[Neuroimaging] ANN: Nibabel release 2.3

Gael Varoquaux gael.varoquaux at normalesup.org
Tue Jun 12 16:37:59 EDT 2018

Congratulations! Thank you for keeping this crucial part of the ecosystem
alive and kicking.

On Tue, Jun 12, 2018 at 06:06:01PM +0000, Christopher Markiewicz wrote:
> Hi all,

> Nibabel 2.3 has been released just in time for OHBM. It's been published to
> PyPI and should be available on conda-forge within the next day.

> Features to look out for in this release are a new image slicing interface and
> TRK/TCK conversion tools. There have also been a number of first-time
> contributors, which is always good to see.

> As always, thanks to all contributors, reviewers and users.

> Please cite using the Zenodo DOI:  https://doi.org/10.5281/zenodo.1287921

> The full changelog follows:

> New feature release for the 2.3 series.

> Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
> Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
> Gerhard (SG) and Eric Larson (EL).

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

> New features
> ------------
> * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)
> * Image slicing for SpatialImages (pr/550) (CM)

> Enhancements
> ------------
> * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB)
> * Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul
>   McCarthy, reviewed by MB, CM)
> * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy,
>   reviewed by CM, MB)
> * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,
>   reviewed by CM, Satra Ghosh, MB, Tim Coalson)
> * Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed
>   by CM, MB)
> * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri
>   Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)
> * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release
>   filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)

> Bug fixes
> ---------
> * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil
>   Goyette, CM, MB)
> * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by
>   CM, MB)
> * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,
>   MB, reviewed by MB, MC, CM)
> * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)
> * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro,
>   reviewed by MC, MB, Eleftherios Garyfallidis, CM)
> * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk,
>   reviewed by MB, CM)
> * Do not crash on non-``ImportError`` failures in optional imports (pr/618)
>   (Yaroslav Halchenko, reviewed by CM)
> * Return original array from ``get_fdata`` for array image, if no cast
>   required (pr/638, MB, reviewed by CM)

> Maintenance
> -----------
> * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB)
> * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM)
> * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM)
> * Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by
>   Yaroslav Halchenko, MB)
> * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615)
>   (Chris Cheng, reviewed by MB, Yaroslav Halchenko)
> * Remove deprecated numpy indexing (EL, reviewed by CM)
> * Update documentation to encourage ``get_fdata`` over ``get_data`` (pr/637,
>   MB, reviewed by CM)

> API changes and deprecations
> ----------------------------
> * Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` will
>   be deprecated in 2.4, for removal in 3.0. Accordingly, support for
>   ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same
>   schedule.
> * Drop-in support for ``indexed_gzip < 0.7`` has been removed.

> Enjoy,
    Gael Varoquaux
    Senior Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

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