Fix CI failures related to conversion of np.floating to dtype #4731

rfezzani · 2020-05-20T11:08:11Z

Description

This PR prevent the conversion using np.floating as it is deprecated in numpy 1.19.

It fixes CI failures in #4730

Checklist

Docstrings for all functions
Gallery example in ./doc/examples (new features only)
Benchmark in ./benchmarks, if your changes aren't covered by an
existing benchmark
Unit tests
Clean style in the spirit of PEP8

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.

sciunto · 2020-05-20T11:30:39Z

looks like it does not fully fix the CI :)

lagru · 2020-05-20T11:46:01Z

skimage/util/dtype.py

@@ -244,6 +244,8 @@ def _convert(image, dtype, force_copy=False, uniform=False):
        if force_copy:
            image = image.copy()
        return image
+    else:
+        dtype = np.float64


Did you mean dtypeobj_out? I think dtype is never used from this point onwards...

Good catch, it should be dtype_out ;)

…into Remove_conversion_to_np_floating

rfezzani · 2020-05-20T22:32:55Z

Ci failures are fixed by #4735

jni

I don't think this is the correct fix. Instead, I think we should change img_as_float's call to _convert(img, np.floating) to _convert(img, np.float). Or np.float64, I'm not sure. np.float64 is the current behaviour, but np.float (ie 32-bit on 32-bit-default platforms, 64-bit on 64-bit-default platforms) is the intended behaviour, I believe.

jni · 2020-05-21T05:49:08Z

To clarify my position: this PR currently takes NumPy's deprecated behaviour and hardcodes it into skimage. Instead, we should follow NumPy's guidance here. Users doing _convert(arr, np.floating) should get the warning (although for some reason I couldn't trigger it locally), users using img_as_float should get the fixed (future) behaviour.

jni

Ignore me! 😂 The np.issubdtype change becomes nearly impossible with my half-baked proposal. 😂

jni · 2020-05-21T06:14:03Z

fwiw, I do think we should consider making img_as_float default to np.float rather than np.float64. But that can be resolved another day, this matches current behaviour.

numpy 1.19 deprecates (See NEP 34) automatic dtype for ragged input. This causes CI failures (please see #4731).

numpy 1.19 deprecates (See NEP 34) automatic dtype for ragged input. This causes CI failures (please see scikit-image#4731).

…-image#4731) * Prevent type conversion to np.floating * Fix conversion to np.floating

* Fix array ragged input numpy deprecation (#4735) numpy 1.19 deprecates (See NEP 34) automatic dtype for ragged input. This causes CI failures (please see #4731). * Fix CI failures related to conversion of np.floating to dtype (#4731) * Prevent type conversion to np.floating * Fix conversion to np.floating Co-authored-by: Riadh Fezzani <rfezzani@gmail.com>

dstansby · 2020-07-13T15:23:52Z

Does anyone know which release number this is targeted for?

sciunto · 2020-07-14T04:42:11Z

@scikit-image/core Do we plan to release a minor version to include this fix?

jni · 2020-07-14T06:30:11Z

Looks like it was backported to the 0.17.x branch, so I think we could release 0.17.3 with this. @emmanuelle could you handle that? I'd be available today and/or Thursday to help if needed.

Prevent type convertion to np.floating

9c4c033

rfezzani mentioned this pull request May 20, 2020

Blacklist cython version 0.29.18 #4730

Merged

hmaarrfk approved these changes May 20, 2020

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lagru added the 🔧 type: Maintenance Refactoring and maintenance of internals label May 20, 2020

lagru reviewed May 20, 2020

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rfezzani changed the title ~~Prevent type convertion to np.floating~~ [WIP] Prevent type convertion to np.floating May 20, 2020

rfezzani changed the title ~~[WIP] Prevent type convertion to np.floating~~ [DO NOT MERGE] Prevent type convertion to np.floating May 20, 2020

rfezzani added 2 commits May 20, 2020 23:37

Merge branch 'master' of https://github.com/scikit-image/scikit-image …

6bedf02

…into Remove_conversion_to_np_floating

Fix conversion to np.floating

b0886db

rfezzani mentioned this pull request May 20, 2020

Fix Ci failures related to array ragged input numpy deprecation #4735

Merged

8 tasks

rfezzani changed the title ~~[DO NOT MERGE] Prevent type convertion to np.floating~~ Fix CI failures related to dtype convertion to np.floating May 20, 2020

jni requested changes May 21, 2020

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jni changed the title ~~Fix CI failures related to dtype convertion to np.floating~~ Fix CI failures related to conversion of np.floating to dtype May 21, 2020

jni approved these changes May 21, 2020

View reviewed changes

jni merged commit fd24648 into scikit-image:master May 21, 2020

jni pushed a commit that referenced this pull request May 21, 2020

Fix array ragged input numpy deprecation (#4735)

daf595f

numpy 1.19 deprecates (See NEP 34) automatic dtype for ragged input. This causes CI failures (please see #4731).

jni pushed a commit to jni/scikit-image that referenced this pull request May 22, 2020

Fix array ragged input numpy deprecation (scikit-image#4735)

f470d7e

numpy 1.19 deprecates (See NEP 34) automatic dtype for ragged input. This causes CI failures (please see scikit-image#4731).

jni pushed a commit to jni/scikit-image that referenced this pull request May 22, 2020

Fix CI failures related to conversion of np.floating to dtype (scikit…

340511b

…-image#4731) * Prevent type conversion to np.floating * Fix conversion to np.floating

jni mentioned this pull request May 22, 2020

Backport NumPy deprecation fixes to v0.17.x #4745

Merged

rfezzani mentioned this pull request May 22, 2020

Add example for 3D adaptive histogram equalization (AHE) #4658

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8 tasks

lagru mentioned this pull request May 25, 2020

2020's calendar of community management #4486

Closed

dstansby mentioned this pull request Jul 13, 2020

Numpy deprecation warning in convert_to_float() #4848

Closed

pllim mentioned this pull request Jul 13, 2020

MNT: Deprecation warnings in satdet with numpy 1.19.0 spacetelescope/acstools#130

Closed

bilderbuchi mentioned this pull request Aug 6, 2020

DeprecationWarning using segmentation.slic #4822

Closed

wangjoshuah mentioned this pull request Sep 29, 2020

fix conversion warning shap/shap#1482

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Fix CI failures related to conversion of np.floating to dtype #4731

Fix CI failures related to conversion of np.floating to dtype #4731

rfezzani commented May 20, 2020

sciunto commented May 20, 2020 •

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jni commented Jul 14, 2020

Fix CI failures related to conversion of np.floating to dtype #4731

Fix CI failures related to conversion of np.floating to dtype #4731

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rfezzani commented May 20, 2020

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