.gitignore

@@ -17,6 +17,7 @@
 .pydevproject
 *.py.orig
 .DS_Store
+.idea/
 
 # Not sure what the next one is for
 *.kpf

.mailmap

@@ -8,6 +8,7 @@
 # This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
 # gives no duplicates.
 Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@m4x.org>
+Anibal Sólon <anibalsolon@gmail.com>
 Ariel Rokem <arokem@gmail.com> arokem <arokem@gmail.com>
 B. Nolan Nichols <nolan.nichols@gmail.com> Nolan Nichols <nolan.nichols@gmail.com>
 Basile Pinsard <basile.pinsard@gmail.com> bpinsard <basile.pinsard@gmail.com>
@@ -52,8 +53,11 @@ Michael Hanke <michael.hanke@gmail.com> <michaelhanke@mvpa1.dartmouth.edu>
 Michiel Cottaar <MichielCottaar@protonmail.com> Michiel Cottaar <MichielCottaar@protonmail.ch>
 Ly Nguyen <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
 Oliver P. Hinds <ohinds@gmail.com> ohinds <ohinds@gmail.com>
+Or Duek <orduek@gmail.com>
 Oscar Esteban <code@oscaresteban.es>
 Paul McCarthy <pauldmccarthy@gmail.com> Paul McCarthy <pauld.mccarthy@gmail.com>
+Roberto Guidotti <robbenson18@gmail.com>
+Roberto Guidotti <robbenson18@gmail.com> <guidotr1@cs-087.org.aalto.fi>
 Satrajit Ghosh <satra@mit.edu> Satrajit Ghosh <satrajit.ghosh@gmail.com>
 Serge Koudoro <skab12@gmail.com> skoudoro <skab12@gmail.com>
 Stephan Gerhard <git@unidesign.ch> Stephan Gerhard <git@github.com>

.travis.yml

@@ -5,6 +5,7 @@
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
 
 os: linux
+arch: amd64
 dist: xenial
 language: python
 cache: pip
@@ -16,16 +17,21 @@ env:
         - INSTALL_TYPE="setup"
         - CHECK_TYPE="test"
         - EXTRA_WHEELS="https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com"
-        - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
+        - NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple"
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
-        - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+        - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --extra-index-url $NIGHTLY_WHEELS"
 
 python:
     - 3.7
     - 3.8
 
 jobs:
   include:
+    - arch: arm64
+      python: 3.6
+      env:
+        - DEPENDS="numpy"
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # Basic dependencies only
     - python: 3.6
       env:

.zenodo.json

@@ -28,6 +28,11 @@
     {
       "name": "McCarthy, Paul"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Jarecka, Dorota",
+      "orcid": "0000-0001-8282-2988"
+    },
     {
       "affiliation": "Center for Open Neuroscience, Dartmouth College",
       "name": "Cheng, Christopher P.",
@@ -77,6 +82,19 @@
       "name": "Kastman, Erik",
       "orcid": "0000-0001-7221-9042"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Kaczmarzyk, Jakub",
+      "orcid": "0000-0002-5544-7577"
+    },
+    {
+      "affiliation": "Department of Computer Science, Aalto University, Espoo, Finland and Department of Neuroscience, Imaging and Clinical Sciences, University G. D'Annunzio, Chieti, Italy",
+      "name": "Guidotti, Roberto",
+      "orcid": "0000-0002-0807-6005"
+    },
+    {
+      "name": "Duek, Or"
+    },
     {
       "affiliation": "The University of Washington eScience Institute",
       "name": "Rokem, Ariel",
@@ -96,6 +114,11 @@
       "name": "Goncalves, Mathias",
       "orcid": "0000-0002-7252-7771"
     },
+    {
+      "affiliation": "Montreal Neurological Institute and Hospital",
+      "name": "Markello, Ross",
+      "orcid": "0000-0003-1057-1336"
+    },
     {
       "affiliation": "Department of Psychology, University of California Davis, CA, USA",
       "name": "Riddell, Cameron",
@@ -118,9 +141,7 @@
       "name": "Lepp\u00e4kangas, Jaakko"
     },
     {
-      "affiliation": "Montreal Neurological Institute and Hospital",
-      "name": "Markello, Ross",
-      "orcid": "0000-0003-1057-1336"
+      "name": "S\u00f3lon, Anibal"
     },
     {
       "name": "van den Bosch, Jasper J.F."
@@ -136,11 +157,6 @@
     {
       "name": "Subramaniam, Krish"
     },
-    {
-      "affiliation": "MIT",
-      "name": "Jarecka, Dorota",
-      "orcid": "0000-0001-8282-2988"
-    },
     {
       "affiliation": "Google",
       "name": "Gorgolewski, Krzysztof J.",
@@ -211,11 +227,6 @@
       "name": "Varoquaux, Gael",
       "orcid": "0000-0003-1076-5122"
     },
-    {
-      "affiliation": "MIT",
-      "name": "Kaczmarzyk, Jakub",
-      "orcid": "0000-0002-5544-7577"
-    },
     {
       "affiliation": "Universit\u00e9 de Sherbrooke",
       "name": "Legarreta, Jon Haitz",
@@ -259,6 +270,9 @@
     {
       "name": "Schwartz, Yannick"
     },
+    {
+      "name": "Baratz, Zvi"
+    },
     {
       "affiliation": "Hospital for Sick Children",
       "name": "Darwin, Benjamin C"
@@ -323,9 +337,6 @@
       "name": "Reddam, Venkateswara Reddy",
       "orcid": "0000-0001-6817-2966"
     },
-    {
-      "name": "Baratz, Zvi"
-    },
     {
       "name": "freec84"
     }

Changelog

@@ -21,10 +21,81 @@ Nibabel releases
 Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
 (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul
 McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
-Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
+Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+3.1.1 (Friday 26 June 2020)
+===========================
+
+Bug-fix release in the 3.1.x series.
+
+These are small compatibility fixes that support ARM64 architecture and
+``indexed_gzip>=1.3.0``.
+
+Bug fixes
+---------
+* Detect ``IndexedGzipFile`` as compressed file type (pr/925) (PM, reviewed by
+  CM)
+* Correctly cast ``nan`` when testing ``array_to_file``, fixing ARM64 builds
+  (pr/862) (CM, reviewed by MB)
+
+
+3.1.0 (Monday 20 April 2020)
+============================
+
+New feature release in the 3.1.x series.
+
+New features
+------------
+* Conformation function (``processing.conform``) and CLI tool
+  (``nib-conform``) to apply shape, orientation and zooms (pr/853) (Jakub
+  Kaczmarzyk, reviewed by CM, YOH)
+* Affine rescaling function (``affines.rescale_affine``) to update
+  dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)
+
+Bug fixes
+---------
+* Delay import of h5py until neded (pr/889) (YOH, reviewed by CM)
+
+Maintenance
+-----------
+* Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
+* Tests converted from nose to pytest (pr/865 + many sub-PRs)
+  (Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon,
+  and Or Duek)
+
+API changes and deprecations
+----------------------------
+* ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
+  (RM, reviewed by CM)
+
+
+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)
 ===========================
 

azure-pipelines.yml

@@ -5,7 +5,6 @@ jobs:
     name: Windows
     vmImage: windows-2019
     matrix:
-      py35-x86:
       py36-x86:
         PYTHON_VERSION: '3.6'
         PYTHON_ARCH: 'x86'

bin/nib-dicomfs

@@ -12,4 +12,4 @@
 from nibabel.cmdline.dicomfs import main
 
 if __name__ == '__main__':
-    main()
+    main()

bin/nib-nifti-dx

@@ -7,7 +7,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-''' Print nifti diagnostics for header files '''
+""" Print nifti diagnostics for header files """
 
 from nibabel.cmdline.nifti_dx import main
 

doc-requirements.txt

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