Merge remote-tracking branch 'upstream/maint/3.0.x'

nipy · Jan 27, 2020 · 6863271 · 6863271
2 parents f300524 + 864fd5e
commit 6863271
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diff --git a/.mailmap b/.mailmap
@@ -13,6 +13,7 @@ B. Nolan Nichols <[email protected]> Nolan Nichols <[email protected]
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
+Benjamin C Darwin <[email protected]>
 Bertrand Thirion <[email protected]> bthirion <[email protected]>
 Cameron Riddell <[email protected]> <[email protected]>
 Christian Haselgrove <[email protected]> Christian Haselgrove <[email protected]>

diff --git a/.zenodo.json b/.zenodo.json
@@ -259,6 +259,10 @@
     {
       "name": "Schwartz, Yannick"
     },
+    {
+      "affiliation": "Hospital for Sick Children",
+      "name": "Darwin, Benjamin C"
+    },
     {
       "affiliation": "INRIA",
       "name": "Thirion, Bertrand",

diff --git a/Changelog b/Changelog
@@ -25,6 +25,22 @@ Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
+3.0.1 (Monday 27 January 2020)
+==============================
+
+Bug fixes
+---------
+* Test failed by using array method on tuple. (pr/860) (Ben Darwin, reviewed by
+  CM)
+* Validate ``ExpiredDeprecationError``\s, promoted by 3.0 release from
+  ``DeprecationWarning``\s. (pr/857) (CM)
+
+Maintenance
+-----------
+* Remove logic accommodating numpy without float16 types. (pr/866) (CM)
+* Accommodate new numpy dtype strings. (pr/858) (CM)
+
+
 3.0.0 (Wednesday 18 December 2019)
 ==================================
 
@@ -66,6 +82,8 @@ Bug fixes
 * Sliced ``Tractogram``s no longer ``apply_affine`` to the original
   ``Tractogram``'s streamlines. (pr/811) (MC, reviewed by Serge Koudoro,
   Philippe Poulin, CM, MB)
+* Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
+  by CM)
 * Re-import externals/netcdf.py from scipy to resolve numpy deprecation
   (pr/821) (CM)
 

diff --git a/doc-requirements.txt b/doc-requirements.txt
@@ -3,4 +3,4 @@
 sphinx
 numpydoc
 texext
-matplotlib>=1.3
+matplotlib >=1.3.1
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -99,7 +99,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2019, %(maintainer)s <%(author_email)s>' % metadata
+copyright = u'2006-2020, %(maintainer)s <%(author_email)s>' % metadata
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -104,6 +104,7 @@ contributed code and discussion (in rough order of appearance):
 * Hao-Ting Wang
 * Dorota Jarecka
 * Chris Gorgolewski
+* Benjamin C Darwin
 
 License reprise
 ===============

diff --git a/doc/source/installation.rst b/doc/source/installation.rst
@@ -89,7 +89,7 @@ Requirements
 *  h5py_ (optional, for MINC2 support)
 *  PyDICOM_ 0.9.9 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
-*  nose_ 0.11 or greater (optional, to run the tests)
+*  nose_ 0.11 or greater and pytest_ (optional, to run the tests)
 *  sphinx_ (optional, to build the documentation)
 
 Get the development sources

diff --git a/doc/source/links_names.txt b/doc/source/links_names.txt
@@ -83,6 +83,7 @@
 .. _emacs_python_mode: http://www.emacswiki.org/cgi-bin/wiki/PythonMode
 .. _doctest-mode: http://ed.loper.org/projects/doctestmode/
 .. _nose: http://somethingaboutorange.com/mrl/projects/nose
+.. _pytest: https://docs.pytest.org/
 .. _`python coverage tester`: http://nedbatchelder.com/code/coverage/
 .. _bitbucket: https://bitbucket.org
 .. _six: http://pythonhosted.org/six

diff --git a/nibabel/casting.py b/nibabel/casting.py
@@ -171,12 +171,6 @@ def shared_range(flt_type, int_type):
 # types.
 # ----------------------------------------------------------------------------
 
-try:
-    _float16 = np.float16
-except AttributeError:  # float16 not present in np < 1.6
-    _float16 = None
-
-
 class FloatingError(Exception):
     pass
 
@@ -242,7 +236,7 @@ def type_info(np_type):
                minexp=info.minexp,
                maxexp=info.maxexp,
                width=width)
-    if np_type in (_float16, np.float32, np.float64,
+    if np_type in (np.float16, np.float32, np.float64,
                    np.complex64, np.complex128):
         return ret
     info_64 = np.finfo(np.float64)

diff --git a/nibabel/tests/test_floating.py b/nibabel/tests/test_floating.py
@@ -15,15 +15,7 @@
 from nose import SkipTest
 from nose.tools import assert_equal, assert_raises, assert_true, assert_false
 
-IEEE_floats = [np.float32, np.float64]
-try:
-    np.float16
-except AttributeError:  # float16 not present in np < 1.6
-    have_float16 = False
-else:
-    have_float16 = True
-if have_float16:
-    IEEE_floats.append(np.float16)
+IEEE_floats = [np.float16, np.float32, np.float64]
 
 LD_INFO = type_info(np.longdouble)
 
@@ -201,8 +193,6 @@ def test_as_int_np_fix():
 
 def test_floor_exact_16():
     # A normal integer can generate an inf in float16
-    if not have_float16:
-        raise SkipTest('No float16')
     assert_equal(floor_exact(2**31, np.float16), np.inf)
     assert_equal(floor_exact(-2**31, np.float16), -np.inf)
 

diff --git a/setup.cfg b/setup.cfg
@@ -42,6 +42,9 @@ packages = find:
 [options.extras_require]
 dicom =
     pydicom >=0.9.9
+dicomfs =
+    %(dicom)s
+    pillow
 dev =
     gitpython
     twine
@@ -52,17 +55,20 @@ doc =
     texext
 minc2 =
     h5py
+spm =
+    scipy
 style =
     flake8
 test =
     coverage
     nose >=0.11
     pytest
 all =
-    %(dicom)s
+    %(dicomfs)s
     %(dev)s
     %(doc)s
     %(minc2)s
+    %(spm)s
     %(style)s
     %(test)s