[Neuroimaging] ANN: Nibabel 3.0 Release Candidate (Please test!)

[bthirion]

Congratulations to all contributors and to you in particular !

Bertrand

On 16/11/2019 18:39, Christopher Markiewicz wrote:
> Hi all,
>
> The first release candidate for Nibabel 3.0 is out. As a major 
> release, there are API changes and a greater than usual opportunity 
> for pain. Therefore, I'm setting a minimum 1 month window (as proposed 
> in https://github.com/nipy/nibabel/issues/734) to help us find bugs, 
> and allow downstream tools to make any necessary adjustments. The only 
> pull requests that will be accepted during this period will be bug 
> fixes or documentation and testing improvements. This window can be 
> extended if needed, so please let me know if you need more time.
>
> I would ask all downstream projects to add pre-release testing if they 
> do not already. Pre-release testing requires specifically requesting 
> pre-release packages from PyPI, so if you have not set up this up in 
> continuous integration configuration, it is very likely that you will 
> not install the correct package. To do this, use the `--pre` flag for 
> pip when installing nibabel.
>
> Please report any issues to https://github.com/nipy/nibabel/issues 
> <https://github.com/nipy/nibabel/issues>.
>
> The most consequential changes in this release are the removal of 
> Python 2 support and the deprecation of the img.get_data() accessor 
> method to retrieve the image data block. The supported APIs for 
> accessing data are img.get_fdata(), which always casts to float, and 
> img.dataobj, which affords more control over the interpretation of the 
> data object.
>
> Additionally, GIFTI images have a new agg_data() method that 
> simplifies the retrieval of DataArrays from GIFTI files into usable 
> numpy arrays. Most, if not all, filenames can now be passed as 
> pathlib.Path objects. And there are significant updates to the 
> streamlines package. Exercising these functionalities will be a 
> valuable contribution during this release candidate phase.
>
> Many thanks to everbody who took the time to investigate and report 
> bugs, propose fixes, review pull requests and review the 
> documentation, including first-time contributors Cameron Riddell, 
> Hao-Ting Wang, Oscar Esteban, Dorota Jarecka, and Chris Gorgolewski. 
> And thanks in advance to your help in making this a smooth upgrade for 
> users.
>
> 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.
>
> # 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)
>
> Enhancements
> ------------
>
> * ``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 ``Tractogram``s no longer ``apply_affine`` to the original 
> ``Tractogram``'s streamlines. (pr/811) (MC, reviewed by Serge Koudoro, 
> Philippe Poulin, CM, MB)
> * Re-import externals/netcdf.py from scipy to resolve numpy 
> deprecation (pr/821) (CM)
>
> Maintenance
> -----------
>
> * 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 ``ArraySequence.data`` in favor of 
> ``ArraySequence.get_data()``, which will return a copy. 
> ``ArraySequence.data`` 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)
>
> -- 
>
> Chris Markiewicz
>
> Center for Reproducible Neuroscience
>
> Stanford University
>
>
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> Neuroimaging at python.org
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