REL: 1.5.0

.travis.yml

@@ -1,22 +1,19 @@
+os: linux
 dist: xenial
-sudo: true
 
 language: python
 # our build matrix
 python:
-- 3.5
 - 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
@@ -31,7 +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:

.zenodo.json

@@ -157,11 +157,6 @@
       "name": "De La Vega, Alejandro",
       "orcid": "0000-0001-9062-3778"
     },
-    {
-      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
-      "name": "Waller, Lea",
-      "orcid": "0000-0002-3239-6957"
-    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -183,6 +178,11 @@
     {
       "name": "Erickson, Drew"
     },
+    {
+      "affiliation": "Neuroscience Program, University of Iowa",
+      "name": "Kent, James D.",
+      "orcid": "0000-0002-4892-2659"
+    },
     {
       "affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
       "name": "Hanke, Michael",
@@ -195,11 +195,6 @@
     {
       "name": "Moloney, Brendan"
     },
-    {
-      "affiliation": "Neuroscience Program, University of Iowa",
-      "name": "Kent, James D.",
-      "orcid": "0000-0002-4892-2659"
-    },
     {
       "affiliation": "SRI International",
       "name": "Nichols, B. Nolan",
@@ -246,6 +241,11 @@
     {
       "name": "Mordom, David"
     },
+    {
+      "affiliation": "University College London",
+      "name": "Mancini, Matteo",
+      "orcid": "0000-0001-7194-4568"
+    },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
       "name": "Guillon, Je\u0301re\u0301my",
@@ -291,16 +291,16 @@
     {
       "name": "Salvatore, John"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Mancini, Matteo",
-      "orcid": "0000-0001-7194-4568"
-    },
     {
       "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay",
       "name": "Gramfort, Alexandre",
       "orcid": "0000-0001-9791-4404"
     },
+    {
+      "affiliation": "Department of Psychology, University of Bielefeld, Bielefeld, Germany.",
+      "name": "Doll, Anna",
+      "orcid": "0000-0002-0799-0831"
+    },
     {
       "name": "Buchanan, Colin"
     },
@@ -393,9 +393,14 @@
       "orcid": "0000-0003-2766-8425"
     },
     {
-      "affiliation": "Department of Psychology, University of Bielefeld, Bielefeld, Germany.",
-      "name": "Doll, Anna",
-      "orcid": "0000-0002-0799-0831"
+      "affiliation": "NIMH, Scientific and Statistical Computing Core",
+      "name": "Glen, Daniel",
+      "orcid": "0000-0001-8456-5647"
+    },
+    {
+      "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
+      "name": "Geisler, Daniel",
+      "orcid": "0000-0003-2076-5329"
     },
     {
       "affiliation": "University of Iowa",
@@ -406,6 +411,11 @@
       "name": "Triplett, William",
       "orcid": "0000-0002-9546-1306"
     },
+    {
+      "affiliation": "The University of Iowa",
+      "name": "Ghayoor, Ali",
+      "orcid": "0000-0002-8858-1254"
+    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Craddock, R. Cameron",
@@ -450,12 +460,12 @@
       "name": "Rothmei, Simon"
     },
     {
-      "name": "Weinstein, Alejandro"
+      "affiliation": "Korea Advanced Institute of Science and Technology",
+      "name": "Kim, Sin",
+      "orcid": "0000-0003-4652-3758"
     },
     {
-      "affiliation": "The University of Iowa",
-      "name": "Ghayoor, Ali",
-      "orcid": "0000-0002-8858-1254"
+      "name": "Weinstein, Alejandro"
     },
     {
       "affiliation": "University of Pennsylvania",
@@ -508,6 +518,11 @@
       "name": "Linkersd\u00f6rfer, Janosch",
       "orcid": "0000-0002-1577-1233"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "name": "Renfro, Mandy"
     },
@@ -521,11 +536,6 @@
     {
       "name": "K\u00fcttner, Ren\u00e9"
     },
-    {
-      "affiliation": "Korea Advanced Institute of Science and Technology",
-      "name": "Kim, Sin",
-      "orcid": "0000-0003-4652-3758"
-    },
     {
       "affiliation": "California Institute of Technology",
       "name": "Pauli, Wolfgang M.",
@@ -536,6 +546,11 @@
       "name": "Glen, Daniel",
       "orcid": "0000-0001-8456-5647"
     },
+    {
+      "affiliation": "Florida International University",
+      "name": "Kimbler, Adam",
+      "orcid": "0000-0001-5885-9596"
+    },
     {
       "affiliation": "University of Pittsburgh",
       "name": "Meyers, Benjamin",
@@ -544,11 +559,6 @@
     {
       "name": "Tarbert, Claire"
     },
-    {
-      "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
-      "name": "Geisler, Daniel",
-      "orcid": "0000-0003-2076-5329"
-    },
     {
       "name": "Ginsburg, Daniel"
     },

doc/changelog/1.X.X-changelog.rst

@@ -1,3 +1,29 @@
+1.5.0 (To be determined)
+=========================
+
+New feature release in the 1.5.x series.
+
+In this release, the example scripts have been split out into their own package:
+`niflow-nipype1-examples <https://github.com/niflows/nipype1-examples>`__.
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.5.0?closed=1>`__)
+
+  * FIX: Partial rollback of N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3188)
+  * FIX: ANTs' tools maintenance overhaul (https://github.com/nipy/nipype/pull/3180)
+  * FIX: load_resultfile crashes if open resultsfile from crashed job (https://github.com/nipy/nipype/pull/3182)
+  * FIX: FSL model.py make multiple F-tests (https://github.com/nipy/nipype/pull/3166)
+  * ENH: Improve workflow connect performance (https://github.com/nipy/nipype/pull/3184)
+  * ENH: Add ``ConstrainedSphericalDeconvolution`` interface to replace ``EstimateFOD`` for MRtrix3's ``dwi2fod`` (https://github.com/nipy/nipype/pull/3176)
+  * ENH: Detect values for EulerNumber interface (https://github.com/nipy/nipype/pull/3173)
+  * ENH: Remove examples from repository (https://github.com/nipy/nipype/pull/3172)
+  * REF: Prefer math.gcd to hand-rolled Euclid's algorithm (https://github.com/nipy/nipype/pull/3177)
+  * REF: Removed all uses of numpy_mmap (https://github.com/nipy/nipype/pull/3121)
+  * DOC: Update links, typos in contributing guide (https://github.com/nipy/nipype/pull/3160)
+  * DOC: Update SelectFiles docstring to match actual behavior (https://github.com/nipy/nipype/pull/3041)
+  * DOC: Updated .zenodo.json file (https://github.com/nipy/nipype/pull/3167)
+  * DOC: Update .zenodo.json (https://github.com/nipy/nipype/pull/3165)
+  * MNT: Update Zenodo ordering based on commit count (https://github.com/nipy/nipype/pull/3169)
+
 1.4.2 (February 14, 2020)
 =========================
 (`Full changelog <https://github.com/nipy/nipype/milestone/1.4.2?closed=1>`__)

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

@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = "1.5.0-dev"
+__version__ = "1.5.0-rc1.post-dev"
 
 
 def get_nipype_gitversion():
@@ -54,12 +54,11 @@ def get_nipype_gitversion():
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.5",
     "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Topic :: Scientific/Engineering",
 ]
-PYTHON_REQUIRES = ">= 3.5"
+PYTHON_REQUIRES = ">= 3.6"
 
 description = "Neuroimaging in Python: Pipelines and Interfaces"
 
@@ -100,7 +99,7 @@ def get_nipype_gitversion():
 # versions
 NIBABEL_MIN_VERSION = "2.1.0"
 NETWORKX_MIN_VERSION = "1.9"
-NUMPY_MIN_VERSION = "1.12"
+NUMPY_MIN_VERSION = "1.13"
 # Numpy bug in python 3.7:
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
 NUMPY_MIN_VERSION_37 = "1.15.3"
@@ -148,7 +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
@@ -158,7 +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