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

[JB Poline]

Indeed - thanks so much
JB

On Sun, Nov 17, 2019 at 4:50 AM bthirion <bertrand.thirion at inria.fr> wrote:

> 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.
>
> 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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