Changelog and refreshed/fixed up patches

Author: yarikoptic

debian/changelog

@@ -1,3 +1,9 @@
+nipype (1.1.8-1) unstable; urgency=medium
+
+  * Fresh upstream release
+
+ -- Yaroslav Halchenko <[email protected]>  Sun, 03 Feb 2019 19:16:00 -0500
+
 nipype (1.1.7-2) neurodebian; urgency=medium
 
   * d/p/deb_no_strict_versions

debian/patches/deb_down_future

@@ -19,10 +19,10 @@ Last-Update: 2017-05-23
  neurdflib
 --- a/nipype/info.py
 +++ b/nipype/info.py
-@@ -109,7 +109,7 @@ SCIPY_MIN_VERSION = '0.14'
+@@ -109,7 +109,7 @@ NUMPY_BAD_VERSION_27 = '1.16.0'
+ SCIPY_MIN_VERSION = '0.14'
  TRAITS_MIN_VERSION = '4.6'
  DATEUTIL_MIN_VERSION = '2.2'
- PYTEST_MIN_VERSION = '3.6'
 -FUTURE_MIN_VERSION = '0.16.0'
 +FUTURE_MIN_VERSION = '0.15.2'
  SIMPLEJSON_MIN_VERSION = '3.8.0'

debian/patches/deb_git_hash

@@ -12,6 +12,6 @@ Last-Update: 2017-05-23
  [commit hash]
  # The line below may contain a valid hash if it has been substituted during 'git archive'
 -archive_subst_hash=%h
-+archive_subst_hash=f2bbcc917899c98102bdeb84db61ea4b84cbf2f5
++archive_subst_hash=70add2941679146307a5bd0769358fc8bcdff17c
  # This line may be modified by the install process
  install_hash=

debian/patches/deb_no_explicit_pydot

@@ -1,13 +1,13 @@
 --- a/nipype/info.py
 +++ b/nipype/info.py
-@@ -150,8 +150,8 @@ REQUIRES = [
-     'pytest>=%s' % PYTEST_MIN_VERSION,
-     'pytest-xdist',
-     'mock',
+@@ -146,8 +146,8 @@ REQUIRES = [
+     'neurdflib',
+     'click>=%s' % CLICK_MIN_VERSION,
+     'funcsigs',
 -    'pydotplus',
 -    'pydot>=%s' % PYDOT_MIN_VERSION,
 +    # 'pydotplus',
 +    # 'pydot>=%s' % PYDOT_MIN_VERSION,
      'packaging',
      'futures',
- ]
+     'configparser',

debian/patches/deb_no_neurdflib

@@ -1,6 +1,6 @@
 --- a/nipype/info.py
 +++ b/nipype/info.py
-@@ -145,7 +145,8 @@ REQUIRES = [
+@@ -144,7 +144,8 @@ REQUIRES = [
      'future>=%s' % FUTURE_MIN_VERSION,
      'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
      'prov>=%s' % PROV_VERSION,
@@ -9,7 +9,7 @@
 +    #'neurdflib',
      'click>=%s' % CLICK_MIN_VERSION,
      'funcsigs',
-     'pytest',
+     # 'pydotplus',
 --- a/requirements.txt
 +++ b/requirements.txt
 @@ -7,7 +7,7 @@ nibabel>=2.1.0

debian/patches/deb_no_strict_versions

@@ -1,13 +1,12 @@
 --- a/nipype/info.py
 +++ b/nipype/info.py
-@@ -106,12 +106,13 @@ NUMPY_MIN_VERSION = '1.9.0'
- # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
+@@ -107,11 +107,12 @@ NUMPY_MIN_VERSION = '1.9.0'
  NUMPY_MIN_VERSION_37 = '1.15.3'
+ NUMPY_BAD_VERSION_27 = '1.16.0'
  SCIPY_MIN_VERSION = '0.14'
 -TRAITS_MIN_VERSION = '4.6'
 +TRAITS_MIN_VERSION = '4.5'
  DATEUTIL_MIN_VERSION = '2.2'
- PYTEST_MIN_VERSION = '3.6'
  FUTURE_MIN_VERSION = '0.15.2'
  SIMPLEJSON_MIN_VERSION = '3.8.0'
 -PROV_VERSION = '1.5.2'
@@ -16,12 +15,3 @@
  CLICK_MIN_VERSION = '6.6.0'
  PYDOT_MIN_VERSION = '1.2.3'
 
-@@ -147,7 +148,7 @@ REQUIRES = [
-     'neurdflib',
-     'click>=%s' % CLICK_MIN_VERSION,
-     'funcsigs',
--    'pytest>=%s' % PYTEST_MIN_VERSION,
-+    'pytest',
-     'pytest-xdist',
-     'mock',
-     # 'pydotplus',

debian/patches/deb_pytest_xdist_no-nauto

@@ -5,13 +5,3 @@ Subject: Disable automatic parallel runs within pytest
 Origin: NeuroDebian
 Last-Update: 2018-03-27
 
---- a/nipype/pytest.ini
-+++ b/nipype/pytest.ini
-@@ -1,6 +1,6 @@
- [pytest]
- norecursedirs = .git build dist doc nipype/external tools examples src
--addopts = --doctest-modules -n auto
-+addopts = --doctest-modules
- doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE
- env =
-     PYTHONHASHSEED=0

debian/patches/deb_simplify_requires

@@ -10,12 +10,25 @@ Last-Update: 2018-08-09
 
 --- a/nipype/info.py
 +++ b/nipype/info.py
-@@ -153,7 +153,7 @@ REQUIRES = [
+@@ -136,9 +136,7 @@ PROVIDES = ['nipype']
+ REQUIRES = [
+     'nibabel>=%s' % NIBABEL_MIN_VERSION,
+     'networkx>=%s' % NETWORKX_MIN_VERSION,
+-    'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
+-    'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
+-    'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
++    'numpy>=%s' % (NUMPY_MIN_VERSION,),
+     'python-dateutil>=%s' % DATEUTIL_MIN_VERSION,
+     'scipy>=%s' % SCIPY_MIN_VERSION,
+     'traits>=%s' % TRAITS_MIN_VERSION,
+@@ -151,8 +149,8 @@ REQUIRES = [
      'pydotplus',
      'pydot>=%s' % PYDOT_MIN_VERSION,
      'packaging',
 -    'futures; python_version == "2.7"',
+-    'configparser; python_version <= "3.4"',
 +    'futures',
++    'configparser',
  ]
 
- if sys.version_info <= (3, 4):
+ TESTS_REQUIRES = [

debian/patches/deb_skip_doctest_pybids

@@ -1,6 +1,6 @@
 --- a/nipype/interfaces/io.py
 +++ b/nipype/interfaces/io.py
-@@ -2747,9 +2747,9 @@ class BIDSDataGrabber(LibraryBaseInterfa
+@@ -2769,9 +2769,9 @@ class BIDSDataGrabber(LibraryBaseInterfa
      from a project, and makes BIDS entities (e.g. subject) available for
      filtering outputs.
 
@@ -13,18 +13,18 @@
      >>> results = bg.run() # doctest: +SKIP
 
 
-@@ -2758,10 +2758,10 @@ class BIDSDataGrabber(LibraryBaseInterfa
+@@ -2780,10 +2780,10 @@ class BIDSDataGrabber(LibraryBaseInterfa
      are filtered on common entities, which can be explicitly defined as
      infields.
 
--    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
+-    >>> bg = BIDSDataGrabber(infields = ['subject'])
 -    >>> bg.inputs.base_dir = 'ds005/'
 -    >>> bg.inputs.subject = '01'
--    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
-+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi']) # doctest: +SKIP
+-    >>> bg.inputs.output_query['dwi'] = dict(datatype='dwi')
++    >>> bg = BIDSDataGrabber(infields = ['subject']) # doctest: +SKIP
 +    >>> bg.inputs.base_dir = 'ds005/' # doctest: +SKIP
 +    >>> bg.inputs.subject = '01' # doctest: +SKIP
-+    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi') # doctest: +SKIP
++    >>> bg.inputs.output_query['dwi'] = dict(datatype='dwi') # doctest: +SKIP
      >>> results = bg.run() # doctest: +SKIP
 
      """