Added distribution badges

[TheChymera]

Added badges for distributions which usually provide more-or-less up-to-date versions of nibabel. I think it would be cool to notify users that they might be able to get nibabel directly via their package managers. Might also encourage people to package nibabel and/or keep it up to date (I know there's a pretty big science packaging effort on Arch's AUR as well, though they seem to have missed nibabel).

@yarikoptic
@liamtimms

[ZviBaratz]

LGTM.
I'm planning to revamp the readme a little sometime next week, so this makes a perfect addition. Thank you very much!

[codecov]

Codecov Report

Base: 92.17% // Head: 92.17% // No change to project coverage 👍

Coverage data is based on head (6553bca) compared to base (fc9a1c1).
Patch has no changes to coverable lines.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1192   +/-   ##
=======================================
  Coverage   92.17%   92.17%           
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  Files          97       97           
  Lines       12341    12341           
  Branches     2535     2535           
=======================================
  Hits        11375    11375           
  Misses        645      645           
  Partials      321      321           

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[ZviBaratz]

@effigies pre-release (windows-latest, 3.11, x64, pip, test, PRE_PIP_FLAGS, REQUIREMENTS, DEFAULT_OPT_DEPENDS) is raising:

FAILED tests/test_nifti1.py::TestNifti1Image::test_slicer - nibabel.spatialimages.HeaderDataError: shape (4, 5, 6, 2, 1, 1, 1, 1) does not fit in dim datatype

this certainly should not have anything to do with this PR, but it also wasn't raised in the latest commit to master 😕
Any ideas?

[liamtimms]

Regarding Arch: I have been keeping the AUR build for nibabel fairly up-to-date since 2019 actually https://aur.archlinux.org/cgit/aur.git/log/?h=python-nibabel

[effigies]

It's a stochastic bug, but I can't understand why it happens. Rerunning the tests will fix it.

[effigies]

I believe there are Fedora and Nix packages as well.

[ZviBaratz]

Fedora and nix are outdated if I understand correctly.

[effigies]

I think nix (4.0.2) is not dramatically far behind, given 5.0.0 was only released a few weeks ago. They may be waiting on deprecation fixes in downstream packages.

[effigies]

cc @ashgillman and @sanjayankur31

[sanjayankur31]

Hi there, the Fedora package should be updated to the latest version soon. I just have to test all the other packages that depend on nibabel to see if they all continue to build/work with the new version (and file bugs if they don't).

[effigies]

No worries on speed. Just wanted to check in in case another maintainer had taken over.

The whole point of having semver releases is to warn that there may be breaking changes, and distributions are welcome to take their time to keep their ecosystem unbroken, so I don't see a lag in adopting a major version as a concern. Anything that's at 4.0.2 is probably currently maintained.

[TheChymera]

@liamtimms thank you for pointing that out :)

Ok, so I added nix and Arch. Fedora is pretty severely out of date, @sanjayankur31 maybe sumbit a PR once it's at least 4.x?

[yarikoptic]

even more badges could always be added

[effigies]

@liamtimms Just looked at https://aur.archlinux.org/cgit/aur.git/commit/?h=python-nibabel&id=efdbaf50ad24c02f807e6cb7f55e34b71a4a8a71 and have a few notes:

1. We do not require six directly, so I would pick it up through the dependency tree, if it's actually needed.
2. setuptools-scm should be a build time, not run time, dependency, and it should be required by hatch-vcs.
3. We do require packaging at runtime, as it's needed to emit deprecation warnings/errors based on the current version.
4. We're currently building docs with Sphinx 5.3.0, so the comment about Sphinx 1.5.6 is out of date.

[liamtimms]

@effigies , thanks so much for this, there was definitely some crust and disorganization leftover in that packaging from a few years ago, plus my confusion about some more recent dependency changes. I've updated the package to reflect these notes now.

[effigies]

@liamtimms Sorry, one update: 5.0 does actually have runtime dependency on setuptools because of pkg_resources. I've removed it in #1190, but it is there in this version. We actually do not have a build-time dependency on it at all.

  depends=('python-numpy>=1.19' 
-          'python-packaging')
+          'python-packaging>=17'
+          'python-setuptools')
 makedepends=('python-hatch-vcs'
-             'python-setuptools'
              'python-build'

(I would run tests to be sure. You should be able to use pytest with pytest-httpserver. If you run doctests, you'll need pytest-doctestplus.)

[effigies]

Oh, and I would suggest using the sdist (.tar.gz) files from PyPI instead of the GitHub archive. You can use the following template: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz

So https://pypi.io/packages/source/n/nibabel/nibabel-5.0.0.tar.gz

[liamtimms]

@effigies just a quick question:

5.0 does actually have runtime dependency on setuptools because of pkg_resources. I've removed it in #1190, but it is there in this version.

is that still true for 5.0.1? Asking because I don't see #1190 mentioned in the release notes for 5.0.1.

[effigies]

Yes. 5.0.1 (and bugfix releases generally) should not change APIs or dependencies.