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MNT CI fix scikit-image dependency for latest numpy #13378

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Merged
merged 3 commits into from
Mar 4, 2019
Merged

MNT CI fix scikit-image dependency for latest numpy #13378

merged 3 commits into from
Mar 4, 2019

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adrinjalali
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The latest numpy has removed _validate_lengths used by skimage. It's fixed in the latest release but not available on conda, hence our circleci/doc build fails.

This PR moves installation of skimage from conda to pip.

@adrinjalali
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related skimage PR: scikit-image/scikit-image#3556

related CI error:

Unexpected failing examples:
/home/circleci/project/examples/cluster/plot_coin_segmentation.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/project/examples/cluster/plot_coin_segmentation.py", line 31, in <module>
    import skimage
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/__init__.py", line 167, in <module>
    from .util.dtype import (img_as_float32,
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/__init__.py", line 8, in <module>
    from .arraycrop import crop
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/arraycrop.py", line 8, in <module>
    from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths'


/home/circleci/project/examples/cluster/plot_coin_ward_segmentation.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/project/examples/cluster/plot_coin_ward_segmentation.py", line 25, in <module>
    import skimage
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/__init__.py", line 176, in <module>
    from .util.lookfor import lookfor
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/__init__.py", line 8, in <module>
    from .arraycrop import crop
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/arraycrop.py", line 8, in <module>
    from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths'


-------------------------------------------------------------------------------

Exception occurred:
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/sphinx_gallery/gen_gallery.py", line 313, in sumarize_failing_examples
    "\n" + "-" * 79)
ValueError: Here is a summary of the problems encountered when running the examples

Unexpected failing examples:
/home/circleci/project/examples/cluster/plot_coin_segmentation.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/project/examples/cluster/plot_coin_segmentation.py", line 31, in <module>
    import skimage
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/__init__.py", line 167, in <module>
    from .util.dtype import (img_as_float32,
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/__init__.py", line 8, in <module>
    from .arraycrop import crop
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/arraycrop.py", line 8, in <module>
    from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths'


/home/circleci/project/examples/cluster/plot_coin_ward_segmentation.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/project/examples/cluster/plot_coin_ward_segmentation.py", line 25, in <module>
    import skimage
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/__init__.py", line 176, in <module>
    from .util.lookfor import lookfor
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/__init__.py", line 8, in <module>
    from .arraycrop import crop
  File "/home/circleci/miniconda/envs/testenv/lib/python3.6/site-packages/skimage/util/arraycrop.py", line 8, in <module>
    from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths'

@adrinjalali
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This has fixed the skimage issue, the failure is due to the 10m limit.

@adrinjalali
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#13379 tackles the example's issue.

qinhanmin2014
qinhanmin2014 approved these changes Mar 4, 2019
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please add a comment, e.g., revert when scikit-image 0.14.2 is available through conda.

@jnothman jnothman merged commit 18920e3 into scikit-learn:master Mar 4, 2019
@adrinjalali adrinjalali deleted the numpy/_validate_lengths branch March 4, 2019 10:10
xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019
@adrinjalali
MNT CI fix scikit-image dependency for latest numpy (scikit-learn#13378)
71e1140
xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019
Revert "MNT CI fix scikit-image dependency for latest numpy (scikit-l…
66a9fda 
…earn#13378)"

This reverts commit 71e1140.
xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019
Revert "MNT CI fix scikit-image dependency for latest numpy (scikit-l…
32ef2f9 
…earn#13378)"

This reverts commit 71e1140.
koenvandevelde pushed a commit to koenvandevelde/scikit-learn that referenced this pull request Jul 12, 2019
@adrinjalali @koenvandevelde
MNT CI fix scikit-image dependency for latest numpy (scikit-learn#13378)
101ed44
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@jnothman jnothman jnothman approved these changes

@qinhanmin2014 qinhanmin2014 qinhanmin2014 approved these changes

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@adrinjalali @jnothman @qinhanmin2014