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nipy/nibabel: 3.0.0rc1

Brett, Matthew; Markiewicz, Christopher J.; Hanke, Michael; Côté, Marc-Alexandre; Cipollini, Ben; McCarthy, Paul; Cheng, Christopher P.; Halchenko, Yaroslav O.; Cottaar, Michiel; Ghosh, Satrajit; Larson, Eric; Wassermann, Demian; Gerhard, Stephan; Lee, Gregory R.; Wang, Hao-Ting; Kastman, Erik; Rokem, Ariel; Madison, Cindee; Morency, Félix C.; Moloney, Brendan; Goncalves, Mathias; Riddell, Cameron; Burns, Christopher; Millman, Jarrod; Gramfort, Alexandre; Leppäkangas, Jaakko; Markello, Ross; van den Bosch, Jasper J.F.; Vincent, Robert D.; Braun, Henry; Subramaniam, Krish; Jarecka, Dorota; Gorgolewski, Krzysztof J.; Raamana, Pradeep Reddy; Nichols, B. Nolan; Baker, Eric M.; Hayashi, Soichi; Pinsard, Basile; Haselgrove, Christian; Hymers, Mark; Esteban, Oscar; Koudoro, Serge; Oosterhof, Nikolaas N.; Amirbekian, Bago; Nimmo-Smith, Ian; Nguyen, Ly; Reddigari, Samir; St-Jean, Samuel; Panfilov, Egor; Garyfallidis, Eleftherios; Varoquaux, Gael; Kaczmarzyk, Jakub; Legarreta, Jon Haitz; Hahn, Kevin S.; Hinds, Oliver P.; Fauber, Bennet; Poline, Jean-Baptiste; Stutters, Jon; Jordan, Kesshi; Cieslak, Matthew; Moreno, Miguel Estevan; Haenel, Valentin; Schwartz, Yannick; Thirion, Bertrand; Papadopoulos Orfanos, Dimitri; Pérez-García, Fernando; Solovey, Igor; Gonzalez, Ivan; Palasubramaniam, Jath; Lecher, Justin; Leinweber, Katrin; Raktivan, Konstantinos; Fischer, Peter; Gervais, Philippe; Gadde, Syam; Ballinger, Thomas; Roos, Thomas; Reddam, Venkateswara Reddy; freec84

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.

3.0.0rc1 (Saturday 16 November 2019)

Release candidate for NiBabel 3.0, initiating a minimum one-month testing window.

Downstream projects are requested to test against the release candidate by installing with pip install --pre nibabel.

New features
  • ArrayProxy method get_scaled() scales data with a dtype of a specified precision, promoting as necessary to avoid overflow. This is to used in img.get_fdata() to control memory usage. (pr/833) (CM, reviewed by Ross Markello)
  • GiftiImage method agg_data() to return usable data arrays (pr/793) (Hao-Ting Wang, reviewed by CM)
  • Accept os.PathLike objects in place of filenames (pr/610) (Cameron Riddell, reviewed by MB, CM)
  • Function to calculate obliquity of affines (pr/815) (Oscar Esteban, reviewed by MB)
  • get_fdata(dtype=np.float32) will attempt to avoid casting data to np.float64 when scaling parameters would otherwise promote the data type unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
  • ArraySequence now supports a large set of Python operators to combine or update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags (pr/818) (Henry Braun, reviewed by CM)
  • Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov, reviewed by MB)
Bug fixes
  • Sliced Tractograms no longer apply_affine to the original Tractogram's streamlines. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Re-import externals/ from scipy to resolve numpy deprecation (pr/821) (CM)
  • Support Python >=3.5.1, including Python 3.8.0 (pr/787) (CM)
  • Manage versioning with slightly customized Versioneer (pr/786) (CM)
  • Reference Nipy Community Code and Nibabel Developer Guidelines in GitHub community documents (pr/778) (CM, reviewed by MB)
API changes and deprecations
  • Deprecate in favor of ArraySequence.get_data(), which will return a copy. now returns a read-only view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Deprecate DataobjImage.get_data() API, to be removed in nibabel 5.0 (pr/794, pr/809) (CM, reviewed by MB)

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