Merge remote-tracking branch 'upstream/maint/2.5.x' into maint/3.0.x

Author: effigies

.travis.yml

@@ -4,11 +4,11 @@
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
 
+os: linux
 dist: xenial
-sudo: true
 language: python
-
 cache: pip
+
 env:
     global:
         - SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
@@ -25,7 +25,7 @@ python:
     - 3.7
     - 3.8
 
-matrix:
+jobs:
   include:
     # Basic dependencies only
     - python: 3.5

Changelog

@@ -25,6 +25,31 @@ Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
+2.5.2 (Wednesday 8 April 2020)
+==============================
+
+Bug-fix release in the 2.5.x series. This is an extended-support series,
+providing bug fixes for Python 2.7 and 3.4.
+
+This and all future releases in the 2.5.x series will be incompatible with
+Python 3.9. The last compatible series of numpy and scipy are 1.16.x and
+1.2.x, respectively.
+
+If you are able to upgrade to Python 3, it is recommended to upgrade to
+NiBabel 3.
+
+Bug fixes
+---------
+* 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)
+
+Maintenance
+-----------
+* Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (CM)
+
+
 3.0.2 (Monday 9 March 2020)
 ===========================
 

doc-requirements.txt

@@ -1,6 +1,6 @@
 # Requirements for building docs
 -r requirements.txt
-sphinx
+sphinx<3
 numpydoc
 texext
 matplotlib >=1.3.1

nibabel/funcs.py

@@ -138,7 +138,7 @@ def concat_images(images, check_affines=True, axis=None):
                     i, len(img.shape), n_dim))
         if not np.all(np.array(img.shape)[idx_mask] == masked_shape):
             raise ValueError('shape {0} for image {1} not compatible with '
-                             'first image shape {2} with axis == {0}'.format(
+                             'first image shape {2} with axis == {3}'.format(
                                  img.shape, i, shape0, axis))
         if check_affines and not np.all(img.affine == affine):
             raise ValueError('Affine for image {0} does not match affine '

nibabel/viewers.py

@@ -184,7 +184,7 @@ def __init__(self, data, affine=None, axes=None, title=None):
                                                 5).astype(int)))
             ax.set_xlim(x[0], x[-1])
             yl = [self._data.min(), self._data.max()]
-            yl = [l + s * np.diff(lims)[0] for l, s in zip(yl, [-1.01, 1.01])]
+            yl = [lim + s * np.diff(lims)[0] for lim, s in zip(yl, [-1.01, 1.01])]
             patch = mpl_patch.Rectangle([-0.5, yl[0]], 1., np.diff(yl)[0],
                                         fill=True, facecolor=(0, 1, 0),
                                         edgecolor=(0, 1, 0), alpha=0.25)