[Neuroimaging] ANN: nibabel 2.4.1

[Christopher Markiewicz]

Hi all,

Just a quick announcement that nibabel has a new bug-fix release, version 2.4.1. The next anticipated release will be 2.5.0, targeted for July, and 2.5.x will be the last of the Python 2-compatible series, with bug-fix-only support through the *end* of 2020.

Probably the highest-impact change in 2.4.1 is that all DataobjImages accept the `mmap` keyword argument on a best-effort basis, so `nibabel.load(fname, mmap=False)` will now succeed for all but GIFTI images. Additionally, GIFTI data arrays are editable again with recent numpy, and FreeSurfer annotation files can be written more reliably.

For a (probably) very small set of users, the `keep_file_open` parameter and `nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` will now raise warnings if set to 'auto'. This was scheduled to happen at 2.4.0, but we missed it. Apologies.

Thanks very much to new contributors Egor Pafilov and Jath Palasubramaniam, as well as Richard Nemec and Dave Allured who helped diagnose and provide fixes to some deeply non-obvious bugs.

Full changelog follows.

----

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.

References like "pr/298" refer to github pull request numbers.

2.4.1 (Monday 27 May 2019)
============================

Contributions from Egor Pafilov, Jath Palasubramaniam, Richard Nemec, and
Dave Allured.

Enhancements
------------
* Enable ``mmap``, ``keep_file_open`` options when loading any
  ``DataobjImage`` (pr/759) (CM, reviewed by PM)

Bug fixes
---------
* Ensure loaded GIFTI files expose writable data arrays (pr/750) (CM,
  reviewed by PM)
* Safer warning registry manipulation when checking for overflows (pr/753)
  (CM, reviewed by MB)
* Correctly write .annot files with duplicate lables (pr/763) (Richard Nemec
  with CM)

Maintenance
-----------
* Fix typo in coordinate systems doc (pr/751) (Egor Panfilov, reviewed by
  CM)
* Replace invalid MINC1 test file with fixed file (pr/754) (Dave Allured
  with CM)
* Update Sphinx config to support recent Sphinx/numpydoc (pr/749) (CM,
  reviewed by PM)
* Pacify ``FutureWarning`` and ``DeprecationWarning`` from h5py, numpy
  (pr/760) (CM)
* Accommodate Python 3.8 deprecation of collections.MutableMapping
  (pr/762) (Jath Palasubramaniam, reviewed by CM)

API changes and deprecations
----------------------------
* Deprecate ``keep_file_open == 'auto'`` (pr/761) (CM, reviewed by PM)

-- 
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University