[Neuroimaging] ANN: nibabel 2.4.1
bertrand.thirion at inria.fr
Tue May 28 13:33:19 EDT 2019
Thx to all contributors !
----- Mail original -----
> De: "Christopher Markiewicz" <markiewicz at stanford.edu>
> À: "Neuroimaging analysis in Python" <neuroimaging at python.org>
> Envoyé: Mardi 28 Mai 2019 16:09:57
> Objet: [Neuroimaging] ANN: nibabel 2.4.1
> 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.
> * 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)
> * Fix typo in coordinate systems doc (pr/751) (Egor Panfilov, reviewed by
> * 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
> Neuroimaging mailing list
> Neuroimaging at python.org
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