<div dir="ltr">Thank you Nibabel devs! We will need to change our minimum requirements for Nibabel in DIPY! Yeah! Fix bugs and move on! <div>:)</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jun 12, 2018 at 2:36 PM Christopher Markiewicz <<a href="mailto:markiewicz@stanford.edu">markiewicz@stanford.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hi all,<br>
<br>
<span class="m_-4758964193409662287il">Nibabel</span> <span class="m_-4758964193409662287il">2.3</span> 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.<br>
<div><br>
</div>
<div>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.<br>
</div>
<div><br>
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<div>As always, thanks to all contributors, reviewers and users.</div>
<div><br>
</div>
Please cite using the Zenodo DOI: <a href="https://doi.org/10.5281/zenodo.1011207" id="m_-4758964193409662287LPlnk604543" class="m_-4758964193409662287OWAAutoLink" target="_blank"></a><a href="https://doi.org/10.5281/zenodo.1287921" class="m_-4758964193409662287OWAAutoLink" id="m_-4758964193409662287LPlnk702021" target="_blank">https://doi.org/10.5281/zenodo.1287921</a></div>
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<div>The full changelog follows:</div>
<div><br>
</div>
<div><br>
</div>
<div>New feature release for the 2.3 series.<br>
<div><br>
Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)<br>
Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan<br>
Gerhard (SG) and Eric Larson (EL).<br>
<br>
References like "pr/298" refer to github pull request numbers.<br>
<br>
New features<br>
------------<br>
* TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)<br>
* Image slicing for SpatialImages (pr/550) (CM)<br>
<br>
Enhancements<br>
------------<br>
* Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB)<br>
* Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul<br>
McCarthy, reviewed by MB, CM)<br>
* Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy,<br>
reviewed by CM, MB)<br>
* Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,<br>
reviewed by CM, Satra Ghosh, MB, Tim Coalson)<br>
* Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed<br>
by CM, MB)<br>
* Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri<br>
Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)<br>
* Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release<br>
filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)<br>
<br>
Bug fixes<br>
---------<br>
* Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil<br>
Goyette, CM, MB)<br>
* Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by<br>
CM, MB)<br>
* Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,<br>
MB, reviewed by MB, MC, CM)<br>
* Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)<br>
* Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro,<br>
reviewed by MC, MB, Eleftherios Garyfallidis, CM)<br>
* Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk,<br>
reviewed by MB, CM)<br>
* Do not crash on non-``ImportError`` failures in optional imports (pr/618)<br>
(Yaroslav Halchenko, reviewed by CM)<br>
* Return original array from ``get_fdata`` for array image, if no cast<br>
required (pr/638, MB, reviewed by CM)<br>
<br>
Maintenance<br>
-----------<br>
* Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB)<br>
* Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM)<br>
* Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM)<br>
* Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by <br>
Yaroslav Halchenko, MB)<br>
* Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615)<br>
(Chris Cheng, reviewed by MB, Yaroslav Halchenko)<br>
* Remove deprecated numpy indexing (EL, reviewed by CM)<br>
* Update documentation to encourage ``get_fdata`` over ``get_data`` (pr/637,<br>
MB, reviewed by CM)<br>
<br>
API changes and deprecations<br>
----------------------------<br>
* Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` will<br>
be deprecated in 2.4, for removal in 3.0. Accordingly, support for<br>
``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same<br>
schedule.<br>
* Drop-in support for ``indexed_gzip < 0.7`` has been removed.</div>
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<div><br>
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<div><br>
</div>
<p></p>
<p style="margin-top:0;margin-bottom:0">Enjoy,</p>
<div id="m_-4758964193409662287Signature">
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<p>-- </p>
<p>Chris Markiewicz</p>
<p>Center for Reproducible Neuroscience</p>
<p>Stanford University</p>
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</blockquote></div>