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Backports for 0.18.3 (pooch 1.5 fix, deprecated scipy.linalg.pinv2 fix)#5531

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grlee77 merged 6 commits intoscikit-image:v0.18.xfrom
grlee77:pooch-fix-backport
Aug 23, 2021
Merged

Backports for 0.18.3 (pooch 1.5 fix, deprecated scipy.linalg.pinv2 fix)#5531
grlee77 merged 6 commits intoscikit-image:v0.18.xfrom
grlee77:pooch-fix-backport

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@grlee77 grlee77 commented Aug 23, 2021

Description

import file_hash from Pooch public API

use pinv instead of deprected scipy.linalg.pinv2 in random_walker

Checklist

For reviewers

  • Check that the PR title is short, concise, and will make sense 1 year
    later.
  • Check that new functions are imported in corresponding __init__.py.
  • Check that new features, API changes, and deprecations are mentioned in
    doc/release/release_dev.rst.

* Handle pooch version 1.5.0

This is compatible with pooch < 1.5.0, too.  If such older compatibility
is not desired, the dependency version could be changed and just the new
code could be kept.

* Flip the order in which we try things.

* undo typo i introduced

* Update skimage/data/__init__.py

Co-authored-by: Gregory R. Lee <grlee77@gmail.com>

Co-authored-by: Mark Harfouche <mark.harfouche@gmail.com>
Co-authored-by: Gregory R. Lee <grlee77@gmail.com>
pyamg uses coarse_solver='pinv2' by default, but SciPy 1.7.0 has deprecated pinv2
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grlee77 commented Aug 23, 2021

Failures are related to two data files that are getting fetched from the main branch rather than this one (They were updated a few months ago on main, but the 0.18.x branch should still be using the older versions)

  skimage/data/_blobs_3d_fiji_skeleton.tif
  skimage/restoration/tests/camera_unsup.npy

@grlee77 grlee77 changed the title Handle pooch version 1.5.0 (#5529) Backports for 0.18.3 (pooch 1.5 fix, deprecated scipy.linalg.pinv2 fix) Aug 23, 2021
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grlee77 commented Aug 23, 2021

As far as I can tell the pooch tests are not going to pass here, but it seems that it should be fine once we have an actual version number that matches a tag. I think I will merge and then follow up, making a 0.18.3rc1 tag to see if that works

@grlee77 grlee77 merged commit 7b721a7 into scikit-image:v0.18.x Aug 23, 2021
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