carpentries-incubator / SDC-BIDS-dMRI

Introduction to dMRI
https://carpentries-incubator.github.io/SDC-BIDS-dMRI/
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ENH: Bump `DIPY` to version 1.7.0 #232

Closed jhlegarreta closed 1 year ago

jhlegarreta commented 1 year ago

Bump DIPY to version 1.7.0.

Previous DIPY versions were using NumPy's testing features relying on nose, which was deprecated in release 1.25.0.

Relevant NumPy documentation: https://github.com/numpy/numpy/blob/dabb12ec5c27846b1ded065b5e61eabb89d029ed/doc/source/release/1.25.0-notes.rst?plain=1#L166 https://github.com/numpy/numpy/blob/dabb12ec5c27846b1ded065b5e61eabb89d029ed/doc/source/release/1.25.0-notes.rst?plain=1#L188

Commit in DIPY removing NumPy's nose testing features: https://github.com/dipy/dipy/pull/2788/commits/d4216cee48a6c08ec97a3ac46a725f582a1fae46

Fixes:

ImportError                               Traceback (most recent call last)
Cell In[1], line 1
----> 1 from dipy.io.gradients import read_bvals_bvecs
      2 from dipy.core.gradients import gradient_table
      4 gt_bvals, gt_bvecs = read_bvals_bvecs(bval, bvec)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/dipy/__init__.py:41
     38 from .testing import setup_test
     40 # Test callable
---> 41 from numpy.testing import Tester
     42 test = Tester().test
     43 bench = Tester().bench

ImportError: cannot import name 'Tester' from 'numpy.testing'
(/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/numpy/testing/__init__.py)

raised, for example, in: https://github.com/carpentries-incubator/SDC-BIDS-dMRI/actions/runs/5593859841/jobs/10228037219#step:13:74

jhlegarreta commented 1 year ago

Testing is partially successful now: https://github.com/carpentries-incubator/SDC-BIDS-dMRI/actions/runs/5599183278/jobs/10239812094#step:13:46

Build failures are unrelated: https://github.com/carpentries-incubator/SDC-BIDS-dMRI/actions/runs/5599183278/jobs/10239812094#step:13:123

Will be addressed in a separate PR.

Merging.