandLine(command="ls -l")
-    assert ci.terminal_output == "allatonce"
+    with mock.patch.object(nib.CommandLine, '_terminal_output'):
+        nib.CommandLine.set_default_terminal_output("allatonce")
+        ci = nib.CommandLine(command="ls -l")
+        assert ci.terminal_output == "allatonce"
 
-    nib.CommandLine.set_default_terminal_output("file")
-    ci = nib.CommandLine(command="ls -l")
-    assert ci.terminal_output == "file"
+        nib.CommandLine.set_default_terminal_output("file")
+        ci = nib.CommandLine(command="ls -l")
+        assert ci.terminal_output == "file"
 
-    # Check default affects derived interfaces
-    ci = BET()
-    assert ci.terminal_output == "file"
+        # Check default affects derived interfaces
+        ci = BET()
+        assert ci.terminal_output == "file"
 
 
 def test_CommandLine_prefix(tmpdir):

nipype/interfaces/fsl/tests/test_base.py

@@ -13,8 +13,7 @@
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_fslversion():
     ver = fsl.Info.version()
-    ver = ver.split(".")
-    assert ver[0] in ["4", "5"]
+    assert ver.split(".", 1)[0].isdigit()
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")

nipype/interfaces/niftyreg/base.py

@@ -19,7 +19,8 @@
 import os
 
 from ... import logging
-from ..base import CommandLine, CommandLineInputSpec, traits, Undefined
+from ..base import (CommandLine, CommandLineInputSpec, traits, Undefined,
+                    PackageInfo)
 from ...utils.filemanip import split_filename
 
 iflogger = logging.getLogger("nipype.interface")
@@ -29,6 +30,14 @@ def get_custom_path(command, env_dir="NIFTYREGDIR"):
     return os.path.join(os.getenv(env_dir, ""), command)
 
 
+class Info(PackageInfo):
+    version_cmd = get_custom_path('reg_aladin') + ' --version'
+
+    @staticmethod
+    def parse_version(raw_info):
+        return raw_info
+
+
 class NiftyRegCommandInputSpec(CommandLineInputSpec):
     """Input Spec for niftyreg interfaces."""
 
@@ -55,9 +64,8 @@ def __init__(self, required_version=None, **inputs):
         self.num_threads = 1
         super(NiftyRegCommand, self).__init__(**inputs)
         self.required_version = required_version
-        _version = self.version_from_command()
+        _version = self.version
         if _version:
-            _version = _version.decode("utf-8")
             if self._min_version is not None and StrictVersion(
                 _version
             ) < StrictVersion(self._min_version):
@@ -91,11 +99,9 @@ def _environ_update(self):
             self.inputs.omp_core_val = Undefined
 
     def check_version(self):
-        _version = self.version_from_command()
+        _version = self.version
         if not _version:
             raise Exception("Niftyreg not found")
-        # Decoding to string:
-        _version = _version.decode("utf-8")
         if StrictVersion(_version) < StrictVersion(self._min_version):
             err = "A later version of Niftyreg is required (%s < %s)"
             raise ValueError(err % (_version, self._min_version))
@@ -107,10 +113,10 @@ def check_version(self):
 
     @property
     def version(self):
-        return self.version_from_command()
+        return Info.version()
 
     def exists(self):
-        return self.version_from_command() is not None
+        return self.version is not None
 
     def _format_arg(self, name, spec, value):
         if name == "omp_core_val":

nipype/interfaces/tests/test_extra_dcm2nii.py

@@ -22,7 +22,7 @@ def _fetch_data(datadir, dicoms):
             """Fetches some test DICOMs using datalad"""
             api.install(path=datadir, source=DICOM_DIR)
             data = os.path.join(datadir, dicoms)
-            api.get(path=data)
+            api.get(path=data, dataset=datadir)
         except IncompleteResultsError as exc:
             pytest.skip("Failed to fetch test data: %s" % str(exc))
         return data
@@ -32,7 +32,6 @@ def _fetch_data(datadir, dicoms):
 
 @pytest.mark.skipif(no_datalad, reason="Datalad required")
 @pytest.mark.skipif(no_dcm2niix, reason="Dcm2niix required")
-@pytest.mark.xfail(reason="Intermittent failures. Let's come back to this later.")
 def test_dcm2niix_dti(fetch_data, tmpdir):
     tmpdir.chdir()
     datadir = tmpdir.mkdir("data").strpath